@article{holland_piepho_2024, title={Don't BLUP Twice}, url={https://doi.org/10.1093/g3journal/jkae250}, DOI={10.1093/g3journal/jkae250}, journal={G3: Genes, Genomes, Genetics}, author={Holland, James B and Piepho, Hans-Peter}, editor={Lipka, AEditor}, year={2024}, month={Nov} }
 @article{washburn_varela_xavier_chen_ertl_gage_holland_lima_romay_lopez-cruz_et al._2024, title={Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates}, url={https://doi.org/10.1101/2024.09.13.612969}, DOI={10.1101/2024.09.13.612969}, abstractNote={Abstract Predicting phenotypes from a combination of genetic and environmental factors is a grand challenge of modern biology. Slight improvements in this area have the potential to save lives, improve food and fuel security, permit better care of the planet, and create other positive outcomes. In 2022 and 2023 the first open-to-the-public Genomes to Fields (G2F) initiative Genotype by Environment (GxE) prediction competition was held using a large dataset including genomic variation, phenotype and weather measurements and field management notes, gathered by the project over nine years. The competition attracted registrants from around the world with representation from academic, government, industry, and non-profit institutions as well as unaffiliated. These participants came from diverse disciplines include plant science, animal science, breeding, statistics, computational biology and others. Some participants had no formal genetics or plant-related training, and some were just beginning their graduate education. The teams applied varied methods and strategies, providing a wealth of modeling knowledge based on a common dataset. The winner’s strategy involved two models combining machine learning and traditional breeding tools: one model emphasized environment using features extracted by Random Forest, Ridge Regression and Least-squares, and one focused on genetics. Other high-performing teams’ methods included quantitative genetics, classical machine learning/deep learning, mechanistic models, and model ensembles. The dataset factors used, such as genetics; weather; and management data, were also diverse, demonstrating that no single model or strategy is far superior to all others within the context of this competition.}, author={Washburn, Jacob D. and Varela, José Ignacio and Xavier, Alencar and Chen, Qiuyue and Ertl, David and Gage, Joseph L. and Holland, James B. and Lima, Dayane Cristina and Romay, Maria Cinta and Lopez-Cruz, Marco and et al.}, year={2024}, month={Sep} }
 @article{washburn_varela_xavier_chen_ertl_gage_holland_lima_romay_lopez-cruz_et al._2024, title={Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates}, url={https://doi.org/10.1093/genetics/iyae195}, DOI={10.1093/genetics/iyae195}, journal={GENETICS}, author={Washburn, Jacob D and Varela, José Ignacio and Xavier, Alencar and Chen, Qiuyue and Ertl, David and Gage, Joseph L and Holland, James B and Lima, Dayane Cristina and Romay, Maria Cinta and Lopez-Cruz, Marco and et al.}, editor={Sillanpää, MikkoEditor}, year={2024}, month={Nov} }
 @article{costa_holland_leon_kaeppler_2024, title={Impact of genotype x environment interaction and selection history on genomic prediction in maize (<i>Zea mays</i> L.)}, volume={10}, ISSN={["1435-0653"]}, url={https://doi.org/10.1002/csc2.21379}, DOI={10.1002/csc2.21379}, abstractNote={Abstract Breeders made remarkable progress in improving productivity and stability of cultivars. Breeding progress relies on selecting favorable alleles for performance and stability to produce productive varieties across diverse environments. In this study, we analyzed the Genomes to Fields Initiative 2018–2019 genotype by environment interaction (G × E) dataset, focusing on three populations of double haploid (DH) lines derived from crossing inbrexpired Plant Variety Protection (ex‐PVP) inbred line PHW65 with inbred lines PHN11, Mo44, and MoG. PHW65 is an Iodent/Lancaster‐type inbred; PHN11 is an Iodent type ex‐PVP line; Mo44 is a tropical‐derived inbred; and MoG is an agronomically poor line derived from the variety Mastadon. Hybrids were produced by crossing the resulting DHs with Stiff Stalk testers PHT69 and LH195. The study's objective was to determine the donor inbreds' relative value and understand the impact of selection history on genomic prediction. We conducted a two‐stage analysis to compare hybrid performance and G × E variance of the populations. G × E variance for yield was significantly lower in the PHW65 × PHN11 population relative to the PHW65 × MoG population. The reduced G × E variance of the PHN11 population led to increased indirect prediction accuracy (when training and testing data are drawn from the same population but different environments). In cross‐validation, the PHN11 population had the greatest indirect prediction accuracy 45% of the time, followed by the Mo44 population (30%) and the MoG population (25%). Results demonstrate that prediction accuracy was greater in the population with the longest history of selection for favorable alleles (PHN11), contributing to greater yield stability.}, journal={CROP SCIENCE}, author={Costa, Martin and Holland, James B. and Leon, Natalia and Kaeppler, Shawn M.}, year={2024}, month={Oct} }
 @article{woore_flint-garcia_holland_2024, title={Phenotypic characterization of Southeastern United States open-pollinated maize landraces}, volume={2}, ISSN={["1435-0653"]}, url={https://doi.org/10.1002/csc2.21198}, DOI={10.1002/csc2.21198}, abstractNote={AbstractMaize (Zea mays L. subsp. mays) is the most important crop in the United States, but maize food and distillation products often rely on varieties that are not bred explicitly for these purposes. Farmers targeting niche food grain markets have expressed interest in historical open‐pollinated varieties of maize, but few such populations are widely available, and even fewer are well‐characterized. We planted field trials of 76 open‐pollinated heirloom varieties available from seed catalogs and the United States Department of Agriculture germplasm collection along with four F1 hybrid cultivars. We measured 24 traits across 3 years and three locations to characterize the selected varieties and measure their phenotypic relationships. We identified a subset of 19 traits with heritability >0.5 and pairwise correlation coefficients not exceeding 0.9 for phenotypic analysis. Our results demonstrate that many historical accessions contain substantial genetic variation that should permit improvement from within‐population selection. Variety name and origin are often not useful indicators of phenotypic relationships or potential crop value, although Hickory King varieties have maintained their identity even following global dispersion. Cluster analysis identifies nine morphologically distinct groups within the varieties tested, which are largely in agreement with previously proposed landrace groupings. Our results suggest a complex intermixing of Southern Dents with other maize types, rather than a clear distinction between Southern Dents and Derived Southern Dents, however. Genetic analysis of larger samples of US open‐pollinated populations will help better define the natural classification of maize indigenous to the United States.}, journal={CROP SCIENCE}, author={Woore, Matthew S. and Flint-Garcia, Sherry A. and Holland, James B.}, year={2024}, month={Feb} }
 @article{hudson_resende jr_messina_holland_brawner_2024, title={Prediction of resistance, virulence, and host-by-pathogen interactions using dual-genome prediction models}, volume={137}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-024-04698-7}, abstractNote={Integrating disease screening data and genomic data for host and pathogen populations into prediction models provides breeders and pathologists with a unified framework to develop disease resistance. Developing disease resistance in crops typically consists of exposing breeding populations to a virulent strain of the pathogen that is causing disease. While including a diverse set of pathogens in the experiments would be desirable for developing broad and durable disease resistance, it is logistically complex and uncommon, and limits our capacity to implement dual (host-by-pathogen)-genome prediction models. Data from an alternative disease screening system that challenges a diverse sweet corn population with a diverse set of pathogen isolates are provided to demonstrate the changes in genetic parameter estimates that result from using genomic data to provide connectivity across sparsely tested experimental treatments. An inflation in genetic variance estimates was observed when among isolate relatedness estimates were included in prediction models, which was moderated when host-by-pathogen interaction effects were incorporated into models. The complete model that included genomic similarity matrices for host, pathogen, and interaction effects indicated that the proportion of phenotypic variation in lesion size that is attributable to host, pathogen, and interaction effects was similar. Estimates of the stability of lesion size predictions for host varieties inoculated with different isolates and the stability of isolates used to inoculate different hosts were also similar. In this pathosystem, genetic parameter estimates indicate that host, pathogen, and host-by-pathogen interaction predictions may be used to identify crop varieties that are resistant to specific virulence mechanisms and to guide the deployment of these sources of resistance into pathogen populations where they will be more effective.}, number={8}, journal={THEORETICAL AND APPLIED GENETICS}, author={Hudson, Owen and Resende Jr, Marcio F. R. and Messina, Charlie and Holland, James and Brawner, Jeremy}, year={2024}, month={Aug} }
 @article{lima_aviles_alpers_mcfarland_kaeppler_ertl_romay_gage_holland_beissinger_et al._2023, title={2018-2019 field seasons of the Maize Genomes to Fields (G2F) G x E project}, volume={24}, ISSN={["2730-6844"]}, url={https://doi.org/10.1186/s12863-023-01129-2}, DOI={10.1186/s12863-023-01129-2}, abstractNote={Abstract
                Objectives
                This report provides information about the public release of the 2018–2019 Maize G X E project of the Genomes to Fields (G2F) Initiative datasets. G2F is an umbrella initiative that evaluates maize hybrids and inbred lines across multiple environments and makes available phenotypic, genotypic, environmental, and metadata information. The initiative understands the necessity to characterize and deploy public sources of genetic diversity to face the challenges for more sustainable agriculture in the context of variable environmental conditions.
              
                Data description
                Datasets include phenotypic, climatic, and soil measurements, metadata information, and inbred genotypic information for each combination of location and year. Collaborators in the G2F initiative collected data for each location and year; members of the group responsible for coordination and data processing combined all the collected information and removed obvious erroneous data. The collaborators received the data before the DOI release to verify and declare that the data generated in their own locations was accurate. ReadMe and description files are available for each dataset. Previous years of evaluation are already publicly available, with common hybrids present to connect across all locations and years evaluated since this project’s inception.
              }, number={1}, journal={BMC GENOMIC DATA}, author={Lima, Dayane Cristina and Aviles, Alejandro Castro and Alpers, Ryan Timothy and McFarland, Bridget A. and Kaeppler, Shawn and Ertl, David and Romay, Maria Cinta and Gage, Joseph L. and Holland, James and Beissinger, Timothy and et al.}, year={2023}, month={May} }
 @article{lima_aviles_alpers_perkins_schoemaker_costa_michel_kaeppler_ertl_romay_et al._2023, title={2020-2021 field seasons of Maize GxE project within the Genomes to Fields Initiative}, volume={16}, ISSN={["1756-0500"]}, DOI={10.1186/s13104-023-06430-y}, abstractNote={Abstract
                Objectives
                This release note describes the Maize GxE project datasets within the Genomes to Fields (G2F) Initiative. The Maize GxE project aims to understand genotype by environment (GxE) interactions and use the information collected to improve resource allocation efficiency and increase genotype predictability and stability, particularly in scenarios of variable environmental patterns. Hybrids and inbreds are evaluated across multiple environments and phenotypic, genotypic, environmental, and metadata information are made publicly available.
              
                Data description
                The datasets include phenotypic data of the hybrids and inbreds evaluated in 30 locations across the US and one location in Germany in 2020 and 2021, soil and climatic measurements and metadata information for all environments (combination of year and location), ReadMe, and description files for each data type. A set of common hybrids is present in each environment to connect with previous evaluations. Each environment had a collaborator responsible for collecting and submitting the data, the GxE coordination team combined all the collected information and removed obvious erroneous data. Collaborators received the combined data to use, verify and declare that the data generated in their own environments was accurate. Combined data is released to the public with minimal filtering to maintain fidelity to the original data.
              }, number={1}, journal={BMC RESEARCH NOTES}, author={Lima, Dayane Cristina and Aviles, Alejandro Castro and Alpers, Ryan Timothy and Perkins, Alden and Schoemaker, Dylan L. and Costa, Martin and Michel, Kathryn J. and Kaeppler, Shawn and Ertl, David and Romay, Maria Cinta and et al.}, year={2023}, month={Sep} }
 @article{dewitt_lyerly_guedira_holland_ward_murphy_boyles_mergoum_babar_shakiba_et al._2023, title={Bearded or smooth? Awns improve yield when wheat experiences heat stress during grain fill}, url={https://doi.org/10.1101/2023.02.27.530138}, DOI={10.1101/2023.02.27.530138}, abstractNote={AbstractThe presence or absence of awns – whether wheat heads are ”bearded” or ”smooth”– is the most visible phenotype distinguishing wheat cultivars. Previous studies suggest that awns may improve yields in heat or water-stressed environments, but the exact contribution of awns to yield differences remains unclear. Here we leverage historical phenotypic, genotypic, and climate data to estimate the yield effects of awns under different environmental conditions over a 12-year period in the Southeast US. Lines were classified as awned or awnless based on sequence data, and observed heading dates were used to associate grain fill periods of each line in each environment with climatic data and grain yield. In most environments, awn suppression was associated with higher yields, but awns were associated with better performance in heat-stressed environments more common at southern locations. Wheat breeders in environments where awns are only beneficial in some years may consider selection for awned lines to reduce year-to-year yield variability, and with an eye towards future climates.}, author={DeWitt, Noah and Lyerly, Jeanette and Guedira, Mohammed and Holland, James B. and Ward, Brian P. and Murphy, J. Paul and Boyles, Richard E. and Mergoum, Mohamed and Babar, Md. Ali and Shakiba, Ehsan and et al.}, year={2023}, month={Mar} }
 @article{dewitt_lyerly_guedira_holland_murphy_ward_boyles_mergoum_babar_shakiba_et al._2023, title={Bearded or smooth? Awns improve yield when wheat experiences heat stress during grain fill in the southeastern United States}, volume={74}, ISSN={["1460-2431"]}, url={https://doi.org/10.1093/jxb/erad318}, DOI={10.1093/jxb/erad318}, abstractNote={Abstract
               The presence or absence of awns—whether wheat heads are ‘bearded’ or ‘smooth’ – is the most visible phenotype distinguishing wheat cultivars. Previous studies suggest that awns may improve yields in heat or water-stressed environments, but the exact contribution of awns to yield differences remains unclear. Here we leverage historical phenotypic, genotypic, and climate data for wheat (Triticum aestivum) to estimate the yield effects of awns under different environmental conditions over a 12-year period in the southeastern USA. Lines were classified as awned or awnless based on sequence data, and observed heading dates were used to associate grain fill periods of each line in each environment with climatic data and grain yield. In most environments, awn suppression was associated with higher yields, but awns were associated with better performance in heat-stressed environments more common at southern locations. Wheat breeders in environments where awns are only beneficial in some years may consider selection for awned lines to reduce year-to-year yield variability, and with an eye towards future climates.}, number={21}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={DeWitt, Noah and Lyerly, Jeanette and Guedira, Mohammed and Holland, James B. and Murphy, J. Paul and Ward, Brian P. and Boyles, Richard E. and Mergoum, Mohamed and Babar, Md Ali and Shakiba, Ehsan and et al.}, editor={Dreisigacker, SusanneEditor}, year={2023}, month={Nov}, pages={6749–6759} }
 @article{samira_lopez_holland_balint-kurti_2023, title={Characterization of a Host-Specific Toxic Activity Produced by Bipolaris cookei, Causal Agent of Target Leaf Spot of Sorghum}, volume={1}, ISSN={["1943-7684"]}, DOI={10.1094/PHYTO-11-22-0427}, journal={PHYTOPATHOLOGY}, author={Samira, Rozalynne and Lopez, Luis Fernando Samayoa and Holland, James and Balint-Kurti, Peter J.}, year={2023}, month={Jan} }
 @article{samira_samayoa_holland_balint-kurti_2023, title={Characterization of a host-specific toxic activity produced by Bipolaris cookei, causal agent of Target Leaf Spot of Sorghum}, volume={113}, ISSN={0031-949X 1943-7684}, url={http://dx.doi.org/10.1094/PHYTO-11-22-0427-R}, DOI={10.1094/PHYTO-11-22-0427-R}, abstractNote={Target leaf spot (TLS) of sorghum, caused by the necrotrophic fungus Bipolaris cookei, can cause severe yield loss in many parts of the world. We grew B. cookei in liquid culture and observed that the resulting culture filtrate (CF) was differentially toxic when infiltrated into the leaves of a population of 288 diverse sorghum lines. In this population, we found a significant correlation between high CF sensitivity and susceptibility to TLS. This suggests that the toxin produced in culture may play a role in the pathogenicity of B. cookei in the field. We demonstrated that the toxic activity is light sensitive and, surprisingly, insensitive to pronase, suggesting that it is not proteinaceous. We identified the two sorghum genetic loci most associated with the response to CF in this population. Screening seedlings with B. cookei CF could be a useful approach for prescreening germplasm for TLS resistance.}, number={7}, journal={Phytopathology®}, publisher={Scientific Societies}, author={Samira, Rozalynne and Samayoa, Luis Fernando and Holland, James and Balint-Kurti, Peter John}, year={2023}, month={Jan}, pages={1301–1306} }
 @article{choquette_weldekidan_brewer_davis_wisser_holland_2023, title={Enhancing adaptation of tropical maize to temperate environments using genomic selection}, volume={6}, ISSN={["2160-1836"]}, url={https://doi.org/10.1093/g3journal/jkad141}, DOI={10.1093/g3journal/jkad141}, abstractNote={Abstract
               Tropical maize can be used to diversify the genetic base of temperate germplasm and help create climate-adapted cultivars. However, tropical maize is unadapted to temperate environments, in which sensitivities to long photoperiods and cooler temperatures result in severely delayed flowering times, developmental defects, and little to no yield. Overcoming this maladaptive syndrome can require a decade of phenotypic selection in a targeted, temperate environment. To accelerate the incorporation of tropical diversity in temperate breeding pools, we tested if an additional generation of genomic selection can be used in an off-season nursery where phenotypic selection is not very effective. Prediction models were trained using flowering time recorded on random individuals in separate lineages of a heterogenous population grown at two northern U.S. latitudes. Direct phenotypic selection and genomic prediction model training was performed within each target environment and lineage, followed by genomic prediction of random intermated progenies in the off-season nursery. Performance of genomic prediction models was evaluated on self-fertilized progenies of prediction candidates grown in both target locations in the following summer season. Prediction abilities ranged from 0.30 to 0.40 among populations and evaluation environments. Prediction models with varying marker effect distributions or spatial field effects had similar accuracies. Our results suggest that genomic selection in a single off-season generation could increase genetic gains for flowering time by more than 50% compared to direct selection in summer seasons only, reducing the time required to change the population mean to an acceptably adapted flowering time by about one-third to one-half.}, journal={G3-GENES GENOMES GENETICS}, author={Choquette, Nicole E. and Weldekidan, Teclemariam and Brewer, Jason and Davis, Scott B. and Wisser, Randall J. and Holland, James B.}, editor={Lipka, AEditor}, year={2023}, month={Jun} }
 @article{choquette_holland_weldekidan_drouault_leon_flint-garcia_lauter_murray_xu_wisser_2023, title={Environment-specific selection alters flowering-time plasticity and results in pervasive pleiotropic responses in maize}, volume={2}, ISSN={["1469-8137"]}, url={https://doi.org/10.1111/nph.18769}, DOI={10.1111/nph.18769}, abstractNote={Summary


Crop genetic diversity for climate adaptations is globally partitioned. We performed experimental evolution in maize to understand the response to selection and how plant germplasm can be moved across geographical zones.

Initialized with a common population of tropical origin, artificial selection on flowering time was performed for two generations at eight field sites spanning 25° latitude, a 2800 km transect. We then jointly tested all selection lineages across the original sites of selection, for the target trait and 23 other traits.

Modeling intergenerational shifts in a physiological reaction norm revealed separate components for flowering‐time plasticity. Generalized and local modes of selection altered the plasticity of each lineage, leading to a latitudinal pattern in the responses to selection that were strongly driven by photoperiod. This transformation led to widespread changes in developmental, architectural, and yield traits, expressed collectively in an environment‐dependent manner. Furthermore, selection for flowering time alone alleviated a maladaptive syndrome and improved yields for tropical maize in the temperate zone.

Our findings show how phenotypic selection can rapidly shift the flowering phenology and plasticity of maize. They also demonstrate that selecting crops to local conditions can accelerate adaptation to climate change.

}, journal={NEW PHYTOLOGIST}, author={Choquette, Nicole E. and Holland, James B. and Weldekidan, Teclemariam and Drouault, Justine and Leon, Natalia and Flint-Garcia, Sherry and Lauter, Nick and Murray, Seth C. and Xu, Wenwei and Wisser, Randall J.}, year={2023}, month={Feb} }
 @article{lima_washburn_varela_chen_gage_romay_holland_ertl_lopez-cruz_aguate_et al._2023, title={Genomes to Fields 2022 Maize genotype by Environment Prediction Competition}, volume={16}, ISSN={["1756-0500"]}, url={https://doi.org/10.1186/s13104-023-06421-z}, DOI={10.1186/s13104-023-06421-z}, abstractNote={Abstract
                Objectives
                The Genomes to Fields (G2F) 2022 Maize Genotype by Environment (GxE) Prediction Competition aimed to develop models for predicting grain yield for the 2022 Maize GxE project field trials, leveraging the datasets previously generated by this project and other publicly available data.
              
                Data description
                This resource used data from the Maize GxE project within the G2F Initiative [1]. The dataset included phenotypic and genotypic data of the hybrids evaluated in 45 locations from 2014 to 2022. Also, soil, weather, environmental covariates data and metadata information for all environments (combination of year and location). Competitors also had access to ReadMe files which described all the files provided. The Maize GxE is a collaborative project and all the data generated becomes publicly available [2]. The dataset used in the 2022 Prediction Competition was curated and lightly filtered for quality and to ensure naming uniformity across years.
              }, number={1}, journal={BMC RESEARCH NOTES}, author={Lima, Dayane Cristina and Washburn, Jacob D. and Varela, Jose Ignacio and Chen, Qiuyue and Gage, Joseph L. and Romay, Maria Cinta and Holland, James and Ertl, David and Lopez-Cruz, Marco and Aguate, Fernando M. and et al.}, year={2023}, month={Jul} }
 @article{tittes_lorant_mcginty_holland_jesus sánchez-gonzález_seetharam_tenaillon_ross-ibarra_2023, title={Not so local: the population genetics of convergent adaptation in maize and teosinte}, url={https://doi.org/10.7554/eLife.92405.1}, DOI={10.7554/eLife.92405.1}, abstractNote={What is the genetic architecture of local adaptation and what is the geographic scale over which it operates? We investigated patterns of local and convergent adaptation in five sympatric population pairs of traditionally cultivated maize and its wild relative teosinte (Zea mays subsp. parviglumis). We found that signatures of local adaptation based on the inference of adaptive fixations and selective sweeps are frequently exclusive to individual populations, more so in teosinte compared to maize. However, for both maize and teosinte, selective sweeps are also frequently shared by several populations, and often between subspecies. We were further able to infer that selective sweeps were shared among populations most often via migration, though sharing via standing variation was also common. Our analyses suggest that teosinte has been a continued source of beneficial alleles for maize, even after domestication, and that maize populations have facilitated adaptation in teosinte by moving beneficial alleles across the landscape. Taken together, our results suggest local adaptation in maize and teosinte has an intermediate geographic scale, one that is larger than individual populations, but smaller than the species range.}, author={Tittes, Silas and Lorant, Anne and McGinty, Sean and Holland, James B. and Jesus Sánchez-González, Jose and Seetharam, Arun and Tenaillon, Maud and Ross-Ibarra, Jeffrey}, year={2023}, month={Nov} }
 @article{tittes_lorant_mcginty_holland_jesus sánchez-gonzález_seetharam_tenaillon_ross-ibarra_2023, title={Not so local: the population genetics of convergent adaptation in maize and teosinte}, url={https://doi.org/10.7554/eLife.92405}, DOI={10.7554/eLife.92405}, abstractNote={What is the genetic architecture of local adaptation and what is the geographic scale over which it operates? We investigated patterns of local and convergent adaptation in five sympatric population pairs of traditionally cultivated maize and its wild relative teosinte (Zea mays subsp. parviglumis). We found that signatures of local adaptation based on the inference of adaptive fixations and selective sweeps are frequently exclusive to individual populations, more so in teosinte compared to maize. However, for both maize and teosinte, selective sweeps are also frequently shared by several populations, and often between subspecies. We were further able to infer that selective sweeps were shared among populations most often via migration, though sharing via standing variation was also common. Our analyses suggest that teosinte has been a continued source of beneficial alleles for maize, even after domestication, and that maize populations have facilitated adaptation in teosinte by moving beneficial alleles across the landscape. Taken together, our results suggest local adaptation in maize and teosinte has an intermediate geographic scale, one that is larger than individual populations, but smaller than the species range.}, author={Tittes, Silas and Lorant, Anne and McGinty, Sean and Holland, James B. and Jesus Sánchez-González, Jose and Seetharam, Arun and Tenaillon, Maud and Ross-Ibarra, Jeffrey}, year={2023}, month={Nov} }
 @article{dobbs_sousa-ortega_holland_snyder_leon_2023, title={Variability structure and heritability of germination timing in <i>Capsella bursa-pastoris</i> (L.) Medik. (Shepherd&apos;s purse)}, volume={12}, ISSN={["1365-3180"]}, url={https://doi.org/10.1111/wre.12605}, DOI={10.1111/wre.12605}, abstractNote={AbstractGermination variability enables weedy species to colonise disturbed habitats and is expected to evolve in response to changing selection pressures. The paucity of information about germination variability in weeds prompted a detailed study of this topic with two agricultural and two non‐agricultural populations of Capsella bursa‐pastoris (Shepherd's purse). Variance in germination time was partitioned amongst and within populations, and amongst racemes and silicles within individual plant, and broad‐sense heritability (H2) was estimated. Agricultural populations exhibited a shorter and more uniform germination timing than non‐agricultural populations. However, differences amongst populations explained 7%–12% of the total variance, while differences amongst individuals and racemes accounted for approximately 40–54% and 10% of the total variance for germination time. For germination time, H2 = 0.4 when averaged across all time points, peaking at H2 = 0.7 at a time coinciding with the exponential phase of the germination curve. Maintaining predominantly intrapopulation variability in germination timing appears to be important for long‐term fitness in this species.}, journal={WEED RESEARCH}, author={Dobbs, April M. and Sousa-Ortega, Carlos and Holland, James B. and Snyder, Lori Unruh and Leon, Ramon G.}, year={2023}, month={Dec} }
 @article{butoto_brewer_holland_2022, title={Empirical comparison of genomic and phenotypic selection for resistance to Fusarium ear rot and fumonisin contamination in maize}, volume={7}, ISSN={["1432-2242"]}, url={https://doi.org/10.1007/s00122-022-04150-8}, DOI={10.1007/s00122-022-04150-8}, abstractNote={GS and PS performed similarly in improving resistance to FER and FUM content. With cheaper and faster genotyping methods, GS has the potential to be more efficient than PS. Fusarium verticillioides is a common maize (Zea mays L.) pathogen that causes Fusarium ear rot (FER) and produces the mycotoxin fumonisin (FUM). This study empirically compared phenotypic selection (PS) and genomic selection (GS) for improving FER and FUM resistance. Three intermating generations of recurrent GS were conducted in the same time frame and from a common base population as two generations of recurrent PS. Lines sampled from each PS and GS cycle were evaluated in three North Carolina environments in 2020. We observed similar cumulative responses to GS and PS, representing decreases of about 50% of mean FER and FUM compared to the base population. The first cycle of GS was more effective than later cycles. PS and GS both achieved about 70% of predicted total gain from selection for FER, but only about 26% of predicted gains for FUM, suggesting that heritability for FUM was overestimated. We observed a 20% decrease in genetic marker variation from PS and 30% decrease from GS. Our greatest challenge was our inability to quickly obtain dense and consistent set of marker genotypes across generations of GS. Practical implementation of GS in individual small-scale breeding programs will require cheaper and faster genotyping methods, and such technological advances will present opportunities to significantly optimize selection and mating schemes for future GS efforts beyond what we were able to achieve in this study.}, journal={THEORETICAL AND APPLIED GENETICS}, author={Butoto, Eric N. and Brewer, Jason C. and Holland, James B.}, year={2022}, month={Jul} }
 @article{rogers_bian_krakowsky_peters_turnbull_nelson_holland_2022, title={Genomic prediction for the Germplasm Enhancement of Maize project}, volume={10}, ISSN={["1940-3372"]}, url={https://doi.org/10.1002/tpg2.20267}, DOI={10.1002/tpg2.20267}, abstractNote={AbstractThe Germplasm Enhancement of Maize (GEM) project was initiated in 1993 as a cooperative effort of public‐ and private‐sector maize (Zea mays L.) breeders to enhance the genetic diversity of the U.S. maize crop. The GEM project selects progeny lines with high topcross yield potential from crosses between elite temperate lines and exotic parents. The GEM project has released hundreds of useful breeding lines based on phenotypic selection within selfing generations and multienvironment yield evaluations of GEM line topcrosses to elite adapted testers. Developing genomic selection (GS) models for the GEM project may contribute to increases in the rate of genetic gain. Here we evaluated the prediction ability of GS models trained on 6 yr of topcross evaluations from the two GEM programs in Raleigh, NC, and Ames, IA, documenting prediction abilities ranging from 0.36 to 0.75 for grain yield and from 0.78 to 0.96 for grain moisture when models were cross‐validated within program and heterotic group. Predicted genetic gain from GS ranged from 0.95 to 2.58 times the gain from phenotypic selection. Prediction ability across program and heterotic group was generally poorer than within groups. Based on observed genomic relationships between GEM breeding lines and their tropical ancestors, GS for either yield or moisture would reduce recovery of exotic germplasm only slightly. Using GS models trained within program, the GEM programs should be able to more effectively deliver on its mission to broaden the genetic base of U.S. germplasm.}, journal={PLANT GENOME}, author={Rogers, Anna R. and Bian, Yang and Krakowsky, Matthew and Peters, David and Turnbull, Clint and Nelson, Paul and Holland, James B.}, year={2022}, month={Oct} }
 @article{billings_jones_rustgi_bridges_holland_hulse-kemp_campbell_2022, title={Outlook for Implementation of Genomics-Based Selection in Public Cotton Breeding Programs}, volume={11}, ISSN={["2223-7747"]}, url={https://doi.org/10.3390/plants11111446}, DOI={10.3390/plants11111446}, abstractNote={Researchers have used quantitative genetics to map cotton fiber quality and agronomic performance loci, but many alleles may be population or environment-specific, limiting their usefulness in a pedigree selection, inbreeding-based system. Here, we utilized genotypic and phenotypic data on a panel of 80 important historical Upland cotton (Gossypium hirsutum L.) lines to investigate the potential for genomics-based selection within a cotton breeding program’s relatively closed gene pool. We performed a genome-wide association study (GWAS) to identify alleles correlated to 20 fiber quality, seed composition, and yield traits and looked for a consistent detection of GWAS hits across 14 individual field trials. We also explored the potential for genomic prediction to capture genotypic variation for these quantitative traits and tested the incorporation of GWAS hits into the prediction model. Overall, we found that genomic selection programs for fiber quality can begin immediately, and the prediction ability for most other traits is lower but commensurate with heritability. Stably detected GWAS hits can improve prediction accuracy, although a significance threshold must be carefully chosen to include a marker as a fixed effect. We place these results in the context of modern public cotton line-breeding and highlight the need for a community-based approach to amass the data and expertise necessary to launch US public-sector cotton breeders into the genomics-based selection era.}, number={11}, journal={PLANTS-BASEL}, author={Billings, Grant T. and Jones, Michael A. and Rustgi, Sachin and Bridges, William C. and Holland, James B. and Hulse-Kemp, Amanda M. and Campbell, B. Todd}, year={2022}, month={Jun} }
 @article{holland_2022, title={Saving Genetic Diversity in Seed Banks}, url={https://doi.org/10.52750/958664}, DOI={10.52750/958664}, abstractNote={In the U.S., most corn crops are hybrids.Jim Holland, Ph.D., discusses how the genetic diversity of the modern corn crop is considerably narrower than open-pollinated crops, and farmers must buy new seed every year from seed companies.Scientists who recognized implications of hybridization began systematically collecting seeds from open-pollinated varieties, classifying them and storing them in seed banks that require strict environmental conditions to maintain viable seeds.There are ongoing efforts to explore and reclaim the food culture surrounding corn in the Southeastern U.S.}, author={Holland, Jim}, year={2022}, month={Aug} }
 @article{holland_2022, title={The History of Maize}, url={https://doi.org/10.52750/273626}, DOI={10.52750/273626}, abstractNote={In this video, Jim Holland, Ph.D., first discusses the characteristics of the wild grass called teosinte, which was domesticated about 9000 years ago in Southern Mexico. Ancient peoples selected natural variants that were more amenable to harvest and consumption by humans, eventually resulting in creating maize, or the corn we know today. He then discusses the spread of maize to most of the Americas, from Canada to Chile.Â}, author={Holland, Jim}, year={2022}, month={Aug} }
 @article{chen_samayoa_yang_olukolu_york_sanchez-gonzalez_xue_glaubitz_bradbury_romay_et al._2021, title={A conserved genetic architecture among populations of the maize progenitor, teosinte, was radically altered by domestication}, volume={118}, ISSN={["1091-6490"]}, DOI={10.1073/pnas.2112970118j1of10}, number={43}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Chen, Qiuyue and Samayoa, Luis Fernando and Yang, Chin Jian and Olukolu, Bode A. and York, Alessandra M. and Sanchez-Gonzalez, Jose de Jesus and Xue, Wei and Glaubitz, Jeffrey C. and Bradbury, Peter J. and Romay, Maria Cinta and et al.}, year={2021}, month={Oct} }
 @article{dewitt_guedira_lauer_murphy_marshall_mergoum_johnson_holland_brown-guedira_2021, title={Characterizing the oligogenic architecture of plant growth phenotypes informs genomic selection approaches in a common wheat population}, volume={22}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-021-07574-6}, abstractNote={Abstract
                Background
                Genetic variation in growth over the course of the season is a major source of grain yield variation in wheat, and for this reason variants controlling heading date and plant height are among the best-characterized in wheat genetics. While the major variants for these traits have been cloned, the importance of these variants in contributing to genetic variation for plant growth over time is not fully understood. Here we develop a biparental population segregating for major variants for both plant height and flowering time to characterize the genetic architecture of the traits and identify additional novel QTL.
              
                Results
                We find that additive genetic variation for both traits is almost entirely associated with major and moderate-effect QTL, including four novel heading date QTL and four novel plant height QTL. FT2 and Vrn-A3 are proposed as candidate genes underlying QTL on chromosomes 3A and 7A, while Rht8 is mapped to chromosome 2D. These mapped QTL also underlie genetic variation in a longitudinal analysis of plant growth over time. The oligogenic architecture of these traits is further demonstrated by the superior trait prediction accuracy of QTL-based prediction models compared to polygenic genomic selection models.
              
                Conclusions
                In a population constructed from two modern wheat cultivars adapted to the southeast U.S., almost all additive genetic variation in plant growth traits is associated with known major variants or novel moderate-effect QTL. Major transgressive segregation was observed in this population despite the similar plant height and heading date characters of the parental lines. This segregation is being driven primarily by a small number of mapped QTL, instead of by many small-effect, undetected QTL. As most breeding populations in the southeast U.S. segregate for known QTL for these traits, genetic variation in plant height and heading date in these populations likely emerges from similar combinations of major and moderate effect QTL. We can make more accurate and cost-effective prediction models by targeted genotyping of key SNPs.
              }, number={1}, journal={BMC GENOMICS}, author={DeWitt, Noah and Guedira, Mohammed and Lauer, Edwin and Murphy, J. Paul and Marshall, David and Mergoum, Mohamed and Johnson, Jerry and Holland, James B. and Brown-Guedira, Gina}, year={2021}, month={May} }
 @article{holland_samayoa_olukolu_yang_chen_stetter_york_jesus sanchez-gonzalez_glaubitz_bradbury_et al._2021, title={Domestication Reshaped the Genetic Basis of Inbreeding Depression in a Maize Landrace Compared to its Wild Relative, Teosinte}, volume={9}, url={https://doi.org/10.1101/2021.09.01.458502}, DOI={10.1101/2021.09.01.458502}, abstractNote={AbstractInbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to rare large-effect variation versus potentially more common variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load predicted from sequence data in the maize population. For many traits - and more commonly in maize - genetic variation among selffertilized families was less than expected based on additive and dominance variance estimated in outcrossed families, suggesting that a negative covariance between additive and homozygous dominance effects limits the variation available to selection under partial inbreeding. We identified quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, smalleffect recessive variation underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following to the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against large effect variants, but polygenic load is harder to purge and segregating mutational burden increased in maize compared to teosinte.}, journal={bioRxiv}, publisher={Cold Spring Harbor Laboratory}, author={Holland, James B. and Samayoa, L.F. and Olukolu, B.A. and Yang, C.J. and Chen, Q. and Stetter, Markus G. and York, Alessandra M. and Jesus Sanchez-Gonzalez, Jose and Glaubitz, Jeffrey C. and Bradbury, Peter J. and et al.}, year={2021}, month={Sep} }
 @article{samayoa_olukolu_yang_chen_stetter_york_sanchez-gonzalez_glaubitz_bradbury_romay_et al._2021, title={Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte}, volume={17}, ISSN={["1553-7404"]}, url={https://doi.org/10.1371/journal.pgen.1009797}, DOI={10.1371/journal.pgen.1009797}, abstractNote={Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to large-effect mutations versus variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load in the maize population that we predicted from sequence data. Parental breeding values were highly consistent between outcross and selfed offspring, indicating that additive effects determine most of the genetic value even in the presence of strong inbreeding depression. We developed a novel linkage scan to identify quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, small-effect partially recessive effects in linkage disequilibrium underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against some large effect variants, but polygenic load is harder to purge and overall segregating mutational burden increased in maize compared to teosinte.}, number={12}, journal={PLOS GENETICS}, publisher={Public Library of Science (PLoS)}, author={Samayoa, Luis Fernando and Olukolu, Bode A. and Yang, Chin Jian and Chen, Qiuyue and Stetter, Markus G. and York, Alessandra M. and Sanchez-Gonzalez, Jose de Jesus and Glaubitz, Jeffrey C. and Bradbury, Peter J. and Romay, Maria Cinta and et al.}, editor={Walsh, BruceEditor}, year={2021}, month={Dec} }
 @article{chiango_jafarikouhini_pradhan_figueiredo_silva_sinclair_holland_2021, title={Drought resilience in CIMMYT maize lines adapted to Africa resulting from transpiration sensitivity to vapor pressure deficit and soil drying}, volume={8}, ISSN={["1542-7536"]}, DOI={10.1080/15427528.2021.1961334}, abstractNote={ABSTRACT Low rainfall limits crop yield, particularly for maize (Zea mays L.) in southern Africa. Consequently, there is a need to identify genetic sources of specific drought-related traits that can contribute to soil water conservation and increased yields under water-limited conditions. In this study, maize genotypes released for production in southern Africa were tested for expression of two soil water-conservation traits: limited transpiration under elevated vapor pressure deficit (VPD) and decreased transpiration rate at high soil water contents earlier in the soil drying cycle. Two genotypes, CML 590 and CML 593, were identified and confirmed to initiate expression of limited-transpiration rate at VPD above about 1.9 kPa. In the soil-drying experiment, Umbelu 8923 and Umbelu 8930 closed their stomata earliest in the soil drying cycle as compared to other tested genotypes. These four genotypes with specific physiological traits for superior response to water deficit are genetic resources for further study to improve maize drought resilience.}, journal={JOURNAL OF CROP IMPROVEMENT}, author={Chiango, H. and Jafarikouhini, N. and Pradhan, D. and Figueiredo, A. and Silva, J. and Sinclair, T. R. and Holland, J.}, year={2021}, month={Aug} }
 @article{butoto_marino_holland_2021, title={Effects of artificial inoculation on trait correlations with resistance to Fusarium ear rot and fumonisin contamination in maize}, volume={5}, ISSN={["1435-0653"]}, url={https://doi.org/10.1002/csc2.20551}, DOI={10.1002/csc2.20551}, abstractNote={AbstractBreeding for resistance to Fusarium ear rot (FER; Fusarium verticillioides Nirenberg) and fumonisin (FUM) contamination in maize (Zea mays L.) is labor intensive, time consuming, and expensive. The objective of this study is to explore three possible shortcuts to improve the efficiency of breeding for resistance to FER and FUM: relying on natural instead of artificial inoculation of Fusarium verticillioides, selecting inbred lines per se instead of topcross hybrids, and using grain test weight (TW) as an indirect selection criterion. We selected the 27 most resistant and 26 most susceptible S0:1 lines from the third cycle of a broad‐based recurrent selection population and topcrossed them to a common inbred line. The resulting topcross hybrids were evaluated in three North Carolina environments under artificial and natural inoculation of F. verticillioides. The entry‐mean heritabilities for FER and FUM are considerably reduced under natural conditions compared to artificial inoculation; therefore, artificial inoculation should be practiced for efficient selection for resistance. We found a high correlation between FER and FUM content of S0:1 lines per se and their topcross hybrids, suggesting that selection among early generation inbred lines per se is an efficient method to improve resistance in their topcross hybrids. The TW of inoculated S0:1 lines per se was strongly and negatively correlated with FER and FUM of their topcross hybrids, suggesting that TW can be utilized as an indirect selection criterion to improve resistance to FER and FUM contamination.}, journal={CROP SCIENCE}, publisher={Wiley}, author={Butoto, Eric N. and Marino, Thiago P. and Holland, James B.}, year={2021}, month={Jun} }
 @article{rogers_holland_2022, title={Environment-specific genomic prediction ability in maize using environmental covariates depends on environmental similarity to training data}, volume={12}, ISSN={["2160-1836"]}, url={https://doi.org/10.1093/g3journal/jkab440}, DOI={10.1093/g3journal/jkab440}, abstractNote={Abstract
               Technology advances have made possible the collection of a wealth of genomic, environmental, and phenotypic data for use in plant breeding. Incorporation of environmental data into environment-specific genomic prediction is hindered in part because of inherently high data dimensionality. Computationally efficient approaches to combining genomic and environmental information may facilitate extension of genomic prediction models to new environments and germplasm, and better understanding of genotype-by-environment (G × E) interactions. Using genomic, yield trial, and environmental data on 1,918 unique hybrids evaluated in 59 environments from the maize Genomes to Fields project, we determined that a set of 10,153 SNP dominance coefficients and a 5-day temporal window size for summarizing environmental variables were optimal for genomic prediction using only genetic and environmental main effects. Adding marker-by-environment variable interactions required dimension reduction, and we found that reducing dimensionality of the genetic data while keeping the full set of environmental covariates was best for environment-specific genomic prediction of grain yield, leading to an increase in prediction ability of 2.7% to achieve a prediction ability of 80% across environments when data were masked at random. We then measured how prediction ability within environments was affected under stratified training-testing sets to approximate scenarios commonly encountered by plant breeders, finding that incorporation of marker-by-environment effects improved prediction ability in cases where training and test sets shared environments, but did not improve prediction in new untested environments. The environmental similarity between training and testing sets had a greater impact on the efficacy of prediction than genetic similarity between training and test sets.}, number={2}, journal={G3-GENES GENOMES GENETICS}, publisher={Oxford University Press (OUP)}, author={Rogers, Anna R. and Holland, James B.}, editor={Lipka, AEditor}, year={2022}, month={Feb} }
 @article{tittes_lorant_mcginty_holland_jesus sánchez-gonzález_seetharam_tenaillon_ross-ibarra_2021, title={Not so local: the population genetics of convergent adaptation in maize and teosinte}, url={https://doi.org/10.1101/2021.09.09.459637}, DOI={10.1101/2021.09.09.459637}, abstractNote={ABSTRACTWhat is the genetic architecture of local adaptation and what is the geographic scale over which it operates? We investigated patterns of local and convergent adaptation in five sympatric population pairs of traditionally cultivated maize and its wild relative teosinte (Zea mayssubsp.parviglumis). We found that signatures of local adaptation based on the inference of adaptive fixations and selective sweeps are frequently exclusive to individual populations, more so in teosinte compared to maize. However, for both maize and teosinte, selective sweeps are also frequently shared by several populations, and often between subspecies. We were further able to infer that selective sweeps were shared among populations most often via migration, though sharing via standing variation was also common. Our analyses suggest that teosinte has been a continued source of beneficial alleles for maize, even after domestication, and that maize populations have facilitated adaptation in teosinte by moving beneficial alleles across the landscape. Taken together, our results suggest local adaptation in maize and teosinte has an intermediate geographic scale, one that is larger than individual populations, but smaller than the species range.}, author={Tittes, Silas and Lorant, Anne and McGinty, Sean and Holland, James B. and Jesus Sánchez-González, Jose and Seetharam, Arun and Tenaillon, Maud and Ross-Ibarra, Jeffrey}, year={2021}, month={Sep} }
 @article{lauer_holland_isik_2022, title={Prediction ability of genome-wide markers in Pinus taeda L. within and between population is affected by relatedness to the training population and trait genetic architecture}, volume={12}, ISSN={["2160-1836"]}, url={https://doi.org/10.1093/g3journal/jkab405}, DOI={10.1093/g3journal/jkab405}, abstractNote={Abstract
               Genomic prediction has the potential to significantly increase the rate of genetic gain in tree breeding programs. In this study, a clonally replicated population (n = 2063) was used to train a genomic prediction model. The model was validated both within the training population and in a separate population (n = 451). The prediction abilities from random (20% vs 80%) cross validation within the training population were 0.56 and 0.78 for height and stem form, respectively. Removal of all full-sib relatives within the training population resulted in ∼50% reduction in their genomic prediction ability for both traits. The average prediction ability for all 451 individual trees was 0.29 for height and 0.57 for stem form. The degree of genetic linkage (full-sib family, half sib family, unrelated) between the training and validation sets had a strong impact on prediction ability for stem form but not for height. A dominant dwarfing allele, the first to be reported in a conifer species, was discovered via genome-wide association studies on linkage Group 5 that conferred a 0.33-m mean height reduction. However, the QTL was family specific. The rapid decay of linkage disequilibrium, large genome size, and inconsistencies in marker-QTL linkage phase suggest that large, diverse training populations are needed for genomic selection in Pinus taeda L.}, number={2}, journal={G3-GENES GENOMES GENETICS}, publisher={Oxford University Press (OUP)}, author={Lauer, Edwin and Holland, James and Isik, Fikret}, editor={Lipka, AEditor}, year={2022}, month={Feb} }
 @article{weldekidan_manching_choquette_leon_flint-garcia_holland_lauter_murray_xu_goodman_et al._2021, title={Registration of tropical populations of maize selected in parallel for early flowering time across the United States}, volume={10}, ISSN={["1940-3496"]}, url={https://doi.org/10.1002/plr2.20181}, DOI={10.1002/plr2.20181}, abstractNote={AbstractTropical strains of maize (Zea mays subsp. mays L.) flower very late in temperate environments. This is a barrier to maize diversification and improvement in regions where a large share of the world's corn production takes place. For investigating early flowering time adaptation, a tightly controlled parallel selection experiment spanning a 28° latitudinal range (∼3,100 km) across the United States was conducted. First, a tropical synthetic population (TropicS‐G0) (Reg. no. GP‐605, PI 698625) of maize was created from seven inbred parents. The molecular genetic diversity in TropicS‐G0 is representative of tropical inbreds that are differentiated from the prevailing germplasm used for hybrid production in the United States. Admixture analysis and genome simulation showed that breeding of TropicS‐G0 captured the parental genomes mostly at random, as intended prior to selection. With TropicS‐G0 as a common base population, a standardized protocol was used to recurrently select for early flowering time at eight locations for two generations, giving rise to location‐specific lineages (TropicS‐G1‐PR, Reg. no. GP‐621, PI 698641; TropicS‐G2‐PR, Reg. no. GP‐622, PI 698642; TropicS‐G2‐FL, Reg. no. GP‐620, PI 698640; TropicS‐G1‐cTX, Reg. no. GP‐618, PI 698638; TropicS‐G2‐cTX, Reg. no. GP‐619, PI 698639; TropicS‐G1‐nTX, Reg. no. GP‐616, PI 698636; TropicS‐G2‐nTX, Reg. no. GP‐617, PI 698637; TropicS‐G1‐NC, Reg. no. GP‐614, PI 698634; TropicS‐G2‐NC, Reg. no. GP‐615, PI 698635; TropicS‐G1‐DE, Reg. no. GP‐610, PI 698630; TropicS‐G1‐IA, Reg. no. GP‐608, PI 698628; TropicS‐G2‐IA, Reg. no. GP‐609, PI 698629; TropicS‐G1‐WI, Reg. no. GP‐606, PI 698626; TropicS‐G2‐WI, Reg. no. GP‐607, PI 698627). Additional generations of selection were performed for the DE lineage (TropicS‐G3‐DE, Reg. no. GP‐611, PI 698631; TropicS‐G4‐DE, Reg. no. GP‐612, PI 698632; TropicS‐G5‐DE, Reg. no. GP‐613, PI 698633). The parallel‐selected maize population is a novel resource for breeders and those seeking to investigate adaptation.}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Weldekidan, Teclemariam and Manching, Heather and Choquette, Nicole and Leon, Natalia and Flint-Garcia, Sherry and Holland, James and Lauter, Nick and Murray, Seth C. and Xu, Wenwei and Goodman, Major M. and et al.}, year={2021}, month={Oct} }
 @article{rogers_dunne_romay_bohn_buckler_ciampitti_edwards_ertl_flint-garcia_gore_et al._2021, title={The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment}, volume={11}, ISSN={["2160-1836"]}, DOI={10.1093/g3journal/jkaa050}, abstractNote={AbstractHigh-dimensional and high-throughput genomic, field performance, and environmental data are becoming increasingly available to crop breeding programs, and their integration can facilitate genomic prediction within and across environments and provide insights into the genetic architecture of complex traits and the nature of genotype-by-environment interactions. To partition trait variation into additive and dominance (main effect) genetic and corresponding genetic-by-environment variances, and to identify specific environmental factors that influence genotype-by-environment interactions, we curated and analyzed genotypic and phenotypic data on 1918 maize (Zea mays L.) hybrids and environmental data from 65 testing environments. For grain yield, dominance variance was similar in magnitude to additive variance, and genetic-by-environment variances were more important than genetic main effect variances. Models involving both additive and dominance relationships best fit the data and modeling unique genetic covariances among all environments provided the best characterization of the genotype-by-environment interaction patterns. Similarity of relative hybrid performance among environments was modeled as a function of underlying weather variables, permitting identification of weather covariates driving correlations of genetic effects across environments. The resulting models can be used for genomic prediction of mean hybrid performance across populations of environments tested or for environment-specific predictions. These results can also guide efforts to incorporate high-throughput environmental data into genomic prediction models and predict values in new environments characterized with the same environmental characteristics.}, number={2}, journal={G3-GENES GENOMES GENETICS}, author={Rogers, Anna R. and Dunne, Jeffrey C. and Romay, Cinta and Bohn, Martin and Buckler, Edward S. and Ciampitti, Ignacio A. and Edwards, Jode and Ertl, David and Flint-Garcia, Sherry and Gore, Michael A. and et al.}, year={2021}, month={Feb} }
 @article{woore_flint-garcia_holland_2021, title={The potential to breed a low-protein maize for protein-restricted diets}, volume={61}, ISSN={["1435-0653"]}, url={https://doi.org/10.1002/csc2.20600}, DOI={10.1002/csc2.20600}, abstractNote={AbstractInborn errors of amino acid metabolism, such as phenylketonuria (PKU), are human genetic conditions that result in an inability to metabolize certain amino acids, requiring lifelong maintenance of a very restrictive low‐protein diet. In the case of PKU, this diet does not permit consumption of most maize (Zea mays L.) products, yet maize is a major part of the human diet and is especially significant in some cultures. Kernel protein content, and to a lesser extent amino acid composition, is variable in maize. Breeding maize for low kernel protein content or low amounts of specific amino acids such as phenylalanine might expand the restrictive diets and improve quality of life for people with amino acid metabolic disorders. To test the potential of breeding low‐protein‐content maize, diverse samples of hybrid or open‐pollinated cultivars and inbreds were evaluated across two locations in two years for grain protein content and amino acid composition. Consistent with previous reports, kernel protein content varied widely across maize varieties and is highly heritable in the broad sense. We found that phenylalanine content (as a proportion of grain weight) and phenylalanine composition (as a proportion of total protein) are also highly heritable in the broad sense. As previously reported, reasonably accurate estimation of protein content is possible with near‐infrared spectrophotometry, whereas measuring phenylalanine content requires a destructive, costly, and time‐consuming laboratory analysis. Because phenylalanine content was strongly correlated with total kernel protein, breeding primarily aimed at reducing grain protein content should permit efficient selection of maize cultivars sufficiently low in phenylalanine to permit broader inclusion in the PKU diet.}, number={6}, journal={CROP SCIENCE}, publisher={Wiley}, author={Woore, Matthew S. and Flint-Garcia, Sherry A. and Holland, James B.}, year={2021}, month={Sep} }
 @article{jarquin_leon_romay_bohn_buckler_ciampitti_edwards_ertl_flint-garcia_gore_et al._2021, title={Utility of Climatic Information via Combining Ability Models to Improve Genomic Prediction for Yield Within the Genomes to Fields Maize Project}, volume={11}, ISSN={["1664-8021"]}, DOI={10.3389/fgene.2020.592769}, abstractNote={Genomic prediction provides an efficient alternative to conventional phenotypic selection for developing improved cultivars with desirable characteristics. New and improved methods to genomic prediction are continually being developed that attempt to deal with the integration of data types beyond genomic information. Modern automated weather systems offer the opportunity to capture continuous data on a range of environmental parameters at specific field locations. In principle, this information could characterize training and target environments and enhance predictive ability by incorporating weather characteristics as part of the genotype-by-environment (G×E) interaction component in prediction models. We assessed the usefulness of including weather data variables in genomic prediction models using a naïve environmental kinship model across 30 environments comprising the Genomes to Fields (G2F) initiative in 2014 and 2015. Specifically four different prediction scenarios were evaluated (i) tested genotypes in observed environments; (ii) untested genotypes in observed environments; (iii) tested genotypes in unobserved environments; and (iv) untested genotypes in unobserved environments. A set of 1,481 unique hybrids were evaluated for grain yield. Evaluations were conducted using five different models including main effect of environments; general combining ability (GCA) effects of the maternal and paternal parents modeled using the genomic relationship matrix; specific combining ability (SCA) effects between maternal and paternal parents; interactions between genetic (GCA and SCA) effects and environmental effects; and finally interactions between the genetics effects and environmental covariates. Incorporation of the genotype-by-environment interaction term improved predictive ability across all scenarios. However, predictive ability was not improved through inclusion of naive environmental covariates in G×E models. More research should be conducted to link the observed weather conditions with important physiological aspects in plant development to improve predictive ability through the inclusion of weather data.}, journal={FRONTIERS IN GENETICS}, author={Jarquin, Diego and Leon, Natalia and Romay, Cinta and Bohn, Martin and Buckler, Edward S. and Ciampitti, Ignacio and Edwards, Jode and Ertl, David and Flint-Garcia, Sherry and Gore, Michael A. and et al.}, year={2021}, month={Mar} }
 @article{stagnati_rahjoo_samayoa_holland_borrelli_busconi_lanubile_marocco_2020, title={A Genome-Wide Association Study To Understand the Effect of Fusarium verticillioides Infection on Seedlings of a Maize Diversity Panel}, volume={10}, ISSN={["2160-1836"]}, url={https://doi.org/10.1534/g3.119.400987}, DOI={10.1534/g3.119.400987}, abstractNote={Abstract
               Fusarium verticillioides, which causes ear, kernel and stem rots, has been reported as the most prevalent species on maize worldwide. Kernel infection by F. verticillioides results in reduced seed yield and quality as well as fumonisin contamination, and may affect seedling traits like germination rate, entire plant seedling length and weight. Maize resistance to Fusarium is a quantitative and complex trait controlled by numerous genes with small effects. In the present work, a Genome Wide Association Study (GWAS) of traits related to Fusarium seedling rot was carried out in 230 lines of a maize association population using 226,446 SNP markers. Phenotypes were scored on artificially infected kernels applying the rolled towel assay screening method and three traits related to disease response were measured in inoculated and not-inoculated seedlings: plant seedling length (PL), plant seedling weight (PW) and germination rate (GERM). Overall, GWAS resulted in 42 SNPs significantly associated with the examined traits. Two and eleven SNPs were associated with PL in inoculated and not-inoculated samples, respectively. Additionally, six and one SNPs were associated with PW and GERM traits in not-inoculated kernels, and further nine and thirteen SNPs were associated to the same traits in inoculated kernels. Five genes containing the significant SNPs or physically closed to them were proposed for Fusarium resistance, and 18 out of 25 genes containing or adjacent to significant SNPs identified by GWAS in the current research co-localized within QTL regions previously reported for resistance to Fusarium seed rot, Fusarium ear rot and fumonisin accumulation. Furthermore, linkage disequilibrium analysis revealed an additional gene not directly observed by GWAS analysis. These findings could aid to better understand the complex interaction between maize and F. verticillioides.}, number={5}, journal={G3-GENES GENOMES GENETICS}, publisher={Oxford University Press (OUP)}, author={Stagnati, Lorenzo and Rahjoo, Vahid and Samayoa, Luis F. and Holland, James B. and Borrelli, Virginia M. G. and Busconi, Matteo and Lanubile, Alessandra and Marocco, Adriano}, year={2020}, month={May}, pages={1685–1696} }
 @article{kuki_barth pinto_bengosi bertagna_tessmann_amaral junior_scapim_holland_2020, title={Association mapping and genomic prediction for ear rot disease caused by Fusarium verticillioides in a tropical maize germplasm}, volume={60}, ISSN={["1435-0653"]}, url={https://doi.org/10.1002/csc2.20272}, DOI={10.1002/csc2.20272}, abstractNote={AbstractFusarium ear rot (FER), caused by Fusarium verticillioides (Sacc.) Nirenberg, is one of the major ear diseases that affect both yield and grain quality in maize (Zea mays L.), especially in tropical environments. Fusarium genetic resistance is a complex trait, controlled by several small‐effect genes and strongly influenced by the environment. We applied a comprehensive genome‐wide association study and genomic prediction for ear rot and starburst symptoms, using 291,633 high‐quality single nucleotide polymorphism (SNPs) markers in 320 tropical maize inbred lines, in two distinct locations in Brazil's southern region. Three SNPs were significantly associated with starburst symptoms, each associated with 6–8% of the phenotypic variance, and with gene models that have expression levels in ears, pericarp, and kernels, corresponding to disease infection period and suggesting some role in FER resistance. No significant SNP was associated with FER, which is an indication that the genetic architecture for this trait is highly polygenic, with potentially many variants having small effects that are not detectable in the association mapping analysis. We observed genomic prediction accuracies ranging from 0.34 to 0.4 for FER and starburst, respectively. Further research is required to validate these significant SNPs and their relationship to genes affecting FER resistance, and also to improve genomic prediction accuracies across different genetic backgrounds.}, number={6}, journal={CROP SCIENCE}, publisher={Wiley}, author={Kuki, Mauricio Carlos and Barth Pinto, Ronald Jose and Bengosi Bertagna, Filipe Augusto and Tessmann, Dauri Jose and Amaral Junior, Antonio Teixeira and Scapim, Carlos Alberto and Holland, James Brendan}, year={2020}, pages={2867–2881} }
 @article{ramstein_larsson_cook_edwards_ersoz_flint-garcia_gardner_holland_lorenz_mcmullen_et al._2020, title={Dominance Effects and Functional Enrichments Improve Prediction of Agronomic Traits in Hybrid Maize}, volume={215}, ISSN={["1943-2631"]}, url={https://doi.org/10.1534/genetics.120.303025}, DOI={10.1534/genetics.120.303025}, abstractNote={Abstract
               Single-cross hybrids have been critical to the improvement of maize (Zea mays L.), but the characterization of their genetic architectures remains challenging. Previous studies of hybrid maize have shown the contribution of within-locus complementation effects (dominance) and their differential importance across functional classes of loci. However, they have generally considered panels of limited genetic diversity, and have shown little benefit from genomic prediction based on dominance or functional enrichments. This study investigates the relevance of dominance and functional classes of variants in genomic models for agronomic traits in diverse populations of hybrid maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the U.S. (1106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1640 hybrids). We investigated three agronomic traits: days to silking (DTS), plant height (PH), and grain yield (GY). Our results point to the presence of dominance for all traits, but also among-locus complementation (epistasis) for DTS and genotype-by-environment interactions for GY. Consistently, dominance improved genomic prediction for PH only. In addition, we assessed enrichment of genetic effects in classes defined by genic regions (gene annotation), structural features (recombination rate and chromatin openness), and evolutionary features (minor allele frequency and evolutionary constraint). We found support for enrichment in genic regions and subsequent improvement of genomic prediction for all traits. Our results suggest that dominance and gene annotations improve genomic prediction across diverse populations in hybrid maize.}, number={1}, journal={GENETICS}, publisher={Genetics Society of America}, author={Ramstein, Guillaume P. and Larsson, Sara J. and Cook, Jason P. and Edwards, Jode W. and Ersoz, Elhan S. and Flint-Garcia, Sherry and Gardner, Candice A. and Holland, James B. and Lorenz, Aaron J. and McMullen, Michael D. and et al.}, year={2020}, month={May}, pages={215–230} }
 @article{diepenbrock_ilut_magallanes-lundback_kandianis_lipka_bradbury_holland_hamilton_wooldridge_vaillancourt_et al._2020, title={Eleven biosynthetic genes explain the majority of natural variation for carotenoid levels in maize grain}, volume={7}, url={https://doi.org/10.1101/2020.07.15.203448}, DOI={10.1101/2020.07.15.203448}, abstractNote={ABSTRACTVitamin A deficiency remains prevalent in parts of Asia, Latin America, and sub-Saharan Africa where maize is a food staple. Extensive natural variation exists for carotenoids in maize grain; to understand its genetic basis, we conducted a joint linkage and genome-wide association study in the U.S. maize nested association mapping panel. Eleven of the 44 detected quantitative trait loci (QTL) were resolved to individual genes. Six of these were correlated expression and effect QTL (ceeQTL), showing strong correlations between RNA-seq expression abundances and QTL allelic effect estimates across six stages of grain development. These six ceeQTL also had the largest percent phenotypic variance explained, and in major part comprised the three to five loci capturing the bulk of genetic variation for each trait. Most of these ceeQTL had strongly correlated QTL allelic effect estimates across multiple traits. These findings provide the most comprehensive genome-level understanding of the genetic and molecular control of carotenoids in any plant system, and a roadmap to accelerate breeding for provitamin A and other priority carotenoid traits in maize grain that should be readily extendable to other cereals.}, publisher={Cold Spring Harbor Laboratory}, author={Diepenbrock, Christine H. and Ilut, Daniel C. and Magallanes-Lundback, Maria and Kandianis, Catherine B. and Lipka, Alexander E. and Bradbury, Peter J. and Holland, James B. and Hamilton, John P. and Wooldridge, Edmund and Vaillancourt, Brieanne and et al.}, year={2020}, month={Jul} }
 @article{diepenbrock_ilut_magallanes-lundback_kandianis_lipka_bradbury_holland_hamilton_wooldridge_vaillancourt_et al._2021, title={Eleven biosynthetic genes explain the majority of natural variation in carotenoid levels in maize grain}, volume={33}, ISSN={["1532-298X"]}, url={https://doi.org/10.1093/plcell/koab032}, DOI={10.1093/plcell/koab032}, abstractNote={Abstract
               Vitamin A deficiency remains prevalent in parts of Asia, Latin America, and sub-Saharan Africa where maize (Zea mays) is a food staple. Extensive natural variation exists for carotenoids in maize grain. Here, to understand its genetic basis, we conducted a joint linkage and genome-wide association study of the US maize nested association mapping panel. Eleven of the 44 detected quantitative trait loci (QTL) were resolved to individual genes. Six of these were correlated expression and effect QTL (ceeQTL), showing strong correlations between RNA-seq expression abundances and QTL allelic effect estimates across six stages of grain development. These six ceeQTL also had the largest percentage of phenotypic variance explained, and in major part comprised the three to five loci capturing the bulk of genetic variation for each trait. Most of these ceeQTL had strongly correlated QTL allelic effect estimates across multiple traits. These findings provide an in-depth genome-level understanding of the genetic and molecular control of carotenoids in plants. In addition, these findings provide a roadmap to accelerate breeding for provitamin A and other priority carotenoid traits in maize grain that should be readily extendable to other cereals.}, number={4}, journal={PLANT CELL}, publisher={Oxford University Press (OUP)}, author={Diepenbrock, Christine H. and Ilut, Daniel C. and Magallanes-Lundback, Maria and Kandianis, Catherine B. and Lipka, Alexander E. and Bradbury, Peter J. and Holland, James B. and Hamilton, John P. and Wooldridge, Edmund and Vaillancourt, Brieanne and et al.}, year={2021}, month={Apr}, pages={882–900} }
 @article{dewitt_guedira_lauer_murphy_marshall_mergoum_johnson_holland_brown-guedira_2020, title={Genetic variation for plant growth traits in a common wheat population is dominated by known variants and novel QTL}, url={https://doi.org/10.1101/2020.12.16.422696}, DOI={10.1101/2020.12.16.422696}, abstractNote={AbstractGenetic variation in growth over the course of the season is a major source of grain yield variation in wheat, and for this reason variants controlling heading date and plant height are among the best-characterized in wheat genetics. While the major variants for these traits have been cloned, the importance of these variants in contributing to genetic variation for plant growth over time is not fully understood. Here we develop a biparental population segregating for major variants for both plant height and flowering time to characterize the genetic architecture of the traits and identify additional novel QTL. We find that additive genetic variation for both traits is almost entirely associated with major and moderate-effect QTL, including four novel heading date QTL and four novel plant height QTL.FT2andVrn-A3are proposed as candidate genes underlying QTL on chromosomes 3A and 7A, whileRht8is mapped to chromosome 2D. These mapped QTL also underlie genetic variation in a longitudinal analysis of plant growth over time. The oligogenic architecture of these traits is further demonstrated by the superior trait prediction accuracy of QTL-based prediction models compared to polygenic genomic selection models. In a population constructed from two modern wheat cultivars adapted to the southeast U.S., almost all additive genetic variation in plant growth traits is associated with known major variants or novel moderate-effect QTL. Major transgressive segregation was observed in this population despite the similar plant height and heading date characters of the parental lines. This segregation is being driven primarily by a small number of mapped QTL, instead of by many small-effect, undetected QTL. As most breeding populations in the southeast U.S. segregate for known QTL for these traits, genetic variation in plant height and heading date in these populations likely emerges from similar combinations of major and moderate effect QTL. We can make more accurate and cost-effective prediction models by targeted genotyping of key SNPs.}, author={DeWitt, Noah and Guedira, Mohammed and Lauer, Edwin and Murphy, J. Paul and Marshall, David and Mergoum, Mohamed and Johnson, Jerry and Holland, James B. and Brown-Guedira, Gina}, year={2020}, month={Dec} }
 @article{woore_holland_2020, title={Genetic variation for response to mixed triazole and strobilurin application in diverse maize}, volume={3}, url={https://doi.org/10.1002/agg2.20054}, DOI={10.1002/agg2.20054}, abstractNote={AbstractStrobilurin and triazole classes of fungicides have been reported to have growth‐regulating effects on crops in the absence of their target pathogens and to increase maize yield. Because the response of maize (Zea mays L.) plants to a commercially marketed mixture of strobilurin and triazole may not be uniform across genotypes, it may be possible to breed selectively for higher yield responses to application of this chemical treatment. To test this hypothesis, diverse samples of maize inbred lines and hybrids were evaluated for response to a combined mixture of a treatment of strobilurin and triazole. Main effects of treatment and genotype and treatment  × genotype interactions were measured on agronomic traits including grain yield and several yield components, lodging, and delayed leaf senescence. Hybrid and inbred genotype main effect variation was significant for all measured traits. Favorable main effects of strobilurin and triazole treatment were observed only for leaf senescence and foliar disease, and genotype × treatment interactions were not significant for yield or yield components. Yield was significantly increased only in two inbred varieties and did not correlate with any known pedigree or genetic relationships. These results suggest that breeding to enhance the response to strobilurin and triazole treatment is not likely to be effective in maize.}, number={1}, journal={Agrosystems, Geosciences & Environment}, publisher={Wiley}, author={Woore, Matthew Smith and Holland, James Brendan}, year={2020}, month={Jan} }
 @article{samira_kimball_samayoa_holland_jamann_brown_stacey_balint-kurti_2020, title={Genome-wide association analysis of the strength of the MAMP-elicited defense response and resistance to target leaf spot in sorghum}, volume={10}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-020-77684-w}, DOI={10.1038/s41598-020-77684-w}, abstractNote={AbstractPlants have the capacity to respond to conserved molecular features known as microbe-associated molecular patterns (MAMPs). The goal of this work was to assess variation in the MAMP response in sorghum, to map loci associated with this variation, and to investigate possible connections with variation in quantitative disease resistance. Using an assay that measures the production of reactive oxygen species, we assessed variation in the MAMP response in a sorghum association mapping population known as the sorghum conversion population (SCP). We identified consistent variation for the response to chitin and flg22—an epitope of flagellin. We identified two SNP loci associated with variation in the flg22 response and one with the chitin response. We also assessed resistance to Target Leaf Spot (TLS) disease caused by the necrotrophic fungus Bipolaris cookei in the SCP. We identified one strong association on chromosome 5 near a previously characterized disease resistance gene. A moderately significant correlation was observed between stronger flg22 response and lower TLS resistance. Possible reasons for this are discussed.}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Samira, Rozalynne and Kimball, Jennifer A. and Samayoa, Luis Fernando and Holland, James B. and Jamann, Tiffany M. and Brown, Patrick J. and Stacey, Gary and Balint-Kurti, Peter J.}, year={2020}, month={Nov} }
 @article{holland_marino_manching_wisser_2020, title={Genomic prediction for resistance to Fusarium ear rot and fumonisin contamination in maize}, volume={60}, ISSN={["1435-0653"]}, url={https://doi.org/10.1002/csc2.20163}, DOI={10.1002/csc2.20163}, abstractNote={AbstractFusarium ear rot (FER) disease of maize (Zea mays L.) is caused by Fusarium verticillioides (Sacc.) Nirenberg, which produces fumonisin (FUM), a mycotoxin linked to human and animal health risks. Extensive field trials, laborious inoculations and ear evaluations, and expensive antibody assays are required to reliably assess resistances to FER and FUM contamination in breeding populations. To evaluate the potential utility of genomic selection (GS) to improve FER and FUM in maize, we genotyped 6086 single nucleotide polymorphisms (SNPs) on 449 S0:1 lines from a recurrent selection population. Two different partitions of the S0:1 evaluation data were made to test the ability of models trained on 251 or 201 lines evaluated at three locations in 2014–2015 to predict FER and FUM of 198 or 248 different lines evaluated at three locations in 2016. Single‐stage univariate and multivariate genomic best linear unbiased predictor (GBLUP) models and two‐stage GBLUP, Bayes Cπ, Bayesian LASSO, and extreme gradient boosting models were compared for prediction. Maximum prediction accuracy for untested lines in a new year was 0.46 for FER and 0.67 for FUM. Bayesian models optimized for predicting traits influenced by major‐effect loci were best for FUM in one set, despite no evidence for significant individual SNP–trait associations from genome‐wide association study (GWAS) in the training sets; otherwise, GBLUP models were best. These results suggest that GS can help improve resistance to FER and FUM contamination in an applied breeding program.}, number={4}, journal={CROP SCIENCE}, publisher={Wiley}, author={Holland, James B. and Marino, Thiago P. and Manching, Heather C. and Wisser, Randall J.}, year={2020}, pages={1863–1875} }
 @article{wagner_roberts_balint‐kurti_holland_2020, title={Heterosis of leaf and rhizosphere microbiomes in field‐grown maize}, volume={228}, ISSN={0028-646X 1469-8137}, url={http://dx.doi.org/10.1111/nph.16730}, DOI={10.1111/nph.16730}, abstractNote={Summary


Macroorganisms’ genotypes shape their phenotypes, which in turn shape the habitat available to potential microbial symbionts. This influence of host genotype on microbiome composition has been demonstrated in many systems; however, most previous studies have either compared unrelated genotypes or delved into molecular mechanisms. As a result, it is currently unclear whether the heritability of host‐associated microbiomes follows similar patterns to the heritability of other complex traits.

We take a new approach to this question by comparing the microbiomes of diverse maize inbred lines and their F1 hybrid offspring, which we quantified in both rhizosphere and leaves of field‐grown plants using 16S‐v4 and ITS1 amplicon sequencing.

We show that inbred lines and hybrids differ consistently in the composition of bacterial and fungal rhizosphere communities, as well as leaf‐associated fungal communities. A wide range of microbiome features display heterosis within individual crosses, consistent with patterns for nonmicrobial maize phenotypes. For leaf microbiomes, these results were supported by the observation that broad‐sense heritability in hybrids was substantially higher than narrow‐sense heritability.

Our results support our hypothesis that at least some heterotic host traits affect microbiome composition in maize.

}, number={3}, journal={New Phytologist}, publisher={Wiley}, author={Wagner, Maggie R. and Roberts, Joseph H. and Balint‐Kurti, Peter and Holland, James B.}, year={2020}, month={Jul}, pages={1055–1069} }
 @article{mcfarland_alkhalifah_bohn_bubert_buckler_ciampitti_edwards_ertl_gage_falcon_et al._2020, title={Maize genomes to fields (G2F): 2014-2017 field seasons: Genotype, phenotype, climatic, soil, and inbred ear image datasets}, volume={13}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85079338248&partnerID=MN8TOARS}, DOI={10.1186/s13104-020-4922-8}, abstractNote={Abstract
                Objectives
                Advanced tools and resources are needed to efficiently and sustainably produce food for an increasing world population in the context of variable environmental conditions. The maize genomes to fields (G2F) initiative is a multi-institutional initiative effort that seeks to approach this challenge by developing a flexible and distributed infrastructure addressing emerging problems. G2F has generated large-scale phenotypic, genotypic, and environmental datasets using publicly available inbred lines and hybrids evaluated through a network of collaborators that are part of the G2F’s genotype-by-environment (G × E) project. This report covers the public release of datasets for 2014–2017.
              
                Data description
                Datasets include inbred genotypic information; phenotypic, climatic, and soil measurements and metadata information for each testing location across years. For a subset of inbreds in 2014 and 2015, yield component phenotypes were quantified by image analysis. Data released are accompanied by README descriptions. For genotypic and phenotypic data, both raw data and a version without outliers are reported. For climatic data, a version calibrated to the nearest airport weather station and a version without outliers are reported. The 2014 and 2015 datasets are updated versions from the previously released files [1] while 2016 and 2017 datasets are newly available to the public.
              }, number={1}, journal={BMC Research Notes}, publisher={Springer Science and Business Media LLC}, author={McFarland, B.A. and Alkhalifah, N. and Bohn, M. and Bubert, J. and Buckler, E.S. and Ciampitti, I. and Edwards, J. and Ertl, D. and Gage, J.L. and Falcon, C.M. and et al.}, year={2020} }
 @article{falcon_kaeppler_spalding_miller_haase_alkhalifah_bohn_buckler_campbell_ciampitti_et al._2020, title={Relative utility of agronomic, phenological, and morphological traits for assessing genotype-by-environment interaction in maize inbreds}, volume={60}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85078817946&partnerID=MN8TOARS}, DOI={10.1002/csc2.20035}, abstractNote={AbstractPlant breeders face the challenge of genotype × environment interaction (G × E) in comprehensively breeding for expanded geographic regions. An improved understanding of G × E sensitivity of traits and the environmental features that effectively discriminate among genotypes will enable more efficient breeding efforts. In this study of 31 maize (Zea mays L.) inbreds grown in 36 environments that are part of the Genomes to Fields Initiative, we measured 14 traits, including flowering date, height, and yield components (i.e., ear and kernel dimensions) to (i) identify traits that are the most sensitive indicators of G × E; (ii) determine how geographic location and weather factors influence environments’ discriminability of inbreds; and (iii) detect patterns of stability in better and worse discriminating environments. Genotype × environment interaction explained between 9.0–20.4% of the phenotypic variance with greater effects in the yield‐component traits. Discriminability of environments varied by trait. Midwest locations (where 26 of the 31 inbreds were developed) were among the most discriminating environments for more traits, while environments in the West and East tended to be less discriminating. Weather factors during silking were significantly different between the most and least discriminating environments more often than average weather across the season or during the period from planting to silking. Stability of genotypes varied by trait, and performance was usually not correlated with stability. The dissection of complex traits, such as yield into component traits, appears to be a useful approach to understand how environmental factors differentially affect phenotype.}, number={1}, journal={Crop Science}, author={Falcon, C.M. and Kaeppler, S.M. and Spalding, E.P. and Miller, N.D. and Haase, N. and AlKhalifah, N. and Bohn, M. and Buckler, E.S. and Campbell, D.A. and Ciampitti, I. and et al.}, year={2020}, pages={62–81} }
 @article{chen_samayoa_yang_bradbury_olukolu_neumeyer_romay_sun_lorant_buckler_et al._2020, title={The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication}, volume={16}, ISSN={["1553-7404"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85085904066&partnerID=MN8TOARS}, DOI={10.1371/journal.pgen.1008791}, abstractNote={The genetics of domestication has been extensively studied ever since the rediscovery of Mendel’s law of inheritance and much has been learned about the genetic control of trait differences between crops and their ancestors. Here, we ask how domestication has altered genetic architecture by comparing the genetic architecture of 18 domestication traits in maize and its ancestor teosinte using matched populations. We observed a strongly reduced number of QTL for domestication traits in maize relative to teosinte, which is consistent with the previously reported depletion of additive variance by selection during domestication. We also observed more dominance in maize than teosinte, likely a consequence of selective removal of additive variants. We observed that large effect QTL have low minor allele frequency (MAF) in both maize and teosinte. Regions of the genome that are strongly differentiated between teosinte and maize (high FST) explain less quantitative variation in maize than teosinte, suggesting that, in these regions, allelic variants were brought to (or near) fixation during domestication. We also observed that genomic regions of high recombination explain a disproportionately large proportion of heritable variance both before and after domestication. Finally, we observed that about 75% of the additive variance in both teosinte and maize is “missing” in the sense that it cannot be ascribed to detectable QTL and only 25% of variance maps to specific QTL. This latter result suggests that morphological evolution during domestication is largely attributable to very large numbers of QTL of very small effect.}, number={5}, journal={PLOS GENETICS}, publisher={Public Library of Science (PLoS)}, author={Chen, Qiuyue and Samayoa, Luis Fernando and Yang, Chin Jian and Bradbury, Peter J. and Olukolu, Bode A. and Neumeyer, Michael A. and Romay, Maria Cinta and Sun, Qi and Lorant, Anne and Buckler, Edward S. and et al.}, editor={Mauricio, RodneyEditor}, year={2020}, month={May} }
 @article{morales_zila_mejia_arbelaez_balint-kurti_holland_nelson_2019, title={Diverse Components of Resistance to Fusarium verticillioides Infection and Fumonisin Contamination in Four Maize Recombinant Inbred Families}, volume={11}, ISSN={["2072-6651"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85061125912&partnerID=MN8TOARS}, DOI={10.3390/toxins11020086}, abstractNote={The fungus Fusarium verticillioides can infect maize ears, causing Fusarium ear rot (FER) and contaminating the grain with fumonisins (FUM), which are harmful to humans and animals. Breeding for resistance to FER and FUM and post-harvest sorting of grain are two strategies for reducing FUM in the food system. Kernel and cob tissues have been previously associated with differential FER and FUM. Four recombinant inbred line families from the maize nested associated mapping population were grown and inoculated with F. verticillioides across four environments, and we evaluated the kernels for external and internal infection severity as well as FUM contamination. We also employed publicly available phenotypes on innate ear morphology to explore genetic relationships between ear architecture and resistance to FER and FUM. The four families revealed wide variation in external symptomatology at the phenotypic level. Kernel bulk density under inoculation was an accurate indicator of FUM levels. Genotypes with lower kernel density—under both inoculated and uninoculated conditions—and larger cobs were more susceptible to infection and FUM contamination. Quantitative trait locus (QTL) intervals could be classified as putatively resistance-specific and putatively shared for ear and resistance traits. Both types of QTL mapped in this study had substantial overlap with previously reported loci for resistance to FER and FUM. Ear morphology may be a component of resistance to F. verticillioides infection and FUM accumulation.}, number={2}, journal={TOXINS}, author={Morales, Laura and Zila, Charles T. and Mejia, Danilo E. Moreta and Arbelaez, Melissa Montoya and Balint-Kurti, Peter J. and Holland, James B. and Nelson, Rebecca J.}, year={2019}, month={Feb} }
 @article{camargo senhorinho_dacal coan_marino_kuki_barth pinto_scapim_holland_2019, title={Genomic-Wide Association Study of Popping Expansion in Tropical Popcorn and Field Corn Germplasm}, volume={59}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85073380607&partnerID=MN8TOARS}, DOI={10.2135/cropsci2019.02.0101}, abstractNote={Popcorn is a popular snack food with higher grain value compared with “field corn” maize (Zea mays L.). In general, popcorn germplasm is less improved than common maize cultivars, with less favorable agronomic performance and greater susceptibility to pests, diseases, and lodging, especially in tropical environments. One approach to expanding and improving popcorn germplasm is to introduce favorable alleles for agronomic performance from field corn. If markers tagging quantitative trait loci (QTLs) associated with popping expansion were identified, they could be selected with markers to maintain popping expansion in breeding populations derived from crosses between field and popcorn germplasm. The objectives of this study were to identify single nucleotide polymorphism (SNP) markers and putative candidate genes associated with higher popping expansion in a diverse sample of popcorn and field corns relevant to Brazilian breeding programs. We applied a comprehensive genome‐wide association study (GWAS) for popping expansion, using 165,089 SNP markers in 183 inbred lines with 2 yr of trial data. Four SNPs were significantly associated with popping expansion, three of which were colocalized to previously reported meta‐QTLs, and one that was novel. Annotated genes closely linked to the associated SNPs were identified with functions related with starch content, which plays an important role in popping expansion quality. If these associations can be validated independently, they can be useful for breeders to select agronomically superior genotypes with greater popping expansion.}, number={5}, journal={CROP SCIENCE}, author={Camargo Senhorinho, Henrique Jose and Dacal Coan, Marlon Matias and Marino, Thiago Pablo and Kuki, Mauricio Carlos and Barth Pinto, Ronald Jose and Scapim, Carlos Alberto and Holland, James Brendan}, year={2019}, pages={2007–2019} }
 @article{guo_yu_li_zhang_zhu_flint-garcia_mcmullen_holland_szalma_wisser_et al._2019, title={Optimal Designs for Genomic Selection in Hybrid Crops}, volume={12}, ISSN={["1752-9867"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85061008767&partnerID=MN8TOARS}, DOI={10.1016/j.molp.2018.12.022}, abstractNote={Improved capacity of genomics and biotechnology has greatly enhanced genetic studies in different areas. Genomic selection exploits the genotype-to-phenotype relationship at the whole-genome level and is being implemented in many crops. Here we show that design-thinking and data-mining techniques can be leveraged to optimize genomic prediction of hybrid performance. We phenotyped a set of 276 maize hybrids generated by crossing founder inbreds of nested association mapping populations for flowering time, ear height, and grain yield. With 10 296 310 SNPs available from the parental inbreds, we explored the patterns of genomic relationships and phenotypic variation to establish training samples based on clustering, graphic network analysis, and genetic mating scheme. Our analysis showed that training set designs outperformed random sampling and earlier methods that either minimize the mean of prediction error variance or maximize the mean of generalized coefficient of determination. Additional analyses of 2556 wheat hybrids from an early-stage hybrid breeding system and 1439 rice hybrids from an established hybrid breeding system validated the approaches. Together, we demonstrated that effective genomic prediction models can be established with a training set 2%-13% of the size of the whole set, enabling an efficient exploration of enormous inference space of genetic combinations.}, number={3}, journal={MOLECULAR PLANT}, author={Guo, Tingting and Yu, Xiaoqing and Li, Xianran and Zhang, Haozhe and Zhu, Chengsong and Flint-Garcia, Sherry and McMullen, Michael D. and Holland, James B. and Szalma, Stephen J. and Wisser, Randall J. and et al.}, year={2019}, month={Mar}, pages={390–401} }
 @article{wisser_fang_holland_teixeira_dougherty_weldekidan_leon_flint-garcia_lauter_murray_et al._2019, title={The Genomic Basis for Short-Term Evolution of Environmental Adaptation in Maize}, volume={213}, ISSN={["1943-2631"]}, url={https://doi.org/10.1534/genetics.119.302780}, DOI={10.1534/genetics.119.302780}, abstractNote={AbstractThe geographical distribution of many crop species spans far beyond their centers of origin and the native range of their wild ancestors. Maize is exemplary of this adaptability, which has contributed to its agricultural...Understanding the evolutionary capacity of populations to adapt to novel environments is one of the major pursuits in genetics. Moreover, for plant breeding, maladaptation is the foremost barrier to capitalizing on intraspecific variation in order to develop new breeds for future climate scenarios in agriculture. Using a unique study design, we simultaneously dissected the population and quantitative genomic basis of short-term evolution in a tropical landrace of maize that was translocated to a temperate environment and phenotypically selected for adaptation in flowering time phenology. Underlying 10 generations of directional selection, which resulted in a 26-day mean decrease in female-flowering time, 60% of the heritable variation mapped to 14% of the genome, where, overall, alleles shifted in frequency beyond the boundaries of genetic drift in the expected direction given their flowering time effects. However, clustering these non-neutral alleles based on their profiles of frequency change revealed transient shifts underpinning a transition in genotype–phenotype relationships across generations. This was distinguished by initial reductions in the frequencies of few relatively large positive effect alleles and subsequent enrichment of many rare negative effect alleles, some of which appear to represent allelic series. With these genomic shifts, the population reached an adapted state while retaining 99% of the standing molecular marker variation in the founding population. Robust selection and association mapping tests highlighted several key genes driving the phenotypic response to selection. Our results reveal the evolutionary dynamics of a finite polygenic architecture conditioning a capacity for rapid environmental adaptation in maize.}, number={4}, journal={GENETICS}, publisher={Genetics Society of America}, author={Wisser, Randall J. and Fang, Zhou and Holland, James B. and Teixeira, Juliana E. C. and Dougherty, John and Weldekidan, Teclemariam and Leon, Natalia and Flint-Garcia, Sherry and Lauter, Nick and Murray, Seth C. and et al.}, year={2019}, month={Dec}, pages={1479–1494} }
 @article{yang_samayoa_bradbury_olukolu_xue_york_tuholski_wang_daskalska_neumeyer_et al._2019, title={The genetic architecture of teosinte catalyzed and constrained maize domestication}, volume={116}, ISBN={0027-8424}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85063274624&partnerID=MN8TOARS}, DOI={10.1073/pnas.1820997116}, abstractNote={
            The process of evolution under domestication has been studied using phylogenetics, population genetics–genomics, quantitative trait locus (QTL) mapping, gene expression assays, and archaeology. Here, we apply an evolutionary quantitative genetic approach to understand the constraints imposed by the genetic architecture of trait variation in teosinte, the wild ancestor of maize, and the consequences of domestication on genetic architecture. Using modern teosinte and maize landrace populations as proxies for the ancestor and domesticate, respectively, we estimated heritabilities, additive and dominance genetic variances, genetic-by-environment variances, genetic correlations, and genetic covariances for 18 domestication-related traits using realized genomic relationships estimated from genome-wide markers. We found a reduction in heritabilities across most traits, and the reduction is stronger in reproductive traits (size and numbers of grains and ears) than vegetative traits. We observed larger depletion in additive genetic variance than dominance genetic variance. Selection intensities during domestication were weak for all traits, with reproductive traits showing the highest values. For 17 of 18 traits, neutral divergence is rejected, suggesting they were targets of selection during domestication. Yield (total grain weight) per plant is the sole trait that selection does not appear to have improved in maize relative to teosinte. From a multivariate evolution perspective, we identified a strong, nonneutral divergence between teosinte and maize landrace genetic variance–covariance matrices (
            
              
                G
              
            
            -matrices). While the structure of
            
              
                G
              
            
            -matrix in teosinte posed considerable genetic constraint on early domestication, the maize landrace
            
              
                G
              
            
            -matrix indicates that the degree of constraint is more unfavorable for further evolution along the same trajectory.
          }, number={12}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Yang, Chin Jian and Samayoa, Luis Fernando and Bradbury, Peter J. and Olukolu, Bode A. and Xue, Wei and York, Alessandra M. and Tuholski, Michael R. and Wang, Weidong and Daskalska, Lora L. and Neumeyer, Michael A. and et al.}, year={2019}, pages={5643–5652} }
 @article{sarinelli_murphy_tyagi_holland_johnson_mergoum_mason_babar_harrison_sutton_et al._2019, title={Training population selection and use of fixed effects to optimize genomic predictions in a historical USA winter wheat panel}, volume={132}, ISSN={["1432-2242"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85060724945&partnerID=MN8TOARS}, DOI={10.1007/s00122-019-03276-6}, abstractNote={The optimization of training populations and the use of diagnostic markers as fixed effects increase the predictive ability of genomic prediction models in a cooperative wheat breeding panel. Plant breeding programs often have access to a large amount of historical data that is highly unbalanced, particularly across years. This study examined approaches to utilize these data sets as training populations to integrate genomic selection into existing pipelines. We used cross-validation to evaluate predictive ability in an unbalanced data set of 467 winter wheat (Triticum aestivum L.) genotypes evaluated in the Gulf Atlantic Wheat Nursery from 2008 to 2016. We evaluated the impact of different training population sizes and training population selection methods (Random, Clustering, PEVmean and PEVmean1) on predictive ability. We also evaluated inclusion of markers associated with major genes as fixed effects in prediction models for heading date, plant height, and resistance to powdery mildew (caused by Blumeria graminis f. sp. tritici). Increases in predictive ability as the size of the training population increased were more evident for Random and Clustering training population selection methods than for PEVmean and PEVmean1. The selection methods based on minimization of the prediction error variance (PEV) outperformed the Random and Clustering methods across all the population sizes. Major genes added as fixed effects always improved model predictive ability, with the greatest gains coming from combinations of multiple genes. Maximum predictabilities among all prediction methods were 0.64 for grain yield, 0.56 for test weight, 0.71 for heading date, 0.73 for plant height, and 0.60 for powdery mildew resistance. Our results demonstrate the utility of combining unbalanced phenotypic records with genome-wide SNP marker data for predicting the performance of untested genotypes.}, number={4}, journal={THEORETICAL AND APPLIED GENETICS}, author={Sarinelli, J. Martin and Murphy, J. Paul and Tyagi, Priyanka and Holland, James B. and Johnson, Jerry W. and Mergoum, Mohamed and Mason, Richard E. and Babar, Ali and Harrison, Stephen and Sutton, Russell and et al.}, year={2019}, month={Apr}, pages={1247–1261} }
 @article{martins_rucker_thomason_wisser_holland_balint-kurti_2019, title={Validation and Characterization of Maize Multiple Disease Resistance QTL}, volume={9}, ISSN={2160-1836}, url={http://dx.doi.org/10.1534/g3.119.400195}, DOI={10.1534/g3.119.400195}, abstractNote={Abstract
               Southern Leaf Blight, Northern Leaf Blight, and Gray Leaf Spot, caused by ascomycete fungi, are among the most important foliar diseases of maize worldwide. Previously, disease resistance quantitative trait loci (QTL) for all three diseases were identified in a connected set of chromosome segment substitution line (CSSL) populations designed for the identification of disease resistance QTL. Some QTL for different diseases co-localized, indicating the presence of multiple disease resistance (MDR) QTL. The goal of this study was to perform an independent test of several of the MDR QTL identified to confirm their existence and derive a more precise estimate of allele additive and dominance effects. Twelve F2:3 family populations were produced, in which selected QTL were segregating in an otherwise uniform genetic background. The populations were assessed for each of the three diseases in replicated trials and genotyped with markers previously associated with disease resistance. Pairwise phenotypic correlations across all the populations for resistance to the three diseases ranged from 0.2 to 0.3 and were all significant at the alpha level of 0.01. Of the 44 QTL tested, 16 were validated (identified at the same genomic location for the same disease or diseases) and several novel QTL/disease associations were found. Two MDR QTL were associated with resistance to all three diseases. This study identifies several potentially important MDR QTL and demonstrates the importance of independently evaluating QTL effects following their initial identification.}, number={9}, journal={G3 Genes|Genomes|Genetics}, publisher={Oxford University Press (OUP)}, author={Martins, Lais B and Rucker, Elizabeth and Thomason, Wade and Wisser, Randall J and Holland, James B and Balint-Kurti, Peter}, year={2019}, month={Sep}, pages={2905–2912} }
 @article{stagnati_lanubile_samayoa_bragalanti_giorni_busconi_holland_marocco_2019, title={A Genome Wide Association Study Reveals Markers and Genes Associated with Resistance to Fusarium verticillioides Infection of Seedlings in a Maize Diversity Panel}, volume={9}, ISSN={["2160-1836"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85061232004&partnerID=MN8TOARS}, DOI={10.1534/g3.118.200916}, abstractNote={Abstract
               Fusarium verticillioides infects maize, causing ear rot, yield loss and contamination by fumonisin mycotoxins. The fungus can be transmitted via kernels and cause systemic infection in maize. Maize resistance to the fungus may occur at different developmental stages, from seedling to maturity. Resistance during kernel germination is part of the plant-pathogen interaction and so far this aspect has not been investigated. In the present study, a genome wide association study (GWAS) of resistance to Fusarium during the seedling developmental stage was conducted in a maize diversity panel using 226,446 SNP markers. Seedling germination and disease phenotypes were scored on artificially inoculated kernels using the rolled towel assay. GWAS identified 164 SNPs significantly associated with the traits examined. Four SNPs were associated with disease severity score after inoculation, 153 were associated with severity in asymptomatic kernels and 7 with the difference between the severity ratings in inoculated and non-inoculated seeds. A set of genes containing or physically near the significant SNPs were identified as candidates for Fusarium resistance at the seedling stage. Functional analysis revealed that many of these genes are directly involved in plant defense against pathogens and stress responses, including transcription factors, chitinase, cytochrome P450, and ubiquitination proteins. In addition, 25 genes were found in high linkage disequilibrium with the associated SNPs identified by GWAS and four of them directly involved in disease resistance. These findings contribute to understanding the complex system of maize-F. verticillioides and may improve genomic selection for Fusarium resistance at the seedling stage.}, number={2}, journal={G3-GENES GENOMES GENETICS}, author={Stagnati, Lorenzo and Lanubile, Alessandra and Samayoa, Luis F. and Bragalanti, Mario and Giorni, Paola and Busconi, Matteo and Holland, James B. and Marocco, Adriano}, year={2019}, month={Feb}, pages={571–579} }
 @article{ovenden_milgate_wade_rebetzke_holland_2018, title={Accounting for Genotype-by-Environment Interactions and Residual Genetic Variation in Genomic Selection for Water-Soluble Carbohydrate Concentration in Wheat}, volume={8}, ISSN={["2160-1836"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85047875467&partnerID=MN8TOARS}, DOI={10.1534/g3.118.200038}, abstractNote={AbstractAbiotic stress tolerance traits are often complex and recalcitrant targets for conventional breeding improvement in many crop species. This study evaluated the potential of genomic selection to predict water-soluble carbohydrate concentration (WSCC), an important drought tolerance trait, in wheat under field conditions. A panel of 358 varieties and breeding lines constrained for maturity was evaluated under rainfed and irrigated treatments across two locations and two years. Whole-genome marker profiles and factor analytic mixed models were used to generate genomic estimated breeding values (GEBVs) for specific environments and environment groups. Additive genetic variance was smaller than residual genetic variance for WSCC, such that genotypic values were dominated by residual genetic effects rather than additive breeding values. As a result, GEBVs were not accurate predictors of genotypic values of the extant lines, but GEBVs should be reliable selection criteria to choose parents for intermating to produce new populations. The accuracy of GEBVs for untested lines was sufficient to increase predicted genetic gain from genomic selection per unit time compared to phenotypic selection if the breeding cycle is reduced by half by the use of GEBVs in off-season generations. Further, genomic prediction accuracy depended on having phenotypic data from environments with strong correlations with target production environments to build prediction models. By combining high-density marker genotypes, stress-managed field evaluations, and mixed models that model simultaneously covariances among genotypes and covariances of complex trait performance between pairs of environments, we were able to train models with good accuracy to facilitate genetic gain from genomic selection.}, number={6}, journal={G3-GENES GENOMES GENETICS}, author={Ovenden, Ben and Milgate, Andrew and Wade, Len J. and Rebetzke, Greg J. and Holland, James B.}, year={2018}, month={Jun}, pages={1909–1919} }
 @article{morales_marino_wenndt_fouts_holland_nelson_2018, title={Dissecting Symptomatology and Fumonisin Contamination Produced by Fusarium verticillioides in Maize Ears}, volume={108}, ISSN={["1943-7684"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85057563477&partnerID=MN8TOARS}, DOI={10.1094/PHYTO-05-18-0167-R}, abstractNote={ The fungus Fusarium verticillioides can infect maize ears, contaminating the grain with mycotoxins, including fumonisins. This global public health threat can be managed by breeding maize varieties that are resistant to colonization by F. verticillioides and by sorting grain after harvest to reduce fumonisin levels in food systems. Here, we employed two F. verticillioides inoculation techniques representing distinct infection pathways to dissect ear symptomatology and morphological resistance mechanisms in a diverse panel of maize inbred lines. The “point” method involved penetrating the ear with a spore-coated toothpick and the “inundative” method introduced a liquid spore suspension under the husk of the ear. We evaluated quantitative and qualitative indicators of external and internal symptom severity as low-cost proxies for fumonisin contamination, and found that kernel bulk density was predictive of fumonisin levels (78 to 84% sensitivity; 97 to 99% specificity). Inundative inoculation resulted in greater disease severity and fumonisin contamination than point inoculation. We also found that the two inoculation methods implicated different ear tissues in defense, with cob morphology being a more important component of resistance under point inoculation. Across both inoculation methods, traits related to cob size were positively associated with disease severity and fumonisin content. Our work demonstrates that (i) the use of diverse modes of inoculation is necessary for combining complementary mechanisms of genetic resistance, (ii) kernel bulk density can be used effectively as a proxy for fumonisin levels, and (iii) trade-offs may exist between yield potential and resistance to fumonisin contamination. }, number={12}, journal={PHYTOPATHOLOGY}, author={Morales, Laura and Marino, Thiago P. and Wenndt, Anthony J. and Fouts, Julia Q. and Holland, James B. and Nelson, Rebecca J.}, year={2018}, month={Dec}, pages={1475–1485} }
 @article{sanchez gonzalez_ruiz corral_medina garcia_ramirez ojeda_cruz larios_holland_miranda medrano_garcia romero_2018, title={Ecogeography of teosinte}, volume={13}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85042214920&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0192676}, abstractNote={Adaptation of crops to climate change has motivated an increasing interest in the potential value of novel traits from wild species; maize wild relatives, the teosintes, harbor traits that may be useful to maize breeding. To study the ecogeographic distribution of teosinte we constructed a robust database of 2363 teosinte occurrences from published sources for the period 1842–2016. A geographical information system integrating 216 environmental variables was created for Mexico and Central America and was used to characterize the environment of each teosinte occurrence site. The natural geographic distribution of teosinte extends from the Western Sierra Madre of the State of Chihuahua, Mexico to the Pacific coast of Nicaragua and Costa Rica, including practically the entire western part of Mesoamerica. The Mexican annuals Zea mays ssp. parviglumis and Zea mays ssp. mexicana show a wide distribution in Mexico, while Zea diploperennis, Zea luxurians, Zea perennis, Zea mays ssp. huehuetenangensis, Zea vespertilio and Zea nicaraguensis had more restricted and distinct ranges, representing less than 20% of the total occurrences. Only 11.2% of teosinte populations are found in Protected Natural Areas in Mexico and Central America. Ecogeographical analysis showed that teosinte can cope with extreme levels of precipitation and temperatures during growing season. Modelling teosinte geographic distribution demonstrated congruence between actual and potential distributions; however, some areas with no occurrences appear to be within the range of adaptation of teosintes. Field surveys should be prioritized to such regions to accelerate the discovery of unknown populations. Potential areas for teosintes Zea mays ssp. mexicana races Chalco, Nobogame, and Durango, Zea mays ssp. huehuetenangensis, Zea luxurians, Zea diploperennis and Zea nicaraguensis are geographically separated; however, partial overlapping occurs between Zea mays ssp. parviglumis and Zea perennis, between Zea mays ssp. parviglumis and Zea diploperennis, and between Zea mays ssp. mexicana race Chalco and Zea mays ssp. mexicana race Central Plateau. Assessing priority of collecting for conservation showed that permanent monitoring programs and in-situ conservation projects with participation of local farmer communities are critically needed; Zea mays ssp. mexicana (races Durango and Nobogame), Zea luxurians, Zea diploperennis, Zea perennis and Zea vespertilio should be considered as the highest priority taxa.}, number={2}, journal={PLOS ONE}, author={Sanchez Gonzalez, Jose de Jesus and Ruiz Corral, Jose Ariel and Medina Garcia, Guillermo and Ramirez Ojeda, Gabriela and Cruz Larios, Lino and Holland, James Brendan and Miranda Medrano, Roberto and Garcia Romero, Giovanni Emmanuel}, year={2018}, month={Feb} }
 @inbook{harnessing maize biodiversity_2018, url={http://dx.doi.org/10.1007/978-3-319-97427-9_20}, DOI={10.1007/978-3-319-97427-9_20}, abstractNote={The phenotypic and genetic diversity of maize worldwide is remarkable. This chapter summarizes decades of studies of the genetic diversity of maize populations from different parts of the world, methods used to group maize into informal hierarchies, and how these groupings partition genetic and trait variation. The USA is the most important maize-producing nation, but the genetic diversity of USA maize is small relative to the available worldwide variation. Tropical maize harbors more genetic variation, but is not adapted to growing in temperate environments. Two distinct approaches to tapping the global reservoir of maize diversity to improve USA and other temperate region maize crops are outlined. One approach, allele mining, involves discovery of alleles with large favorable effects on traits in exotic germplasm, followed by marker-aided backcrossing or gene editing to introduce specific unique alleles into elite breeding populations. Alternatively, for traits conditioned mostly by many small-effect polygenes, rapid genomic selection for adaptation followed by combining ability within pure exotic populations could be used to create adapted and improved versions of exotic populations before they are crossed to elite adapted inbreds to make new breeding populations.}, booktitle={Compendium of Plant Genomes}, year={2018} }
 @article{alkhalifah_campbell_falcon_gardiner_miller_romay_walls_walton_yeh_bohn_et al._2018, title={Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets}, volume={11}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85049778367&partnerID=MN8TOARS}, DOI={10.1186/s13104-018-3508-1}, abstractNote={Crop improvement relies on analysis of phenotypic, genotypic, and environmental data. Given large, well-integrated, multi-year datasets, diverse queries can be made: Which lines perform best in hot, dry environments? Which alleles of specific genes are required for optimal performance in each environment? Such datasets also can be leveraged to predict cultivar performance, even in uncharacterized environments. The maize Genomes to Fields (G2F) Initiative is a multi-institutional organization of scientists working to generate and analyze such datasets from existing, publicly available inbred lines and hybrids. G2F's genotype by environment project has released 2014 and 2015 datasets to the public, with 2016 and 2017 collected and soon to be made available.Datasets include DNA sequences; traditional phenotype descriptions, as well as detailed ear, cob, and kernel phenotypes quantified by image analysis; weather station measurements; and soil characterizations by site. Data are released as comma separated value spreadsheets accompanied by extensive README text descriptions. For genotypic and phenotypic data, both raw data and a version with outliers removed are reported. For weather data, two versions are reported: a full dataset calibrated against nearby National Weather Service sites and a second calibrated set with outliers and apparent artifacts removed.}, number={1}, journal={BMC Research Notes}, author={Alkhalifah, N. and Campbell, D.A. and Falcon, C.M. and Gardiner, J.M. and Miller, N.D. and Romay, M.C. and Walls, R. and Walton, R. and Yeh, C.-T. and Bohn, M. and et al.}, year={2018} }
 @article{holland_2018, title={Plant Genetics: Two Steps on the Path to Maize Adaptation}, volume={28}, ISSN={["1879-0445"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85053555135&partnerID=MN8TOARS}, DOI={10.1016/j.cub.2018.07.049}, abstractNote={Two distinct variations in the promoter of a key flowering time gene were selected during the spread of maize from its tropical origin to northern North America.}, number={18}, journal={CURRENT BIOLOGY}, author={Holland, James B.}, year={2018}, month={Sep}, pages={R1098–R1101} }
 @article{wills_fang_york_holland_doebley_2018, title={Defining the Role of the MADS-Box Gene, Zea Agamous-like1, a Target of Selection During Maize Domestication}, volume={109}, ISSN={["1465-7333"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85044226393&partnerID=MN8TOARS}, DOI={10.1093/jhered/esx073}, abstractNote={AbstractGenomic scans for genes that show the signature of past selection have been widely applied to a number of species and have identified a large number of selection candidate genes. In cultivated maize (Zea mays ssp. mays) selection scans have identified several hundred candidate domestication genes by comparing nucleotide diversity and differentiation between maize and its progenitor, teosinte (Z. mays ssp. parviglumis). One of these is a gene called zea agamous-like1 (zagl1), a MADS-box transcription factor, that is known for its function in the control of flowering time. To determine the trait(s) controlled by zagl1 that was (were) the target(s) of selection during maize domestication, we created a set of recombinant chromosome isogenic lines that differ for the maize versus teosinte alleles of zagl1 and which carry cross-overs between zagl1 and its neighbor genes. These lines were grown in a randomized trial and scored for flowering time and domestication related traits. The results indicated that the maize versus teosinte alleles of zagl1 affect flowering time as expected, as well as multiple traits related to ear size with the maize allele conferring larger ears with more kernels. Our results suggest that zagl1 may have been under selection during domestication to increase the size of the maize ear.}, number={3}, journal={JOURNAL OF HEREDITY}, author={Wills, David M. and Fang, Zhou and York, Alessandra M. and Holland, James B. and Doebley, John F.}, year={2018}, month={May}, pages={333–338} }
 @article{bian_holland_2017, title={Enhancing genomic prediction with genome-wide association studies in multiparental maize populations}, volume={118}, ISSN={["1365-2540"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85012882558&partnerID=MN8TOARS}, DOI={10.1038/hdy.2017.4}, abstractNote={Genome-wide association mapping using dense marker sets has identified some nucleotide variants affecting complex traits that have been validated with fine-mapping and functional analysis. However, many sequence variants associated with complex traits in maize have small effects and low repeatability. In contrast to genome-wide association study (GWAS), genomic prediction (GP) is typically based on models incorporating information from all available markers, rather than modeling effects of individual loci. We considered methods to integrate results of GWASs into GP models in the context of multiple interconnected families. We compared association tests based on a biallelic additive model constraining the effect of a single-nucleotide polymorphism (SNP) to be equal across all families in which it segregates to a model in which the effect of a SNP can vary across families. Association SNPs were then included as fixed effects into a GP model that also included the random effects of the whole genome background. Simulation studies revealed that the effectiveness of this joint approach depends on the extent of polygenicity of the traits. Congruent with this finding, cross-validation studies indicated that GP including the fixed effects of the most significantly associated SNPs along with the polygenic background was more accurate than the polygenic background model alone for moderately complex but not highly polygenic traits measured in the maize nested association mapping population. Individual SNPs with strong and robust association signals can effectively improve GP. Our approach provides a new integrative modeling approach for both reliable gene discovery and robust GP.}, number={6}, journal={HEREDITY}, author={Bian, Y. and Holland, J. B.}, year={2017}, month={Jun}, pages={585–593} }
 @book{isik_holland_maltecca_2017, title={Genetic Data Analysis for Plant and Animal Breeding}, ISBN={9783319551753 9783319551777}, url={http://dx.doi.org/10.1007/978-3-319-55177-7}, DOI={10.1007/978-3-319-55177-7}, publisher={Springer International Publishing}, author={Isik, Fikret and Holland, James and Maltecca, Christian}, year={2017} }
 @article{ovenden_milgate_wade_rebetzke_holland_2017, title={Genome-Wide Associations for Water-Soluble Carbohydrate Concentration and Relative Maturity in Wheat Using SNP and DArT Marker Arrays}, volume={7}, ISSN={["2160-1836"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85027256280&partnerID=MN8TOARS}, DOI={10.1534/g3.117.039842}, abstractNote={Abstract
               Improving water-use efficiency by incorporating drought avoidance traits into new wheat varieties is an important objective for wheat breeding in water-limited environments. This study uses genome wide association studies (GWAS) to identify candidate loci for water-soluble carbohydrate accumulation—an important drought-avoidance characteristic in wheat. Phenotypes from a multi-environment trial with experiments differing in water availability and separate single nucleotide polymorphism (SNP) and diversity arrays technology (DArT) marker sets were used to perform the analyses. Significant associations for water-soluble carbohydrate accumulation were identified on chromosomes 1A, 1B, 1D, 2D, and 4A. Notably, these loci did not collocate with the major loci identified for relative maturity. Loci on chromosome 1D collocated with markers previously associated with the high molecular weight glutenin Glu-D1 locus. Genetic × environmental interactions impacted the results strongly, with significant associations for carbohydrate accumulation identified only in the water-deficit experiments. The markers associated with carbohydrate accumulation may be useful for marker-assisted selection of drought tolerance in wheat.}, number={8}, journal={G3-GENES GENOMES GENETICS}, author={Ovenden, Ben and Milgate, Andrew and Wade, Len J. and Rebetzke, Greg J. and Holland, James B.}, year={2017}, month={Aug}, pages={2821–2830} }
 @article{swarts_gutaker_benz_blake_bukowski_holland_kruse-peeples_lepak_prim_romay_et al._2017, title={Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America}, volume={357}, ISSN={["1095-9203"]}, url={https://doi.org/10.1126/science.aam9425}, DOI={10.1126/science.aam9425}, abstractNote={Estimating temperate adaptation in ancient maize
          
            Maize as a staple food crop in temperate North America required adaptation to a shorter growing season. On its first introduction in the southwestern United States ∼4000 years ago, maize was extensively grown in the lowlands. Cultivation in the temperate uplands did not occur for another 2000 years. Swarts
            et al.
            used ancient DNA data from 1900-year-old maize cobs found in a temperate cave in the southwestern United States and mapped the ancient flowering phenotype. The ancient maize samples were marginally adapted to temperate regions as a result of selection on standing variation.
          
          
            Science
            , this issue p.
            512
          }, number={6350}, journal={SCIENCE}, publisher={American Association for the Advancement of Science (AAAS)}, author={Swarts, Kelly and Gutaker, Rafal M. and Benz, Bruce and Blake, Michael and Bukowski, Robert and Holland, James and Kruse-Peeples, Melissa and Lepak, Nicholas and Prim, Lynda and Romay, M. Cinta and et al.}, year={2017}, month={Aug}, pages={512–515} }
 @article{jamann_sood_wisser_holland_2017, title={High-Throughput Resequencing of Maize Landraces at Genomic Regions Associated with Flowering Time}, volume={12}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85008367807&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0168910}, abstractNote={Despite the reduction in the price of sequencing, it remains expensive to sequence and assemble whole, complex genomes of multiple samples for population studies, particularly for large genomes like those of many crop species. Enrichment of target genome regions coupled with next generation sequencing is a cost-effective strategy to obtain sequence information for loci of interest across many individuals, providing a less expensive approach to evaluating sequence variation at the population scale. Here we evaluate amplicon-based enrichment coupled with semiconductor sequencing on a validation set consisting of three maize inbred lines, two hybrids and 19 landrace accessions. We report the use of a multiplexed panel of 319 PCR assays that target 20 candidate loci associated with photoperiod sensitivity in maize while requiring 25 ng or less of starting DNA per sample. Enriched regions had an average on-target sequence read depth of 105 with 98% of the sequence data mapping to the maize ‘B73’ reference and 80% of the reads mapping to the target interval. Sequence reads were aligned to B73 and 1,486 and 1,244 variants were called using SAMtools and GATK, respectively. Of the variants called by both SAMtools and GATK, 30% were not previously reported in maize. Due to the high sequence read depth, heterozygote genotypes could be called with at least 92.5% accuracy in hybrid materials using GATK. The genetic data are congruent with previous reports of high total genetic diversity and substantial population differentiation among maize landraces. In conclusion, semiconductor sequencing of highly multiplexed PCR reactions is a cost-effective strategy for resequencing targeted genomic loci in diverse maize materials.}, number={1}, journal={PLOS ONE}, author={Jamann, Tiffany M. and Sood, Shilpa and Wisser, Randall J. and Holland, James B.}, year={2017}, month={Jan} }
 @article{ovenden_milgate_lisle_wade_rebetzke_holland_2017, title={Selection for water-soluble carbohydrate accumulation and investigation of genetic x environment interactions in an elite wheat breeding population}, volume={130}, ISSN={["1432-2242"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85028760357&partnerID=MN8TOARS}, DOI={10.1007/s00122-017-2969-2}, abstractNote={Water-soluble carbohydrate accumulation can be selected in wheat breeding programs with consideration of genetic × environmental interactions and relationships with other important characteristics such as relative maturity and nitrogen concentration, although the correlation between WSC traits and grain yield is low and inconsistent. The potential to increase the genetic capacity for water-soluble carbohydrate (WSC) accumulation is an opportunity to improve the drought tolerance capability of rainfed wheat varieties, particularly in environments where terminal drought is a significant constraint to wheat production. A population of elite breeding germplasm was characterized to investigate the potential for selection of improved WSC concentration and total amount in water deficit and well-watered environments. Accumulation of WSC involves complex interactions with other traits and the environment. For both WSC concentration (WSCC) and total WSC per area (WSCA), strong genotype × environment interactions were reflected in the clear grouping of experiments into well-watered and water deficit environment clusters. Genetic correlations between experiments were high within clusters. Heritability for WSCC was larger than for WSCA, and significant associations were observed in both well-watered and water deficit experiment clusters between the WSC traits and nitrogen concentration, tillering, grains per m 2 , and grain size. However, correlations between grain yield and WSCC or WSCA were weak and variable, suggesting that selection for these traits is not a better strategy for improving yield under drought than direct selection for yield.}, number={11}, journal={THEORETICAL AND APPLIED GENETICS}, author={Ovenden, Ben and Milgate, Andrew and Lisle, Chris and Wade, Len J. and Rebetzke, Greg J. and Holland, James B.}, year={2017}, month={Nov}, pages={2445–2461} }
 @article{gage_jarquin_romay_lorenz_buckler_kaeppler_alkhalifah_bohn_campbell_edwards_et al._2017, title={The effect of artificial selection on phenotypic plasticity in maize}, volume={8}, ISSN={["2041-1723"]}, url={https://doi.org/10.1038/s41467-017-01450-2}, DOI={10.1038/s41467-017-01450-2}, abstractNote={AbstractRemarkable productivity has been achieved in crop species through artificial selection and adaptation to modern agronomic practices. Whether intensive selection has changed the ability of improved cultivars to maintain high productivity across variable environments is unknown. Understanding the genetic control of phenotypic plasticity and genotype by environment (G × E) interaction will enhance crop performance predictions across diverse environments. Here we use data generated from the Genomes to Fields (G2F) Maize G × E project to assess the effect of selection on G × E variation and characterize polymorphisms associated with plasticity. Genomic regions putatively selected during modern temperate maize breeding explain less variability for yield G × E than unselected regions, indicating that improvement by breeding may have reduced G × E of modern temperate cultivars. Trends in genomic position of variants associated with stability reveal fewer genic associations and enrichment of variants 0–5000 base pairs upstream of genes, hypothetically due to control of plasticity by short-range regulatory elements.}, number={1}, journal={NATURE COMMUNICATIONS}, publisher={Springer Nature}, author={Gage, Joseph L. and Jarquin, Diego and Romay, Cinta and Lorenz, Aaron and Buckler, Edward S. and Kaeppler, Shawn and Alkhalifah, Naser and Bohn, Martin and Campbell, Darwin A. and Edwards, Jode and et al.}, year={2017}, month={Nov} }
 @article{morales_wenndt_marino_holland_nelson_2017, title={Variation in the Fusarium verticilloides-maize pathosystem and implications for sorting mycotoxin-contaminated maize grain}, volume={107}, number={2}, journal={Phytopathology}, author={Morales, L. and Wenndt, A. and Marino, T. and Holland, J. and Nelson, R.}, year={2017}, pages={11–11} }
 @article{xue_bradbury_casstevens_holland_2016, title={Genetic Architecture of Domestication-Related Traits in Maize}, volume={204}, ISSN={["1943-2631"]}, url={https://doi.org/10.1534/genetics.116.191106}, DOI={10.1534/genetics.116.191106}, abstractNote={AbstractStrong directional selection occurred during the domestication of maize from its wild ancestor teosinte, reducing its genetic diversity, particularly at genes controlling domestication-related traits. Nevertheless, variability for some domestication-related traits is maintained in maize. The genetic basis of this could be sequence variation at the same key genes controlling maize–teosinte differentiation (due to lack of fixation or arising as new mutations after domestication), distinct loci with large effects, or polygenic background variation. Previous studies permit annotation of maize genome regions associated with the major differences between maize and teosinte or that exhibit population genetic signals of selection during either domestication or postdomestication improvement. Genome-wide association studies and genetic variance partitioning analyses were performed in two diverse maize inbred line panels to compare the phenotypic effects and variances of sequence polymorphisms in regions involved in domestication and improvement to the rest of the genome. Additive polygenic models explained most of the genotypic variation for domestication-related traits; no large-effect loci were detected for any trait. Most trait variance was associated with background genomic regions lacking previous evidence for involvement in domestication. Improvement sweep regions were associated with more trait variation than expected based on the proportion of the genome they represent. Selection during domestication eliminated large-effect genetic variants that would revert maize toward a teosinte type. Small-effect polygenic variants (enriched in the improvement sweep regions of the genome) are responsible for most of the standing variation for domestication-related traits in maize.}, number={1}, journal={GENETICS}, publisher={Genetics Society of America}, author={Xue, Shang and Bradbury, Peter J. and Casstevens, Terry and Holland, James B.}, year={2016}, month={Sep}, pages={99-+} }
 @article{andres_coneva_frank_tuttle_samayoa_han_kaur_zhu_fang_bowman_et al._2017, title={Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.)}, volume={114}, DOI={10.1101/062612}, abstractNote={AbstractLeaf shape is spectacularly diverse. As the primary source of photo-assimilate in major crops, understanding the evolutionary and environmentally induced changes in leaf morphology are critical to improving agricultural productivity. The role of leaf shape in cotton domestication is unique, as breeders have purposefully selected for entire and lobed leaf morphs resulting from a single locus,okra(L-D1). Theokralocus is not only of agricultural importance in cotton (Gossypium hirsutumL.), but through pioneering chimeric and morphometric studies it has contributed to fundamental knowledge about leaf development. Here we show that the major leaf shapes of cotton at theL-D1locus are controlled by a HD-Zip transcription factor most similar toLate Meristem Identity1 (LMI1)gene. The classicalokraleaf shape gene has133-bp tandem duplication in the promoter, correlated with elevated expression, while an 8-bp deletion in the third exon of the presumed wild-typenormalleaf causes a frame-shifted and truncated coding sequence. Virus-induced gene silencing (VIGS) of thisLMI1-likegene in anokravariety was sufficient to induce normal leaf formation. An intermediate leaf shape allele,sub-okra, lacks both the promoter duplication and the exonic deletion. Our results indicate thatsub-okrais the ancestral leaf shape of tetraploid cotton andnormalis a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton.}, number={1}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Andres, R. J. and Coneva, V. and Frank, M. H. and Tuttle, J. R. and Samayoa, L. F. and Han, S. W. and Kaur, B. and Zhu, L. L. and Fang, Hui and Bowman, D. T. and et al.}, year={2017}, pages={E57–66} }
 @article{andres_coneva_frank_tuttle_samayoa_han_kaur_zhu_fang_bowman_et al._2016, title={Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.)}, volume={114}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/PNAS.1613593114}, DOI={10.1073/pnas.1613593114}, abstractNote={Significance
          
            Leaves are the primary source of photoassimilate in crop plants. A precise understanding of the genetic architecture underlying leaf morphology is critical to engineering climate-resilient crop varieties. An ideal cotton cultivar would produce a lower canopy of broad,
            normal
            leaves before transitioning to an upper canopy of highly lobed,
            okra
            leaves. Here we show that the major leaf shapes of cotton are controlled by the
            okra
            locus, which encodes an HD-Zip transcription factor
            Gossypium hirsutum
            LATE MERISTEM IDENTITY1-D1b
            (
            GhLMI1-D1b
            ). Using gene silencing, we temporarily induced normal leaf formation in
            okra
            , thus validating the candidate gene and creating the leaf shape ideotype in cotton. This study, identifying a single locus responsible for cotton leaf shape, expands the genetic toolbox for breeders to produce superior cotton varieties.
          }, number={1}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Andres, Ryan J. and Coneva, Viktoriya and Frank, Margaret H. and Tuttle, John R. and Samayoa, Luis Fernando and Han, Sang-Won and Kaur, Baljinder and Zhu, Linglong and Fang, Hui and Bowman, Daryl T. and et al.}, year={2016}, month={Dec}, pages={E57–E66} }
 @article{rebetzke_richards_holland_2017, title={Population extremes for assessing trait value and correlated response of genetically complex traits}, volume={201}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84996607156&partnerID=MN8TOARS}, DOI={10.1016/j.fcr.2016.10.019}, abstractNote={Physiological studies have led to the identification of many traits hypothesized to be useful for breeding improved crop performance. The effect of selection for these traits on yield across breeding populations and across target environments is generally unknown, such that crop breeders may have difficulty in prioritizing evaluation resources among potentially many traits. A simple method to estimate the effect on crop performance from selection on a proposed trait would facilitate trait adoption toward implementation and delivery in improved varieties. The response to indirect selection for different traits can be accurately predicted with nearly-isogenic lines differing for only small regions of the genome and those traits under investigation. An alternative approach better suited to complex, polygenic traits is the assessment of direct and indirect response in ‘tails’ representing phenotypic extremes from a distribution for a target trait. The smaller set of lines representing the two tail groups can then be evaluated more extensively for yield or other expensive and difficult to phenotype traits. Assuming an infinitesimal model appropriate for polygenic traits, we used simulations to understand the influence of population size, proportion of lines sampled in each tail group, trait heritability, and the genotypic correlation between the selection and evaluation trait on the resulting difference between tail means. The power of the tail comparison test was closely related to the heritability of the selection trait and its genotypic correlation with the evaluation trait, demonstrating that the tail comparison test can appropriately evaluate and rank the potential utility of different selection traits. Increasing the entry-mean heritability through multiple environment testing can be coupled with larger population and tail group sizes to increase power and confidence in assessment of both selection and response trait values. We assessed the selection of phenotypic distribution tails for water productivity traits in wheat. Reduced-tillering tails were associated with an average 14% reduction in tiller number and significantly reduced yields (−5%), particularly at wider row-spacings. High vigour tails were associated with a 49% increase in early ground cover, 40% increase in NDVI score, and greater yields (+18%) across all sampled environments. Assessment of population tails across multiple genetic backgrounds will guide selection in commercial breeding programs and facilitate trait delivery in improved cultivars.}, journal={Field Crops Research}, author={Rebetzke, G.J. and Richards, R.A. and Holland, J.B.}, year={2017}, pages={122–132} }
 @article{olukolu_bian_de vries_tracy_wisser_holland_balint-kurti_2016, title={The Genetics of Leaf Flecking in Maize and Its Relationship to Plant Defense and Disease Resistance}, volume={172}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.15.01870}, DOI={10.1104/pp.15.01870}, abstractNote={Leaf flecking in maize may be related to disease resistance and to a diverse set of metabolic pathways. Physiological leaf spotting, or flecking, is a mild-lesion phenotype observed on the leaves of several commonly used maize (Zea mays) inbred lines and has been anecdotally linked to enhanced broad-spectrum disease resistance. Flecking was assessed in the maize nested association mapping (NAM) population, comprising 4,998 recombinant inbred lines from 25 biparental families, and in an association population, comprising 279 diverse maize inbreds. Joint family linkage analysis was conducted with 7,386 markers in the NAM population. Genome-wide association tests were performed with 26.5 million single-nucleotide polymorphisms (SNPs) in the NAM population and with 246,497 SNPs in the association population, resulting in the identification of 18 and three loci associated with variation in flecking, respectively. Many of the candidate genes colocalizing with associated SNPs are similar to genes that function in plant defense response via cell wall modification, salicylic acid- and jasmonic acid-dependent pathways, redox homeostasis, stress response, and vesicle trafficking/remodeling. Significant positive correlations were found between increased flecking, stronger defense response, increased disease resistance, and increased pest resistance. A nonlinear relationship with total kernel weight also was observed whereby lines with relatively high levels of flecking had, on average, lower total kernel weight. We present evidence suggesting that mild flecking could be used as a selection criterion for breeding programs trying to incorporate broad-spectrum disease resistance.}, number={3}, journal={Plant Physiology}, publisher={Oxford University Press (OUP)}, author={Olukolu, Bode A. and Bian, Yang and De Vries, Brian and Tracy, William F. and Wisser, Randall J. and Holland, James B. and Balint-Kurti, Peter J.}, year={2016}, month={Sep}, pages={1787–1803} }
 @article{holland_graham_murphy_lynn_2015, title={Charles W. Stuber: Maize Geneticist and Pioneer of Marker-Assisted Selection}, volume={39}, DOI={10.1002/9781119107743.ch1}, abstractNote={This chapter contains sections titled: BIOGRAPHICAL SKETCH SCIENTIFIC ACHIEVEMENTS LEADERSHIP BEFORE AND AFTER RETIREMENT AWARDS AND HONORS IMPACT ON BREEDING PARADIGMS IN THE PRIVATE SECTOR IMPACT ON STUDENTS AND POSTDOCS}, journal={Plant breeding reviews, vol 39}, author={Holland, James and Graham, G. I. and Murphy, J. P. and Lynn, M.}, year={2015}, pages={1–22} }
 @book{holland_graham_murphy_senior_2015, title={Charles W. Stuber: Maize Geneticist and Pioneer of Marker-Assisted Selection}, volume={39}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84977447531&partnerID=MN8TOARS}, DOI={10.1002/9781119107743.ch01}, abstractNote={This chapter contains sections titled: BIOGRAPHICAL SKETCH SCIENTIFIC ACHIEVEMENTS LEADERSHIP BEFORE AND AFTER RETIREMENT AWARDS AND HONORS IMPACT ON BREEDING PARADIGMS IN THE PRIVATE SECTOR IMPACT ON STUDENTS AND POSTDOCS}, number={1}, journal={Plant Breeding Reviews}, author={Holland, J.B. and Graham, G.I. and Murphy, J.P. and Senior, M.L.}, year={2015}, pages={1–22} }
 @article{bian_holland_2015, title={Ensemble Learning of QTL Models Improves Prediction of Complex Traits}, volume={5}, ISSN={["2160-1836"]}, url={https://doi.org/10.1534/g3.115.021121}, DOI={10.1534/g3.115.021121}, abstractNote={Abstract
               Quantitative trait locus (QTL) models can provide useful insights into trait genetic architecture because of their straightforward interpretability but are less useful for genetic prediction because of the difficulty in including the effects of numerous small effect loci without overfitting. Tight linkage between markers introduces near collinearity among marker genotypes, complicating the detection of QTL and estimation of QTL effects in linkage mapping, and this problem is exacerbated by very high density linkage maps. Here we developed a thinning and aggregating (TAGGING) method as a new ensemble learning approach to QTL mapping. TAGGING reduces collinearity problems by thinning dense linkage maps, maintains aspects of marker selection that characterize standard QTL mapping, and by ensembling, incorporates information from many more markers-trait associations than traditional QTL mapping. The objective of TAGGING was to improve prediction power compared with QTL mapping while also providing more specific insights into genetic architecture than genome-wide prediction models. TAGGING was compared with standard QTL mapping using cross validation of empirical data from the maize (Zea mays L.) nested association mapping population. TAGGING-assisted QTL mapping substantially improved prediction ability for both biparental and multifamily populations by reducing both the variance and bias in prediction. Furthermore, an ensemble model combining predictions from TAGGING-assisted QTL and infinitesimal models improved prediction abilities over the component models, indicating some complementarity between model assumptions and suggesting that some trait genetic architectures involve a mixture of a few major QTL and polygenic effects.}, number={10}, journal={G3-GENES GENOMES GENETICS}, publisher={Genetics Society of America}, author={Bian, Yang and Holland, James B.}, year={2015}, month={Oct}, pages={2073–2084} }
 @article{nelson_krakowsky_coles_holland_bubeck_smith_goodman_2016, title={Genetic Characterization of the North Carolina State University Maize Lines}, volume={56}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84952837677&partnerID=MN8TOARS}, DOI={10.2135/cropsci2015.09.0532}, abstractNote={ABSTRACTSince 1980, 150 North Carolina State University (NCSU) maize (Zea mays L.) inbreds have been developed and released on the basis of superior performance for topcross yield and other traits of agronomic importance. During this time, there has been great emphasis placed on breeding with exotic germplasm, with 86 NCSU inbreds having at least 50% exotic parentage and 40 of those having all‐tropical parentage. Maize germplasm released by NCSU represents a potentially useful resource for increasing maize diversity and performance in the United States. The objectives of this study were to characterize the genetic relationships among inbreds released from this unique breeding program and to compare them genetically with inbreds from other public and private breeding programs. The NCSU maize inbreds can be classified into five germplasm pools: Lancaster, Temperate‐adapted all tropical (TAAT), Lancaster × Tropical, Stiff Stalk, and Southern non‐Stiff Stalk; detailed analysis of pedigree records and molecular marker genotypes reveals additional substructure within each of these pools. There is general agreement among the four cluster analyses performed, three using single nucleotide polymorphism (SNP) data and one using pedigree‐derived coefficients of coancestry. We introduce a novel application of Procrustes analysis to identify disagreements between pedigree and marker similarities. The NCSU maize breeding germplasm includes diverse genetic backgrounds, as evidenced by the number of unique alleles compared with publically available inbreds from both public and off‐protection, private‐sector sources.}, number={1}, journal={CROP SCIENCE}, author={Nelson, P. T. and Krakowsky, M. D. and Coles, N. D. and Holland, J. B. and Bubeck, D. M. and Smith, J. S. C. and Goodman, M. M.}, year={2016}, pages={259–275} }
 @article{samayoa_malvar_olukolu_holland_butron_2015, title={Genome-wide association study reveals a set of genes associated with resistance to the Mediterranean corn borer (Sesamia nonagrioides L.) in a maize diversity panel}, volume={15}, ISSN={["1471-2229"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84924054437&partnerID=MN8TOARS}, DOI={10.1186/s12870-014-0403-3}, abstractNote={Corn borers are the primary maize pest; their feeding on the pith results in stem damage and yield losses. In this study, we performed a genome-wide association study (GWAS) to identify SNPs associated with resistance to Mediterranean corn borer in a maize diversity panel using a set of more than 240,000 SNPs. Twenty five SNPs were significantly associated with three resistance traits: 10 were significantly associated with tunnel length, 4 with stem damage, and 11 with kernel resistance. Allelic variation at each significant SNP was associated with from 6 to 9% of the phenotypic variance. A set of genes containing or physically close to these SNPs are proposed as candidate genes for borer resistance, supported by their involvement in plant defense-related mechanisms in previously published evidence. The linkage disequilibrium decayed (r 2 < 0.10) rapidly within short distance, suggesting high resolution of GWAS associations. Most of the candidate genes found in this study are part of signaling pathways, others act as regulator of expression under biotic stress condition, and a few genes are encoding enzymes with antibiotic effect against insects such as the cystatin1 gene and the defensin proteins. These findings contribute to the understanding the complex relationship between plant-insect interactions.}, number={1}, journal={BMC PLANT BIOLOGY}, author={Samayoa, Luis Fernando and Malvar, Rosa Ana and Olukolu, Bode A. and Holland, James B. and Butron, Ana}, year={2015}, month={Feb} }
 @article{ogut_bian_bradbury_holland_2015, title={Joint-multiple family linkage analysis predicts within-family variation better than single-family analysis of the maize nested association mapping population}, volume={114}, ISSN={["1365-2540"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84922607318&partnerID=MN8TOARS}, DOI={10.1038/hdy.2014.123}, abstractNote={Quantitative trait locus (QTL) mapping has been used to dissect the genetic architecture of complex traits and predict phenotypes for marker-assisted selection. Many QTL mapping studies in plants have been limited to one biparental family population. Joint analysis of multiple biparental families offers an alternative approach to QTL mapping with a wider scope of inference. Joint-multiple population analysis should have higher power to detect QTL shared among multiple families, but may have lower power to detect rare QTL. We compared prediction ability of single-family and joint-family QTL analysis methods with fivefold cross-validation for 6 diverse traits using the maize nested association mapping population, which comprises 25 biparental recombinant inbred families. Joint-family QTL analysis had higher mean prediction abilities than single-family QTL analysis for all traits at most significance thresholds, and was always better at more stringent significance thresholds. Most robust QTL (detected in >50% of data samples) were restricted to one family and were often not detected at high frequency by joint-family analysis, implying substantial genetic heterogeneity among families for complex traits in maize. The superior predictive ability of joint-family QTL models despite important genetic differences among families suggests that joint-family models capture sufficient smaller effect QTL that are shared across families to compensate for missing some rare large-effect QTL.}, number={6}, journal={HEREDITY}, author={Ogut, F. and Bian, Y. and Bradbury, P. J. and Holland, J. B.}, year={2015}, month={Jun}, pages={552–563} }
 @article{holland_2015, title={MAGIC maize: a new resource for plant genetics}, volume={16}, ISSN={["1474-760X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84941204292&partnerID=MN8TOARS}, DOI={10.1186/s13059-015-0713-2}, abstractNote={A multiparent advanced-generation intercross population of maize has been developed to help plant geneticists identify sequence variants affecting important agricultural traits.}, number={1}, journal={GENOME BIOLOGY}, author={Holland, James B.}, year={2015}, month={Sep} }
 @article{balint-kurti_holland_2015, title={New insight into a complex plant–fungal pathogen interaction}, volume={47}, ISSN={1061-4036 1546-1718}, url={http://dx.doi.org/10.1038/ng.3203}, DOI={10.1038/ng.3203}, abstractNote={The coevolution of plants and microbes has shaped plant mechanisms that detect and repel pathogens. A newly identified plant gene confers partial resistance to a fungal pathogen not by preventing initial infection but by limiting its spread through the plant.}, number={2}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={Balint-Kurti, Peter J and Holland, James B}, year={2015}, month={Jan}, pages={101–103} }
 @misc{jamann_balint-kurti_holland_2015, title={QTL Mapping Using High-Throughput Sequencing}, volume={1284}, ISBN={9781493924431 9781493924448}, ISSN={1064-3745 1940-6029}, url={http://dx.doi.org/10.1007/978-1-4939-2444-8_13}, DOI={10.1007/978-1-4939-2444-8_13}, abstractNote={Quantitative trait locus (QTL) mapping in plants dates to the 1980s (Stuber et al. Crop Sci 27: 639–648, 1987; Paterson et al. Nature 335: 721–726, 1988), but earlier studies were often hindered by the expense and time required to identify large numbers of polymorphic genetic markers that differentiated the parental genotypes and then to genotype them on large segregating mapping populations. High-throughput sequencing has provided an efficient means to discover single nucleotide polymorphisms (SNPs) that can then be assayed rapidly on large populations with array-based techniques (Gupta et al. Heredity 101: 5–18, 2008). Alternatively, high-throughput sequencing methods such as restriction site-associated DNA sequencing (RAD-Seq) (Davey et al. Nat Rev Genet 12: 499–510, 2011; Baird et al. PloS ONE 3: e3376, 2008) and genotyping-by-sequencing (GBS) (Elshire et al. PLoS One 6: 2011; Glaubitz et al. PLoS One 9: e90346, 2014) can be used to identify and genotype polymorphic markers directly. Linkage disequilibrium (LD) between markers and causal variants is needed to detect QTL. The earliest QTL mapping methods used backcross and F2 generations of crosses between inbred lines, which have high levels of linkage disequilibrium (dependent entirely on the recombination frequency between chromosomal positions), to ensure that QTL would have sufficiently high linkage disequilibrium with one or more markers on sparse genetic linkage maps. The downside of this approach is that resolution of QTL positions is poor. The sequencing technology revolution, by facilitating genotyping of vastly more markers than was previously feasible, has allowed researchers to map QTL in situations of lower linkage disequilibrium, and consequently, at higher resolution. We provide a review of methods to identify QTL with higher precision than was previously possible. We discuss modifications of the traditional biparental mapping population that provide higher resolution of QTL positions, QTL fine-mapping procedures, and genome-wide association studies, all of which are greatly facilitated by high-throughput sequencing methods. Each of these procedures has many variants, and consequently many details to consider; we focus our chapter on the consequences of practical decisions that researchers make when designing QTL mapping studies and when analyzing the resulting data. The ultimate goal of many of these studies is to resolve a QTL to its causal sequence variation.}, journal={Methods in Molecular Biology}, publisher={Springer New York}, author={Jamann, Tiffany M. and Balint-Kurti, Peter J. and Holland, James B.}, year={2015}, pages={257–285} }
 @article{pratt_holland_balint-kurti_coles_zwonitzer_casey_mcmullen_2015, title={Registration of the Ki14 × B73 Recombinant Inbred Mapping Population of Maize}, volume={9}, ISSN={1936-5209}, url={http://dx.doi.org/10.3198/jpr2014.06.0041crmp}, DOI={10.3198/jpr2014.06.0041crmp}, abstractNote={The Ohio Agricultural Research and Development Center released Ki14 × B73 maize (Zea mays L.) mapping population (Reg. No. MP-2, MGS 9025066 MAP; Maize Genetics COOP Stock Center no. Z042), a set of 119 recombinant inbred lines (RILs), in 2007. The mapping population was derived from a biparental cross between tropical inbred Ki14 (NCRPIS accession Ames 27259) and temperate inbred B73 (Reg. No. PL-17, PI 550473). One hundred sixteen of the original RILs were used for mapping quantitative trait loci associated with host resistance to foliar pathogens inciting southern corn leaf blight [caused by Cochliobolus heterostrophus (Drechs.)], gray leaf spot, (caused by Cercospora zeae-maydis Tehon & E.Y. Daniels), and northern corn leaf blight [caused by Setosphaeria turcica (Luttrell) K.J. Leonard & E.G. Suggs], three traits associated with maturity—days to anthesis, days to silking, and anther silk interval—and two morphological traits, plant and ear height. The genetic marker data included 765 single nucleotide polymorphisms and 74 simple sequence repeat markers genotyped on all the RILs and constructed into a genetic map. It is envisioned that the high level of host resistance of Ki14 and the agronomic performance of B73 will invite use of the population as a germplasm source for improved host resistance of temperate zone, and increased yield potential, of tropical zone maize. Distribution of the RIL mapping population will allow public access to this resource for continued mapping, gene discovery, and plant breeding.}, number={2}, journal={Journal of Plant Registrations}, publisher={Wiley}, author={Pratt, R. C. and Holland, J. B. and Balint-Kurti, P. J. and Coles, N. D. and Zwonitzer, J. C. and Casey, M. A. and McMullen, M. D.}, year={2015}, month={Mar}, pages={262–265} }
 @article{horne_eller_holland_2016, title={Responses to Recurrent Index Selection for Reduced Fusarium Ear Rot and Lodging and for Increased Yield in Maize}, volume={56}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84952760963&partnerID=MN8TOARS}, DOI={10.2135/cropsci2015.06.0333}, abstractNote={ABSTRACTFusarium ear rot, caused by the pathogen Fusarium verticillioides, damages maize (Zea mays L.) grain production and is associated with contamination of grain by fumonisin, a mycotoxin harmful to both humans and animals. Recurrent selection may be an effective way to combine improvements in resistance to Fusarium ear rot with improved grain yield and lodging resistance. To test this hypothesis, three cycles of recurrent index selection based on evaluating S0:1 lines for Fusarium ear rot, grain yield, and lodging were implemented in a genetically broad‐based population. Direct intrapopulation response to selection in the target traits was measured by comparing lines sampled from Cycle 0 and Cycle 3 populations. In addition, indirect response for fumonisin contamination was also measured along with indirect response for agronomic traits when crossed to commercial inbred tester, FR1064. Results indicate significant direct gain from selection for Fusarium ear rot, but no significant gains for yield or lodging resistance. Indirect gains were also observed for Fusarium ear rot resistance in topcrosses to an unrelated tester line and for fumonisin contamination both within the selection population and in topcrosses. Our results are the first demonstration of the indirect effect of selection against Fusarium ear rot on reduction of fumonisin contamination. Heritabilities for target traits did not decrease over generations, indicating potential for further genetic gain from selection in this population.}, number={1}, journal={CROP SCIENCE}, author={Horne, David W. and Eller, Magen S. and Holland, James B.}, year={2016}, pages={85–94} }
 @article{olukolu_wang_vontimitta_venkata_marla_ji_gachomo_chu_negeri_benson_et al._2014, title={A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways}, volume={10}, ISSN={1553-7404}, url={http://dx.doi.org/10.1371/journal.pgen.1004562}, DOI={10.1371/journal.pgen.1004562}, abstractNote={Much remains unknown of molecular events controlling the plant hypersensitive defense response (HR), a rapid localized cell death that limits pathogen spread and is mediated by resistance (R-) genes. Genetic control of the HR is hard to quantify due to its microscopic and rapid nature. Natural modifiers of the ectopic HR phenotype induced by an aberrant auto-active R-gene (Rp1-D21), were mapped in a population of 3,381 recombinant inbred lines from the maize nested association mapping population. Joint linkage analysis was conducted to identify 32 additive but no epistatic quantitative trait loci (QTL) using a linkage map based on more than 7000 single nucleotide polymorphisms (SNPs). Genome-wide association (GWA) analysis of 26.5 million SNPs was conducted after adjusting for background QTL. GWA identified associated SNPs that colocalized with 44 candidate genes. Thirty-six of these genes colocalized within 23 of the 32 QTL identified by joint linkage analysis. The candidate genes included genes predicted to be in involved programmed cell death, defense response, ubiquitination, redox homeostasis, autophagy, calcium signalling, lignin biosynthesis and cell wall modification. Twelve of the candidate genes showed significant differential expression between isogenic lines differing for the presence of Rp1-D21. Low but significant correlations between HR-related traits and several previously-measured disease resistance traits suggested that the genetic control of these traits was substantially, though not entirely, independent. This study provides the first system-wide analysis of natural variation that modulates the HR response in plants.}, number={8}, journal={PLoS Genetics}, publisher={Public Library of Science (PLoS)}, author={Olukolu, Bode A. and Wang, Guan-Feng and Vontimitta, Vijay and Venkata, Bala P. and Marla, Sandeep and Ji, Jiabing and Gachomo, Emma and Chu, Kevin and Negeri, Adisu and Benson, Jacqueline and et al.}, editor={McDowell, John M.Editor}, year={2014}, month={Aug}, pages={e1004562} }
 @inbook{goodman_holland_sánchez g_2014, title={Breeding and genetic diversity}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85020851622&partnerID=MN8TOARS}, DOI={10.1201/b17274}, abstractNote={Since the beginnings in the early part of the 20th Century, hybrid maize breeding has continued to evolve as new genetic understanding of traits and new technologies have become available. We review some of the early innovations that were involved in the transition of maize from an open pollinated crop to a hybrid crop and from the use of the Double Cross hybrid system to the Single Cross hybrid system. Today molecular technologies have opened up many new opportunities. These technologies and our understanding of trait genetics have enabled the further evolution of maize breeding methodology to include a range of molecular breeding methods. High throughput genotyping at the DNA sequence level has enabled the use of both marker assisted breeding for specifi c traits and whole genome prediction methodology for complex quantitative traits. The characterization of trait functional diversity and understanding its underlying genetic bases at the molecular level will continue to offer new tools to assist hybrid maize breeding. Furthermore, recent transgenic approaches provide new opportunities for commercial maize hybrid development.}, booktitle={Genetics, Genomics and Breeding of Maize}, author={Goodman, M.M. and Holland, J.B. and Sánchez G, J.J.}, year={2014}, pages={14–50} }
 @inbook{holland_2014, title={Breeding: Plants, Modern}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85042835077&partnerID=MN8TOARS}, DOI={10.1016/B978-0-444-52512-3.00226-6}, abstractNote={Historically, plant breeding has progressed from the initial domestication of crops to highly intensive and effective cultivar improvement methods that integrate genomic information with phenotypic evaluations of breeding populations. Plant breeders employ a wide variety of breeding methods, the choice of which is largely driven by the mating system of the species, and the type of cultivar that can be disseminated easily to farmers. Recent improvements in breeding methods include statistical methods that can combine information across different breeding families and the application of genomic information to improve selection response under certain circumstances.}, booktitle={Encyclopedia of Agriculture and Food Systems}, author={Holland, J.B.}, year={2014}, pages={187–200} }
 @article{peiffer_romay_gore_flint-garcia_zhang_millard_gardner_mcmullen_holland_bradbury_et al._2014, title={Causes and Consequences of Genetic Background Effects Illuminated by Integrative Genomic Analysis}, volume={196}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.113.159426}, abstractNote={Abstract
               The phenotypic consequences of individual mutations are modulated by the wild-type genetic background in which they occur. Although such background dependence is widely observed, we do not know whether general patterns across species and traits exist or about the mechanisms underlying it. We also lack knowledge on how mutations interact with genetic background to influence gene expression and how this in turn mediates mutant phenotypes. Furthermore, how genetic background influences patterns of epistasis remains unclear. To investigate the genetic basis and genomic consequences of genetic background dependence of the scallopedE3 allele on the Drosophila melanogaster wing, we generated multiple novel genome-level datasets from a mapping-by-introgression experiment and a tagged RNA gene expression dataset. In addition we used whole genome resequencing of the parental lines—two commonly used laboratory strains—to predict polymorphic transcription factor binding sites for SD. We integrated these data with previously published genomic datasets from expression microarrays and a modifier mutation screen. By searching for genes showing a congruent signal across multiple datasets, we were able to identify a robust set of candidate loci contributing to the background-dependent effects of mutations in sd. We also show that the majority of background-dependent modifiers previously reported are caused by higher-order epistasis, not quantitative noncomplementation. These findings provide a useful foundation for more detailed investigations of genetic background dependence in this system, and this approach is likely to prove useful in exploring the genetic basis of other traits as well.}, number={4}, journal={GENETICS}, author={Peiffer, J. A. and Romay, M. C. and Gore, M. A. and Flint-Garcia, S. A. and Zhang, Z. W. and Millard, M. J. and Gardner, C. A. C. and McMullen, M. D. and Holland, James and Bradbury, P. J. and et al.}, year={2014}, month={Apr}, pages={1321-+} }
 @article{zila_ogut_romay_gardner_buckler_holland_2014, title={Genome-wide association study of Fusarium ear rot disease in the USA maize inbred line collection}, volume={14}, ISSN={["1471-2229"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84964314102&partnerID=MN8TOARS}, DOI={10.1186/s12870-014-0372-6}, abstractNote={Resistance to Fusarium ear rot of maize is a quantitative and complex trait. Marker-trait associations to date have had small additive effects and were inconsistent between previous studies, likely due to the combined effects of genetic heterogeneity and low power of detection of many small effect variants. The complexity of inheritance of resistance hinders the use marker-assisted selection for ear rot resistance. We conducted a genome-wide association study (GWAS) for Fusarium ear rot resistance in a panel of 1687 diverse inbred lines from the USDA maize gene bank with 200,978 SNPs while controlling for background genetic relationships with a mixed model and identified seven single nucleotide polymorphisms (SNPs) in six genes associated with disease resistance in either the complete inbred panel (1687 lines with highly unbalanced phenotype data) or in a filtered inbred panel (734 lines with balanced phenotype data). Different sets of SNPs were detected as associated in the two different data sets. The alleles conferring greater disease resistance at all seven SNPs were rare overall (below 16%) and always higher in allele frequency in tropical maize than in temperate dent maize. Resampling analysis of the complete data set identified one robust SNP association detected as significant at a stringent p-value in 94% of data sets, each representing a random sample of 80% of the lines. All associated SNPs were in exons, but none of the genes had predicted functions with an obvious relationship to resistance to fungal infection. GWAS in a very diverse maize collection identified seven SNP variants each associated with between 1% and 3% of trait variation. Because of their small effects, the value of selection on these SNPs for improving resistance to Fusarium ear rot is limited. Selection to combine these resistance alleles combined with genomic selection to improve the polygenic background resistance might be fruitful. The genes associated with resistance provide candidate gene targets for further study of the biological pathways involved in this complex disease resistance.}, number={1}, journal={BMC PLANT BIOLOGY}, publisher={Springer Science \mathplus Business Media}, author={Zila, Charles T. and Ogut, Funda and Romay, Maria C. and Gardner, Candice A. and Buckler, Edward S. and Holland, James B.}, year={2014}, month={Dec} }
 @article{teixeira_weldekidan_leon_flint-garcia_holland_lauter_murray_xu_hessel_kleintop_et al._2015, title={Hallauer's Tuson: a decade of selection for tropical-to-temperate phenological adaptation in maize}, volume={114}, ISSN={["1365-2540"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84927567459&partnerID=MN8TOARS}, DOI={10.1038/hdy.2014.90}, abstractNote={Crop species exhibit an astounding capacity for environmental adaptation, but genetic bottlenecks resulting from intense selection for adaptation and productivity can lead to a genetically vulnerable crop. Improving the genetic resiliency of temperate maize depends upon the use of tropical germplasm, which harbors a rich source of natural allelic diversity. Here, the adaptation process was studied in a tropical maize population subjected to 10 recurrent generations of directional selection for early flowering in a single temperate environment in Iowa, USA. We evaluated the response to this selection across a geographical range spanning from 43.05° (WI) to 18.00° (PR) latitude. The capacity for an all-tropical maize population to become adapted to a temperate environment was revealed in a marked fashion: on average, families from generation 10 flowered 20 days earlier than families in generation 0, with a nine-day separation between the latest generation 10 family and the earliest generation 0 family. Results suggest that adaptation was primarily due to selection on genetic main effects tailored to temperature-dependent plasticity in flowering time. Genotype-by-environment interactions represented a relatively small component of the phenotypic variation in flowering time, but were sufficient to produce a signature of localized adaptation that radiated latitudinally, in partial association with daylength and temperature, from the original location of selection. Furthermore, the original population exhibited a maladaptive syndrome including excessive ear and plant heights along with later flowering; this was reduced in frequency by selection for flowering time.}, number={2}, journal={HEREDITY}, author={Teixeira, J. E. C. and Weldekidan, T. and Leon, N. and Flint-Garcia, S. and Holland, J. B. and Lauter, N. and Murray, S. C. and Xu, W. and Hessel, D. A. and Kleintop, A. E. and et al.}, year={2015}, month={Feb}, pages={229–240} }
 @article{hirsch_flint-garcia_beissinger_eichten_deshpande_barry_mcmullen_holland_buckler_buckler_et al._2014, title={Insights into the effects of long-term artificial selection on seed size in maize}, volume={198}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84907998638&partnerID=MN8TOARS}, DOI={10.1534/genetics.114.167155}, abstractNote={Abstract
               Grain produced from cereal crops is a primary source of human food and animal feed worldwide. To understand the genetic basis of seed-size variation, a grain yield component, we conducted a genome-wide scan to detect evidence of selection in the maize Krug Yellow Dent long-term divergent seed-size selection experiment. Previous studies have documented significant phenotypic divergence between the populations. Allele frequency estimates for ∼3 million single nucleotide polymorphisms (SNPs) in the base population and selected populations were estimated from pooled whole-genome resequencing of 48 individuals per population. Using FST values across sliding windows, 94 divergent regions with a median of six genes per region were identified. Additionally, 2729 SNPs that reached fixation in both selected populations with opposing fixed alleles were identified, many of which clustered in two regions of the genome. Copy-number variation was highly prevalent between the selected populations, with 532 total regions identified on the basis of read-depth variation and comparative genome hybridization. Regions important for seed weight in natural variation were identified in the maize nested association mapping population. However, the number of regions that overlapped with the long-term selection experiment did not exceed that expected by chance, possibly indicating unique sources of variation between the two populations. The results of this study provide insights into the genetic elements underlying seed-size variation in maize and could also have applications for other cereal crops.}, number={1}, journal={Genetics}, author={Hirsch, C.N. and Flint-Garcia, S.A. and Beissinger, T.M. and Eichten, S.R. and Deshpande, S. and Barry, K. and McMullen, M.D. and Holland, James and Buckler, E.S. and Buckler, E.S. and et al.}, year={2014}, pages={409-} }
 @article{bian_yang_balint-kurti_wisser_holland_2014, title={Limits on the reproducibility of marker associations with southern leaf blight resistance in the maize nested association mapping population}, volume={15}, ISSN={["1471-2164"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84924290940&partnerID=MN8TOARS}, DOI={10.1186/1471-2164-15-1068}, abstractNote={A previous study reported a comprehensive quantitative trait locus (QTL) and genome wide association study (GWAS) of southern leaf blight (SLB) resistance in the maize Nested Association Mapping (NAM) panel. Since that time, the genomic resources available for such analyses have improved substantially. An updated NAM genetic linkage map has a nearly six-fold greater marker density than the previous map and the combined SNPs and read-depth variants (RDVs) from maize HapMaps 1 and 2 provided 28.5 M genomic variants for association analysis, 17 fold more than HapMap 1. In addition, phenotypic values of the NAM RILs were re-estimated to account for environment-specific flowering time covariates and a small proportion of lines were dropped due to genotypic data quality problems. Comparisons of original and updated QTL and GWAS results confound the effects of linkage map density, GWAS marker density, population sample size, and phenotype estimates. Therefore, we evaluated the effects of changing each of these parameters individually and in combination to determine their relative impact on marker-trait associations in original and updated analyses. Of the four parameters varied, map density caused the largest changes in QTL and GWAS results. The updated QTL model had better cross-validation prediction accuracy than the previous model. Whereas joint linkage QTL positions were relatively stable to input changes, the residual values derived from those QTL models (used as inputs to GWAS) were more sensitive, resulting in substantial differences between GWAS results. The updated NAM GWAS identified several candidate genes consistent with previous QTL fine-mapping results. The highly polygenic nature of resistance to SLB complicates the identification of causal genes. Joint linkage QTL are relatively stable to perturbations of data inputs, but their resolution is generally on the order of tens or more Mbp. GWAS associations have higher resolution, but lower power due to stringent thresholds designed to minimize false positive associations, resulting in variability of detection across studies. The updated higher density linkage map improves QTL estimation and, along with a much denser SNP HapMap, greatly increases the likelihood of detecting SNPs in linkage with causal variants. We recommend use of the updated genetic resources and results but emphasize the limited repeatability of small-effect associations.}, number={1}, journal={BMC GENOMICS}, publisher={Springer Science \mathplus Business Media}, author={Bian, Yang and Yang, Qin and Balint-Kurti, Peter J. and Wisser, Randall J. and Holland, James B.}, year={2014}, month={Dec} }
 @article{yu_roy_kamal_cho_kwon_cho_so_holland_woo_2014, title={Protein profiling reveals novel proteins in pollen and pistil of W22 (ga1; Ga1) in maize}, volume={2}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84947263088&partnerID=MN8TOARS}, DOI={10.3390/proteomes2020258}, abstractNote={Gametophytic factors mediate pollen-pistil interactions in maize (Zea mays L.) and play active roles in limiting gene flow among maize populations and between maize and teosinte. This study was carried out to identify proteins and investigate the mechanism of gametophytic factors using protein analysis. W22 (ga1); which did not carry a gametophytic factor and W22 (Ga1), a near iso-genic line, were used for the proteome investigation. SDS-PAGE was executed to investigate proteins in the pollen and pistil of W22 (ga1) and W22 (Ga1). A total of 44 differentially expressed proteins were identified in the pollen and pistil on SDS-PAGE using LTQ-FTICR MS. Among the 44 proteins, a total of 24 proteins were identified in the pollen of W22 (ga1) and W22 (Ga1) whereas 20 differentially expressed proteins were identified from the pistil of W22 (ga1) and W22 (Ga1). However, in pollen, 2 proteins were identified only in the W22 (ga1) and 12 proteins only in the W22 (Ga1) whereas 10 proteins were confirmed from the both of W22 (ga1) and W22 (Ga1). In contrary, 10 proteins were appeared only in the pistil of W22 (ga1) and 7 proteins from W22 (Ga1) while 3 proteins confirmed in the both of W22 (ga1) and W22 (Ga1). Moreover, the identified proteins were generally involved in hydrolase activity, nucleic acid binding and nucleotide binding. These results help to reveal the mechanism of gametophytic factors and provide a valuable clue for the pollen and pistil research in maize.}, number={2}, journal={Proteomes}, author={Yu, J. and Roy, S.K. and Kamal, A.H.M. and Cho, K. and Kwon, S.-J. and Cho, S.-W. and So, Y.-S. and Holland, J.B. and Woo, S.H.}, year={2014}, pages={258–271} }
 @article{peiffer_romay_gore_flint-garcia_zhang_millard_gardner_mcmullen_holland_bradbury_et al._2014, title={The Genetic Architecture Of Maize Height}, volume={196}, ISSN={["1943-2631"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84901312138&partnerID=MN8TOARS}, DOI={10.1534/genetics.113.159152}, abstractNote={Abstract
               Height is one of the most heritable and easily measured traits in maize (Zea mays L.). Given a pedigree or estimates of the genomic identity-by-state among related plants, height is also accurately predictable. But, mapping alleles explaining natural variation in maize height remains a formidable challenge. To address this challenge, we measured the plant height, ear height, flowering time, and node counts of plants grown in >64,500 plots across 13 environments. These plots contained >7300 inbreds representing most publically available maize inbreds in the United States and families of the maize Nested Association Mapping (NAM) panel. Joint-linkage mapping of quantitative trait loci (QTL), fine mapping in near isogenic lines (NILs), genome-wide association studies (GWAS), and genomic best linear unbiased prediction (GBLUP) were performed. The heritability of maize height was estimated to be >90%. Mapping NAM family-nested QTL revealed the largest explained 2.1 ± 0.9% of height variation. The effects of two tropical alleles at this QTL were independently validated by fine mapping in NIL families. Several significant associations found by GWAS colocalized with established height loci, including brassinosteroid-deficient dwarf1, dwarf plant1, and semi-dwarf2. GBLUP explained >80% of height variation in the panels and outperformed bootstrap aggregation of family-nested QTL models in evaluations of prediction accuracy. These results revealed maize height was under strong genetic control and had a highly polygenic genetic architecture. They also showed that multiple models of genetic architecture differing in polygenicity and effect sizes can plausibly explain a population’s variation in maize height, but they may vary in predictive efficacy.}, number={4}, journal={GENETICS}, author={Peiffer, Jason A. and Romay, Maria C. and Gore, Michael A. and Flint-Garcia, Sherry A. and Zhang, Zhiwu and Millard, Mark J. and Gardner, Candice A. C. and McMullen, Michael D. and Holland, James B. and Bradbury, Peter J. and et al.}, year={2014}, month={Apr}, pages={1337-+} }
 @article{santa-cruz_kump_arellano_goodman_krakowsky_holland_balint-kurti_2014, title={Yield effects of two southern leaf blight resistance loci in maize hybrids}, volume={54}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84898430312&partnerID=MN8TOARS}, DOI={10.2135/cropsci2013.08.0553}, abstractNote={ABSTRACTIn this study we examined the effects of two quantitative trait loci (QTL) for southern leaf blight (SLB) resistance on several agronomic traits including disease resistance and yield. B73–3B and B73–6A are two near‐isogenic lines (NILs) in the background of the maize (Zea mays L.) inbred B73, each carrying one introgression (called 3B and 6A respectively) encompassing a QTL for SLB resistance. Sets of isohybrid triplets were developed by crossing B73, B73–3B, and B73–6A to several inbred lines. A subset of these triplets for which the B73–3B and/or B73–6A hybrid was significantly more SLB resistant than the B73 check hybrid was selected and assessed in multi‐environment yield trials with and without disease. In the presence of SLB, 3B was associated with an approximately 3% yield increase over B73. 6A was associated with a yield advantage in the presence of SLB in specific pedigrees where the 6A resistance phenotype was highly expressed. Results suggested that both introgressions might confer a yield cost in the absence of SLB, but only introgression 6A was associated with a statistically significant reduction. We present evidence to suggest that the yield cost is associated with the resistance phenotype rather than with linkage drag.}, number={3}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Santa-Cruz, Jose H. and Kump, Kristen L. and Arellano, Consuelo and Goodman, Major M. and Krakowsky, Matthew D. and Holland, James B. and Balint-Kurti, Peter J.}, year={2014}, pages={882–894} }
 @article{zila_fernando samayoa_santiago_butron_holland_2013, title={A Genome-Wide Association Study Reveals Genes Associated with Fusarium Ear Rot Resistance in a Maize Core Diversity Panel}, volume={3}, ISSN={["2160-1836"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84888996046&partnerID=MN8TOARS}, DOI={10.1534/g3.113.007328}, abstractNote={Abstract
               Fusarium ear rot is a common disease of maize that affects food and feed quality globally. Resistance to the disease is highly quantitative, and maize breeders have difficulty incorporating polygenic resistance alleles from unadapted donor sources into elite breeding populations without having a negative impact on agronomic performance. Identification of specific allele variants contributing to improved resistance may be useful to breeders by allowing selection of resistance alleles in coupling phase linkage with favorable agronomic characteristics. We report the results of a genome-wide association study to detect allele variants associated with increased resistance to Fusarium ear rot in a maize core diversity panel of 267 inbred lines evaluated in two sets of environments. We performed association tests with 47,445 single-nucleotide polymorphisms (SNPs) while controlling for background genomic relationships with a mixed model and identified three marker loci significantly associated with disease resistance in at least one subset of environments. Each associated SNP locus had relatively small additive effects on disease resistance (±1.1% on a 0–100% scale), but nevertheless were associated with 3 to 12% of the genotypic variation within or across environment subsets. Two of three identified SNPs colocalized with genes that have been implicated with programmed cell death. An analysis of associated allele frequencies within the major maize subpopulations revealed enrichment for resistance alleles in the tropical/subtropical and popcorn subpopulations compared with other temperate breeding pools.}, number={11}, journal={G3-GENES GENOMES GENETICS}, author={Zila, Charles T. and Fernando Samayoa, L. and Santiago, Rogelio and Butron, Ana and Holland, James B.}, year={2013}, month={Nov}, pages={2095–2104} }
 @article{romay_millard_glaubitz_peiffer_swarts_casstevens_elshire_acharya_mitchell_flint-garcia_et al._2013, title={Comprehensive genotyping of the USA national maize inbred seed bank}, volume={14}, ISSN={["1474-760X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84878685948&partnerID=MN8TOARS}, DOI={10.1186/gb-2013-14-6-r55}, abstractNote={Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world.The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits.The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.}, number={6}, journal={GENOME BIOLOGY}, author={Romay, Maria C. and Millard, Mark J. and Glaubitz, Jeffrey C. and Peiffer, Jason A. and Swarts, Kelly L. and Casstevens, Terry M. and Elshire, Robert J. and Acharya, Charlotte B. and Mitchell, Sharon E. and Flint-Garcia, Sherry A. and et al.}, year={2013} }
 @article{willcox_davis_warburton_windham_abbas_betrán_holland_williams_2013, title={Confirming quantitative trait loci for aflatoxin resistance from Mp313E in different genetic backgrounds}, volume={32}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84879211529&partnerID=MN8TOARS}, DOI={10.1007/s11032-012-9821-9}, number={1}, journal={Molecular Breeding}, author={Willcox, M.C. and Davis, G.L. and Warburton, M.L. and Windham, G.L. and Abbas, H.K. and Betrán, J. and Holland, J.B. and Williams, W.P.}, year={2013}, pages={15–26} }
 @inbook{sood_flint-garcia_willcox_holland_2014, title={Mining natural variation for maize improvement: Selection on phenotypes and genes}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84951209506&partnerID=MN8TOARS}, DOI={10.1007/978-94-007-7572-5_25}, booktitle={Genomics of Plant Genetic Resources: Volume 1. Managing, Sequencing and Mining Genetic Resources}, author={Sood, S. and Flint-Garcia, S. and Willcox, M.C. and Holland, J.B.}, year={2014}, pages={615–649} }
 @article{olukolu_negeri_dhawan_venkata_sharma_garg_gachomo_marla_chu_hasan_et al._2013, title={A Connected Set of Genes Associated with Programmed Cell Death Implicated in Controlling the Hypersensitive Response in Maize}, volume={193}, ISSN={["0016-6731"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84876366651&partnerID=MN8TOARS}, DOI={10.1534/genetics.112.147595}, abstractNote={Abstract
               Rp1-D21 is a maize auto-active resistance gene conferring a spontaneous hypersensitive response (HR) of variable severity depending on genetic background. We report an association mapping strategy based on the Mutant Assisted Gene Identification and Characterization approach to identify naturally occurring allelic variants associated with phenotypic variation in HR. Each member of a collection of 231 diverse inbred lines of maize constituting a high-resolution association mapping panel were crossed to a parental stock heterozygous for Rp1-D21, and the segregating F1 generation testcrosses were evaluated for phenotypes associated with lesion severity for 2 years at two locations. A genome-wide scan for associations with HR was conducted with 47,445 SNPs using a linear mixed model that controlled for spurious associations due to population structure. Since the ability to identify candidate genes and the resolution of association mapping are highly influenced by linkage disequilibrium (LD), we examined the extent of genome-wide LD. On average, marker pairs separated by >10 kbp had an r2 value of <0.1. Genomic regions surrounding SNPs significantly associated with HR traits were locally saturated with additional SNP markers to establish local LD structure and precisely identify candidate genes. Six significantly associated SNPs at five loci were detected. At each locus, the associated SNP was located within or immediately adjacent to candidate causative genes predicted to play significant roles in the control of programmed cell death and especially in ubiquitin pathway-related processes.}, number={2}, journal={GENETICS}, author={Olukolu, Bode A. and Negeri, Adisu and Dhawan, Rahul and Venkata, Bala P. and Sharma, Pankaj and Garg, Anshu and Gachomo, Emma and Marla, Sandeep and Chu, Kevin and Hasan, Anna and et al.}, year={2013}, month={Feb}, pages={609-+} }
 @article{hung_holland_2012, title={Diallel Analysis of Resistance to Fusarium Ear Rot and Fumonisin Contamination in Maize}, volume={52}, ISSN={["0011-183X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84864723417&partnerID=MN8TOARS}, DOI={10.2135/cropsci2012.03.0154}, abstractNote={ABSTRACTThe fungus Fusarium verticillioides infects maize (Zea mays L.) ears and kernels, resulting in Fusarium ear rot disease, reduced grain yields, and contamination of grain with the mycotoxin fumonisin. Hybrid maize breeding programs involve selection for both inbred and hybrid performance; the emphasis placed on inbred versus hybrid selection depends on heritability of and the genetic correlation between resistance in the different generations. The objectives of this study were to assess the importance of general combing ability (GCA) and specific combining ability (SCA) for resistance to Fusarium ear rot and fumonisin contamination and to estimate the correlation between resistance measured in inbred and hybrid generations. We evaluated a diallel mating of 18 inbred lines from different heterotic groups with different levels of resistance. Hybrids had 27% less ear rot and 30% less fumonisin content than their inbred parents, demonstrating the importance of hybrid vigor to disease resistance. Both GCA and SCA were significant for yield and disease resistance, and inbred performance per se and corresponding GCA in hybrids were significantly correlated (r ≥ 0.78). Genetic variation for resistance was greater in inbred lines than among hybrids, however. These results suggest that the most efficient way to improve Fusarium ear rot and fumonisin contamination resistances in hybrids is to evaluate and select among inbred lines before using resources to create and evaluate hybrids.}, number={5}, journal={CROP SCIENCE}, author={Hung, Hsiao-Yi and Holland, James B.}, year={2012}, month={Sep}, pages={2173–2181} }
 @article{chia_song_bradbury_costich_de leon_doebley_elshire_gaut_geller_glaubitz_et al._2012, title={Maize HapMap2 identifies extant variation from a genome in flux}, volume={44}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84863007735&partnerID=MN8TOARS}, DOI={10.1038/ng.2313}, abstractNote={Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize.}, number={7}, journal={Nature Genetics}, author={Chia, J.-M. and Song, C. and Bradbury, P.J. and Costich, D. and De Leon, N. and Doebley, J. and Elshire, R.J. and Gaut, B. and Geller, L. and Glaubitz, J.C. and et al.}, year={2012}, pages={803–807} }
 @article{veturi_kump_walsh_ott_poland_kolkman_balint-kurti_holland_wisser_2012, title={Multivariate Mixed Linear Model Analysis of Longitudinal Data: An Information-Rich Statistical Technique for Analyzing Plant Disease Resistance}, volume={102}, ISSN={["1943-7684"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84871758907&partnerID=MN8TOARS}, DOI={10.1094/phyto-10-11-0268}, abstractNote={ The mixed linear model (MLM) is an advanced statistical technique applicable to many fields of science. The multivariate MLM can be used to model longitudinal data, such as repeated ratings of disease resistance taken across time. In this study, using an example data set from a multi-environment trial of northern leaf blight disease on 290 maize lines with diverse levels of resistance, multivariate MLM analysis was performed and its utility was examined. In the population and environments tested, genotypic effects were highly correlated across disease ratings and followed an autoregressive pattern of correlation decay. Because longitudinal data are often converted to the univariate measure of area under the disease progress curve (AUDPC), comparisons between univariate MLM analysis of AUDPC and multivariate MLM analysis of longitudinal data were made. Univariate analysis had the advantage of simplicity and reduced computational demand, whereas multivariate analysis enabled a comprehensive perspective on disease development, providing the opportunity for unique insights into disease resistance. To aid in the application of multivariate MLM analysis of longitudinal data on disease resistance, annotated program syntax for model fitting is provided for the software ASReml. }, number={11}, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Veturi, Yogasudha and Kump, Kristen and Walsh, Ellie and Ott, Oliver and Poland, Jesse and Kolkman, Judith M. and Balint-Kurti, Peter J. and Holland, James B. and Wisser, Randall J.}, year={2012}, month={Nov}, pages={1016–1025} }
 @article{hizbai_gardner_wight_dhanda_molnar_johnson_fregeau-reid_yan_rossnagel_holland_et al._2012, title={Quantitative Trait Loci Affecting Oil Content, Oil Composition, and Other Agronomically Important Traits in Oat}, volume={5}, ISSN={["1940-3372"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84883812915&partnerID=MN8TOARS}, DOI={10.3835/plantgenome2012.07.0015}, abstractNote={Groat oil content and composition are important determinants of oat (Avena sativa L.) quality. We investigated these traits in a population of 146 recombinant inbred lines from a cross between ‘Dal’ (high oil) and ‘Exeter’ (low oil). A linkage map consisting of 475 Diversity Arrays Technology (DArT) markers spanning 1271.8 cM across 40 linkage groups was constructed. Quantitative trait locus (QTL) analysis for groat oil content and composition was conducted using grain samples grown at Aberdeen, ID, in 1997. Quantitative trait locus analysis for multiple agronomic traits was also conducted using data collected from hill plots and field plots in Ottawa, ON, in 2010. Using simple and composite interval mapping methods, QTLs for oil content, palmitic acid (16:0), stearic acid (18:0), oleic acid (18:1), linoleic acid (18:2), and linolenic acid (18:3) were identified. Two of the loci associated with oil content were associated with all of the fatty acids examined in this study, and most oil‐related QTL showed similar patterns of effect on the fatty acid profile. These results suggest the presence of pleiotropic effects on oil‐related traits through influences at specific nodes of the oil synthesis pathway. In addition, 12 QTL‐associated markers (likely representing nine unique regions) were associated with plant height, heading date, lodging, and protein content.}, number={3}, journal={PLANT GENOME}, author={Hizbai, Biniam T. and Gardner, K. M. and Wight, C. P. and Dhanda, R. K. and Molnar, S. J. and Johnson, D. and Fregeau-Reid, J. and Yan, W. and Rossnagel, B. G. and Holland, J. B. and et al.}, year={2012}, month={Nov}, pages={164–175} }
 @article{hung_shannon_tian_bradbury_chen_flint-garcia_mcmullen_ware_buckler_doebley_et al._2012, title={ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize}, volume={109}, ISSN={["0027-8424"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84863955846&partnerID=MN8TOARS}, DOI={10.1073/pnas.1203189109}, abstractNote={
            Teosinte, the progenitor of maize, is restricted to tropical environments in Mexico and Central America. The pre-Columbian spread of maize from its center of origin in tropical Southern Mexico to the higher latitudes of the Americas required postdomestication selection for adaptation to longer day lengths. Flowering time of teosinte and tropical maize is delayed under long day lengths, whereas temperate maize evolved a reduced sensitivity to photoperiod. We measured flowering time of the maize nested association and diverse association mapping panels in the field under both short and long day lengths, and of a maize-teosinte mapping population under long day lengths. Flowering time in maize is a complex trait affected by many genes and the environment. Photoperiod response is one component of flowering time involving a subset of flowering time genes whose effects are strongly influenced by day length. Genome-wide association and targeted high-resolution linkage mapping identified
            ZmCCT
            , a homologue of the rice photoperiod response regulator
            Ghd7,
            as the most important gene affecting photoperiod response in maize. Under long day lengths
            ZmCCT
            alleles from diverse teosintes are consistently expressed at higher levels and confer later flowering than temperate maize alleles. Many maize inbred lines, including some adapted to tropical regions, carry
            ZmCCT
            alleles with no sensitivity to day length. Indigenous farmers of the Americas were remarkably successful at selecting on genetic variation at key genes affecting the photoperiod response to create maize varieties adapted to vastly diverse environments despite the hindrance of the geographic axis of the Americas and the complex genetic control of flowering time.
          }, number={28}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Hung, Hsiao-Yi and Shannon, Laura M. and Tian, Feng and Bradbury, Peter J. and Chen, Charles and Flint-Garcia, Sherry A. and McMullen, Michael D. and Ware, Doreen and Buckler, Edward S. and Doebley, John F. and et al.}, year={2012}, month={Jul}, pages={E1913–E1921} }
 @article{wisser_balint-kurti_holland_2011, title={A novel genetic framework for studying response to artificial selection}, volume={9}, ISSN={["1479-2621"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79960130677&partnerID=MN8TOARS}, DOI={10.1017/s1479262111000359}, abstractNote={Response to selection is fundamental to plant breeding. To gain insight into the genetic basis of response to selection, we propose a new experimental genetic framework allowing for the identification of trait-specific genomic loci underlying population improvement and the characterization of allelic frequency responses at those loci. This is achieved by employing a sampling scheme for recurrently selected populations that allows for the simultaneous application of genetic association mapping and analysis of allelic frequency change across generations of selection. The combined method unites advantages of the two approaches, permitting the estimation of trait-specific allelic effects by association mapping and the detection of rare favourable alleles by their significant enrichment over generations of selection. Our aim is to develop a framework applicable for many crop species in order to gain a broader and deeper understanding of the genetic architecture of response to artificial selection.}, number={2}, journal={PLANT GENETIC RESOURCES-CHARACTERIZATION AND UTILIZATION}, publisher={Cambridge University Press (CUP)}, author={Wisser, Randall J. and Balint-Kurti, Peter J. and Holland, James B.}, year={2011}, month={Jul}, pages={281–283} }
 @article{coles_zila_holland_2011, title={Allelic Effect Variation at Key Photoperiod Response Quantitative Trait Loci in Maize}, volume={51}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79955539611&partnerID=MN8TOARS}, DOI={10.2135/cropsci2010.08.0488}, abstractNote={Tropical maize (Zea mays L.) represents a valuable genetic resource containing unique alleles not present in elite temperate maize. The strong delay in flowering in response to long daylength photoperiods exhibited by most tropical maize hinders its incorporation into temperate maize breeding programs. We tested the hypothesis that diverse tropical inbreds carry alleles with similar effects at four key photoperiod response quantitative trait loci (QTL) previously identified in maize. Four tropical maize inbreds were each crossed and backcrossed twice to the temperate recurrent parent B73 to establish four sets of introgression lines. Evaluation of these lines under long daylengths demonstrated that all four QTL have significant effects on flowering time or height in these lines, but the functional allelic effects varied substantially across the tropical donor lines. At the most important photoperiod response QTL on chromosome 10, one tropical line allele even promoted earlier flowering relative to the B73 allele. Significant allelic effect differences among tropical founders were also demonstrated directly in an F2 population derived from the cross of Ki14 and CML254. The chromosome 10 photoperiod response QTL position was validated in a set of heterogeneous inbred families evaluated in field tests and in controlled environments.}, number={3}, journal={CROP SCIENCE}, author={Coles, N. D. and Zila, C. T. and Holland, J. B.}, year={2011}, month={May}, pages={1036–1049} }
 @article{jumbo_weldekidan_holland_hawk_2011, title={Comparison of Conventional, Modified Single Seed Descent, and Doubled Haploid Breeding Methods for Maize Inbred Line Development Using Germplasm Enhancement of Maize Breeding Crosses}, volume={51}, ISSN={["0011-183X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79959605955&partnerID=MN8TOARS}, DOI={10.2135/cropsci2010.10.0594}, abstractNote={ABSTRACTBreeding crosses from the Germplasm Enhancement of Maize (GEM) project between exotic accessions and elite Corn Belt Dent inbreds provide a unique opportunity for broadening the genetic base of the U.S. maize (Zea mays L.) crop by incorporating favorable exotic alleles in elite genetic backgrounds. Genetic gains in the GEM program could be enhanced by identifying more efficient breeding procedures for this purpose. We compared four breeding methods, conventional Germplasm Enhancement of Maize (CG), conventional mass (CM), modified single seed descent (MSSD), and doubled haploid (DH) methods, for their relative capacity to produce superior maize inbred lines and hybrids from three GEM breeding crosses: (ANTIG01 × N16) × DE4, (AR16035 × S02) × S09, and (DKXL212 × S09) × S43b. Testcross evaluations of 50 selected lines from each combination of cross and breeding method were conducted across multiple environments, generally revealing no differences among breeding methods. The MSSD and CM methods had higher proportions of the top 10 lines for grain yield and yield:moisture ratio in the second year testcross reevaluations of about the top 28% of lines. Hybrids from MSSD lines tended to have higher grain moisture, but MSSD hybrids with high yield:moisture ratio could still be identified. The MSSD method may be an effective and efficient alternative to both pedigree and DH methods for developing high performing lines from the GEM breeding crosses as it requires relatively fewer resources.}, number={4}, journal={CROP SCIENCE}, author={Jumbo, McDonald and Weldekidan, Teclemariam and Holland, James B. and Hawk, James A.}, year={2011}, month={Jul}, pages={1534–1543} }
 @article{brown_upadyayula_mahone_tian_bradbury_myles_holland_flint-garcia_mcmullen_buckler_et al._2011, title={Distinct Genetic Architectures for Male and Female Inflorescence Traits of Maize}, volume={7}, ISSN={["1553-7404"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-81755187332&partnerID=MN8TOARS}, DOI={10.1371/journal.pgen.1002383}, abstractNote={We compared the genetic architecture of thirteen maize morphological traits in a large population of recombinant inbred lines. Four traits from the male inflorescence (tassel) and three traits from the female inflorescence (ear) were measured and studied using linkage and genome-wide association analyses and compared to three flowering and three leaf traits previously studied in the same population. Inflorescence loci have larger effects than flowering and leaf loci, and ear effects are larger than tassel effects. Ear trait models also have lower predictive ability than tassel, flowering, or leaf trait models. Pleiotropic loci were identified that control elongation of ear and tassel, consistent with their common developmental origin. For these pleiotropic loci, the ear effects are larger than tassel effects even though the same causal polymorphisms are likely involved. This implies that the observed differences in genetic architecture are not due to distinct features of the underlying polymorphisms. Our results support the hypothesis that genetic architecture is a function of trait stability over evolutionary time, since the traits that changed most during the relatively recent domestication of maize have the largest effects.}, number={11}, journal={PLOS GENETICS}, author={Brown, Patrick J. and Upadyayula, Narasimham and Mahone, Gregory S. and Tian, Feng and Bradbury, Peter J. and Myles, Sean and Holland, James B. and Flint-Garcia, Sherry and McMullen, Michael D. and Buckler, Edward S. and et al.}, year={2011}, month={Nov} }
 @article{cook_mcmullen_holland_tian_bradbury_ross-ibarra_buckler_flint-garcia_2012, title={Genetic Architecture of Maize Kernel Composition in the Nested Association Mapping and Inbred Association Panels}, volume={158}, ISSN={["1532-2548"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84856582669&partnerID=MN8TOARS}, DOI={10.1104/pp.111.185033}, abstractNote={Abstract
               The maize (Zea mays) kernel plays a critical role in feeding humans and livestock around the world and in a wide array of industrial applications. An understanding of the regulation of kernel starch, protein, and oil is needed in order to manipulate composition to meet future needs. We conducted joint-linkage quantitative trait locus mapping and genome-wide association studies (GWAS) for kernel starch, protein, and oil in the maize nested association mapping population, composed of 25 recombinant inbred line families derived from diverse inbred lines. Joint-linkage mapping revealed that the genetic architecture of kernel composition traits is controlled by 21–26 quantitative trait loci. Numerous GWAS associations were detected, including several oil and starch associations in acyl-CoA:diacylglycerol acyltransferase1-2, a gene that regulates oil composition and quantity. Results from nested association mapping were verified in a 282 inbred association panel using both GWAS and candidate gene association approaches. We identified many beneficial alleles that will be useful for improving kernel starch, protein, and oil content.}, number={2}, journal={PLANT PHYSIOLOGY}, author={Cook, Jason P. and McMullen, Michael D. and Holland, James B. and Tian, Feng and Bradbury, Peter and Ross-Ibarra, Jeffrey and Buckler, Edward S. and Flint-Garcia, Sherry A.}, year={2012}, month={Feb}, pages={824–834} }
 @article{tian_bradbury_brown_hung_sun_flint-garcia_rocheford_mcmullen_holland_buckler_2011, title={Genome-wide association study of leaf architecture in the maize nested association mapping population}, volume={43}, ISSN={["1546-1718"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79251561130&partnerID=MN8TOARS}, DOI={10.1038/ng.746}, abstractNote={US maize yield has increased eight-fold in the past 80 years, with half of the gain attributed to selection by breeders. During this time, changes in maize leaf angle and size have altered plant architecture, allowing more efficient light capture as planting density has increased. Through a genome-wide association study (GWAS) of the maize nested association mapping panel, we determined the genetic basis of important leaf architecture traits and identified some of the key genes. Overall, we demonstrate that the genetic architecture of the leaf traits is dominated by small effects, with little epistasis, environmental interaction or pleiotropy. In particular, GWAS results show that variations at the liguleless genes have contributed to more upright leaves. These results demonstrate that the use of GWAS with specially designed mapping populations is effective in uncovering the basis of key agronomic traits.}, number={2}, journal={NATURE GENETICS}, author={Tian, Feng and Bradbury, Peter J. and Brown, Patrick J. and Hung, Hsiaoyi and Sun, Qi and Flint-Garcia, Sherry and Rocheford, Torbert R. and McMullen, Michael D. and Holland, James B. and Buckler, Edward S.}, year={2011}, month={Feb}, pages={159–U113} }
 @article{kump_bradbury_wisser_buckler_belcher_oropeza-rosas_zwonitzer_kresovich_mcmullen_ware_et al._2011, title={Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population}, volume={43}, ISSN={["1061-4036"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79251575784&partnerID=MN8TOARS}, DOI={10.1038/ng.747}, abstractNote={Nested association mapping (NAM) offers power to resolve complex, quantitative traits to their causal loci. The maize NAM population, consisting of 5,000 recombinant inbred lines (RILs) from 25 families representing the global diversity of maize, was evaluated for resistance to southern leaf blight (SLB) disease. Joint-linkage analysis identified 32 quantitative trait loci (QTLs) with predominantly small, additive effects on SLB resistance. Genome-wide association tests of maize HapMap SNPs were conducted by imputing founder SNP genotypes onto the NAM RILs. SNPs both within and outside of QTL intervals were associated with variation for SLB resistance. Many of these SNPs were within or near sequences homologous to genes previously shown to be involved in plant disease resistance. Limited linkage disequilibrium was observed around some SNPs associated with SLB resistance, indicating that the maize NAM population enables high-resolution mapping of some genome regions.}, number={2}, journal={NATURE GENETICS}, publisher={Nature Publishing Group}, author={Kump, Kristen L. and Bradbury, Peter J. and Wisser, Randall J. and Buckler, Edward S. and Belcher, Araby R. and Oropeza-Rosas, Marco A. and Zwonitzer, John C. and Kresovich, Stephen and McMullen, Michael D. and Ware, Doreen and et al.}, year={2011}, month={Feb}, pages={163–U120} }
 @article{bloom_holland_2011, title={Genomic localization of the maize cross-incompatibility gene, Gametophyte factor 1 (ga1)}, volume={56}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84857675839&partnerID=MN8TOARS}, number={4}, journal={Maydica}, author={Bloom, J.C. and Holland, J.B.}, year={2011}, pages={379–387} }
 @article{negeri_coles_holland_balint-kurti_2011, title={Mapping QTL controlling southern leaf blight resistance by joint analysis of three related recombinant inbred line populations}, volume={51}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79959615426&partnerID=MN8TOARS}, DOI={10.2135/cropsci2010.12.0672}, abstractNote={ABSTRACTSouthern leaf blight (SLB) is a foliar necrotrophic disease of maize (Zea mays L.) caused by the ascomycete fungus Cochliobolus heterostrophus (Drechs.) Drechs. It is particularly important in warm humid parts of the world where maize is cultivated, such as the southern Atlantic coast area of the United States and parts of India, Africa, and Western Europe. Quantitative trait loci (QTL) for resistance to SLB disease caused by C. heterostrophus race O were identified in three maize recombinant inbred populations assessed in two environments: Clayton, NC, in the summer and Homestead, FL, in the winter. The three populations were derived from the crosses B73 × CML254, CML254 × B97, and B97 × Ki14. Each of these populations was derived from a cross between a temperate maize line (B73 or B97) and a tropical maize line (Ki14 or CML254). Quantitative trait loci were identified by separate analysis of each population and by joint connected and disconnected analyses of all the populations. The most significant QTL identified were on chromosomes 3, 8, 9,and 10. Joint analysis led to more precise position estimates than separate analysis in each case. Results are discussed in the context of previous SLB QTL analysis studies and a recent flowering time QTL study that used the same populations. The chromosome 8 and 9 QTL colocalized with previously identified flowering time QTL which suggested that the perceived effect on SLB resistance at these QTL may have been mediated through an effect on flowering time}, number={4}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Negeri, Adisu T. and Coles, Nathan D. and Holland, James B. and Balint-Kurti, Peter J.}, year={2011}, pages={1571–1579} }
 @article{wisser_kolkman_patzoldt_holland_yu_krakowsky_nelson_balint-kurti_2011, title={Multivariate analysis of maize disease resistances suggests a pleiotropic genetic basis and implicates a GST gene}, volume={108}, ISSN={["0027-8424"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79956318799&partnerID=MN8TOARS}, DOI={10.1073/pnas.1011739108}, abstractNote={
            Plants are attacked by pathogens representing diverse taxonomic groups, such that genes providing multiple disease resistance (MDR) are expected to be under positive selection pressure. To address the hypothesis that naturally occurring allelic variation conditions MDR, we extended the framework of structured association mapping to allow for the analysis of correlated complex traits and the identification of pleiotropic genes. The multivariate analytical approach used here is directly applicable to any species and set of traits exhibiting correlation. From our analysis of a diverse panel of maize inbred lines, we discovered high positive genetic correlations between resistances to three globally threatening fungal diseases. The maize panel studied exhibits rapidly decaying linkage disequilibrium that generally occurs within 1 or 2 kb, which is less than the average length of a maize gene. The positive correlations therefore suggested that functional allelic variation at specific genes for MDR exists in maize. Using a multivariate test statistic, a glutathione
            S
            -transferase (
            GST
            ) gene was found to be associated with modest levels of resistance to all three diseases. Resequencing analysis pinpointed the association to a histidine (basic amino acid) for aspartic acid (acidic amino acid) substitution in the encoded protein domain that defines GST substrate specificity and biochemical activity. The known functions of GSTs suggested that variability in detoxification pathways underlie natural variation in maize MDR.
          }, number={18}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Wisser, Randall J. and Kolkman, Judith M. and Patzoldt, Megan E. and Holland, James B. and Yu, Jianming and Krakowsky, Matthew and Nelson, Rebecca J. and Balint-Kurti, Peter J.}, year={2011}, month={May}, pages={7339–7344} }
 @article{holland_coles_2011, title={QTL controlling masculinization of ear tips in a maize (Zea mays L.) intraspecific cross}, volume={1}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84883041575&partnerID=MN8TOARS}, DOI={10.1534/g3.111.000786}, abstractNote={Abstract
               Maize is unique among cereal grasses because of its monoecious flowering habit. Male flowers are normally restricted to the tassel that terminates the primary shoot, whereas female flowers occur as ears at the terminal nodes of lateral branches. We observed Ki14, a tropical maize inbred that produces an ear tipped by a staminate (male) spike under certain environmental conditions, such as long daylengths. Recombinant inbred lines derived from the cross between temperate line B97, which was never observed to produce a staminate ear tip, and Ki14 segregated for the trait under long daylengths. Some progeny lines that had even longer staminate tips than Ki14 were male fertile. We mapped three QTL controlling staminate ear tip using a two-part (binomial plus normal) model. A major QTL on chromosome 3 had a large effect on penetrance of the trait (whether a line would produce staminate ear tips or not) as well as its severity (the length of the staminate tip). This QTL seems to be linked to, but at a distinct position from, a previously mapped QTL controlling the proportion of staminate florets in ears in progeny from crosses between maize and teosinte. Two additional QTL affecting staminate ear tip severity overlapped with QTL controlling photoperiod response previously mapped in this population. Alleles conferring photoperiod sensitivity for delayed flowering at these QTL seem to enhance the production of staminate ear tips under long daylengths.}, number={5}, journal={G3: Genes, Genomes, Genetics}, author={Holland, J.B. and Coles, N.D.}, year={2011}, pages={337–341} }
 @article{avendano lopez_sanchez gonzalez_ruiz corral_de la cruz larios_santacruz-ruvalcaba_sanchez hernandez_holland_2011, title={Seed Dormancy in Mexican Teosinte}, volume={51}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79961182540&partnerID=MN8TOARS}, DOI={10.2135/cropsci2010.09.0538}, abstractNote={Seed dormancy in wild Zea species may affect fitness and relate to ecological adaptation. The primary objective of this study was to characterize the variation in seed germination of the wild species of the genus Zea that currently grow in México and to relate this variation to their ecological zones of adaptation. In addition, we compared methods to break dormancy and measured the germination responses of seeds to environment factors that are related to seasonal changes. Teosinte populations representing all the taxonomic and racial groups known in México were collected during the period 2003 to 2008 in twelve states of México. Seed dormancy was classified according to the rate of its loss (depth of dormancy). Results indicated that more than 90% of populations studied had some degree of seed dormancy. Nondormant populations are distributed predominantly in semicold areas, while deep and very deep seed dormancy was found in populations distributed in hot and very hot environments in well defined geographic regions of the Balsas River Basin and in San Felipe Usila, Oaxaca. Mechanical seed scarification was the best method to break dormancy.}, number={5}, journal={CROP SCIENCE}, author={Avendano Lopez, Adriana Natividad and Sanchez Gonzalez, Jose de Jesus and Ruiz Corral, Jose Ariel and De La Cruz Larios, Lino and Santacruz-Ruvalcaba, Fernando and Sanchez Hernandez, Carla Vanessa and Holland, James B.}, year={2011}, month={Sep}, pages={2056–2066} }
 @article{sanchez g_cruz l_vidal m_ron p_taba_santacruz-ruvalcaba_sood_holland_ruiz c_carvajal_et al._2011, title={THREE NEW TEOSINTES (ZEA SPP., POACEAE) FROM MEXICO}, volume={98}, ISSN={["1537-2197"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84857141107&partnerID=MN8TOARS}, DOI={10.3732/ajb.1100193}, abstractNote={•Premise of the study:Teosinte species are the closest relatives of maize and represent an important but increasingly rare genetic resource for maize improvement and the study of evolution by domestication. Three morphologically and ecologically distinct teosinte populations were recently discovered in México. The taxonomic status of these rare and endangered populations was investigated by detailed comparisons to previously characterized wildZeaspecies.•Methods:Three new teosinte populations were compared to known teosinte taxa on the basis of morphological, ecogeographic, cytological, and molecular characteristics. Phenetic and phylogenetic analyses were performed using morphological and molecular data, respectively.•Key results:The newly discovered populations are distinct from each other and from otherZeaspecies to represent three new entities based on their unique combinations of morphological, ecological, ploidy, and DNA markers. A perennial diploid population from Nayarit is distinguished by early maturing plants, and having male inflorescences with few tassel branches and long spikelets. A perennial tetraploid population from Michoacán is characterized by tall and late maturing plants, and having male inflorescences with many branches. An annual diploid population from Oaxaca is characterized by having male inflorescences with fewer branches and longer spikelets than those found in the sister taxaZ. luxuriansandZ. nicaraguensis, plants with high thermal requirements, and very long seed dormancy.•Conclusions:Evidence from multiple independent sources suggests placement of the three new populations of teosinte as distinct entities within sectionLuxuriantesof the genusZea. However, more extensive DNA marker or sequence data are required to resolve the taxonomy of this genus.}, number={9}, journal={AMERICAN JOURNAL OF BOTANY}, author={Sanchez G, J. J. and Cruz L, L. De and Vidal M, V. A. and Ron P, J. and Taba, S. and Santacruz-Ruvalcaba, F. and Sood, S. and Holland, J. B. and Ruiz C, J. A. and Carvajal, S. and et al.}, year={2011}, month={Sep}, pages={1537–1548} }
 @article{hung_browne_guill_coles_eller_garcia_lepak_melia-hancock_oropeza-rosas_salvo_et al._2012, title={The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population}, volume={108}, ISSN={["1365-2540"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84859947989&partnerID=MN8TOARS}, DOI={10.1038/hdy.2011.103}, abstractNote={Appropriate selection of parents for the development of mapping populations is pivotal to maximizing the power of quantitative trait loci detection. Trait genotypic variation within a family is indicative of the family's informativeness for genetic studies. Accurate prediction of the most useful parental combinations within a species would help guide quantitative genetics studies. We tested the reliability of genotypic and phenotypic distance estimators between pairs of maize inbred lines to predict genotypic variation for quantitative traits within families derived from biparental crosses. We developed 25 families composed of ∼200 random recombinant inbred lines each from crosses between a common reference parent inbred, B73, and 25 diverse maize inbreds. Parents and families were evaluated for 19 quantitative traits across up to 11 environments. Genetic distances (GDs) among parents were estimated with 44 simple sequence repeat and 2303 single-nucleotide polymorphism markers. GDs among parents had no predictive value for progeny variation, which is most likely due to the choice of neutral markers. In contrast, we observed for about half of the traits measured a positive correlation between phenotypic parental distances and within-family genetic variance estimates. Consequently, the choice of promising segregating populations can be based on selecting phenotypically diverse parents. These results are congruent with models of genetic architecture that posit numerous genes affecting quantitative traits, each segregating for allelic series, with dispersal of allelic effects across diverse genetic material. This architecture, common to many quantitative traits in maize, limits the predictive value of parental genotypic or phenotypic values on progeny variance.}, number={5}, journal={HEREDITY}, author={Hung, H-Y and Browne, C. and Guill, K. and Coles, N. and Eller, M. and Garcia, A. and Lepak, N. and Melia-Hancock, S. and Oropeza-Rosas, M. and Salvo, S. and et al.}, year={2012}, month={May}, pages={490–499} }
 @inbook{holland_nelson_2010, title={Dedication: Major M. Goodman: Maize Geneticist and Breeder}, volume={33}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84948148719&partnerID=MN8TOARS}, DOI={10.1002/9780470535486.ch1}, abstractNote={This chapter contains sections titled: Biographical Sketch Scientific Achievements Service to Humankind Mentor and Colleague Publications of Major Goodman Literature Cited}, booktitle={Plant Breeding Reviews}, author={Holland, J.B. and Nelson, P.T.}, year={2010}, pages={1–29} }
 @article{glover_reganold_bell_borevitz_brummer_buckler_cox_cox_crews_culman_et al._2010, title={Increased Food and Ecosystem Security via Perennial Grains}, volume={328}, ISSN={["1095-9203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77954078282&partnerID=MN8TOARS}, DOI={10.1126/science.1188761}, abstractNote={Perennial grains hold promise, especially for marginal landscapes or with limited resources where annual versions struggle.}, number={5986}, journal={SCIENCE}, author={Glover, J. D. and Reganold, J. P. and Bell, L. W. and Borevitz, J. and Brummer, E. C. and Buckler, E. S. and Cox, C. M. and Cox, T. S. and Crews, T. E. and Culman, S. W. and et al.}, year={2010}, month={Jun}, pages={1638–1639} }
 @article{glover_reganold_bell_borevitz_brummer_buckler_cox_cox_crews_culman_et al._2010, title={Response}, volume={330}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77957375418&partnerID=MN8TOARS}, number={6000}, journal={Science}, author={Glover, J.D. and Reganold, J.P. and Bell, L.W. and Borevitz, J. and Brummer, E.C. and Buckler, E.S. and Cox, C.M. and Cox, T.S. and Crews, T.E. and Culman, S.W. and et al.}, year={2010}, pages={33–34} }
 @article{eller_payne_holland_2010, title={Selection for Reduced Fusarium Ear Rot and Fumonisin Content in Advanced Backcross Maize Lines and Their Topeross Hybrids}, volume={50}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-78650082599&partnerID=MN8TOARS}, DOI={10.2135/cropsci2009.11.0683}, abstractNote={Backcross breeding is an important method to improve elite cultivars for traits controlled by a small number of loci but has been used less frequently to improve quantitatively controlled traits. Resistances to Fusarium ear rot [caused by Fusarium verticillioides (Sacc.) Nirenberg (teleomorph Gibberella moniliformis Wineland)] and contamination by the associated mycotoxin fumonisin in maize (Zea mays L.) are quantitatively inherited. We backcrossed the more resistant but unadapted inbred GE440 for four generations to the susceptible but agronomically elite commercial inbred FR1064. A selected set of 19 BC4F1:3 lines had greater resistance to ear rot and fumonisin content than their recurrent parent FR1064. Topcrosses of the selected lines had greater resistance to Fusarium ear rot and similar grain yield compared to the topcross of the recurrent parent FR1064. We also genotyped selected lines at DNA markers linked to ear rot and fumonisin resistance quantitative trait loci (QTL) identified in the BC1 generation of this cross to determine which QTL demonstrated allele frequency shifts due to selection. Markers linked to QTL on chromosomes 1 and 4 inherited the GE440 allele significantly more often than expected by random chance.}, number={6}, journal={CROP SCIENCE}, author={Eller, Magen S. and Payne, Gary A. and Holland, James B.}, year={2010}, pages={2249–2260} }
 @article{yan_holland_2010, title={A heritability-adjusted GGE biplot for test environment evaluation}, volume={171}, ISSN={["0014-2336"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-76149125761&partnerID=MN8TOARS}, DOI={10.1007/s10681-009-0030-5}, abstractNote={Test environment evaluation has become an increasingly important issue in plant breeding. In the context of indirect selection, a test environment can be characterized by two parameters: the heritability in the test environment and its genetic correlation with the target environment. In the context of GGE biplot analysis, a test environment is similarly characterized by two parameters: its discrimination power and its similarity with other environments. This paper investigates the relationships between GGE biplots based on different data scaling methods and the theory of indirect selection, and introduces a heritability-adjusted (HA) GGE biplot. We demonstrate that the vector length of an environment in the HA-GGE biplot approximates the square root heritability ( $$ \sqrt H $$ ) within the environment and that the cosine of the angle between the vectors of two environments approximates the genetic correlation (r) between them. Moreover, projections of vectors of test environments onto that of a target environment approximate values of $$ r\sqrt H $$ , which are proportional to the predicted genetic gain expected in the target environment from indirect selection in the test environments at a constant selection intensity. Thus, the HA-GGE biplot graphically displays the relative utility of environments in terms of selection response. Therefore, the HA-GGE biplot is the preferred GGE biplot for test environment evaluation. It is also the appropriate GGE biplot for genotype evaluation because it weights information from the different environments proportional to their within-environment square root heritability. Approximation of the HA-GGE biplot by other types of GGE biplots was discussed.}, number={3}, journal={EUPHYTICA}, author={Yan, Weikai and Holland, James B.}, year={2010}, month={Feb}, pages={355–369} }
 @article{gonzalo_holland_vyn_mcintyre_2010, title={Direct mapping of density response in a population of B73 x Mo17 recombinant inbred lines of maize (Zea Mays L.)}, volume={104}, ISSN={["1365-2540"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77952673698&partnerID=MN8TOARS}, DOI={10.1038/hdy.2009.140}, abstractNote={Maize yield per unit area has dramatically increased over time as have plant population densities, but the genetic basis for plant response to density is unknown as is its stability over environments. To elucidate the genetic basis of plant response to density in maize, we mapped QTL for plant density-related traits in a population of 186 recombinant inbred lines (RILs) derived from the cross of inbred lines B73 and Mo17. All RILs were evaluated for growth, development, and yield traits at moderate (50 000 plants per hectare) and high (100 000 plants per hectare) plant densities. The results show that genetic control of the traits evaluated is multigenic in their response to density. Five of the seven loci significant for final height showed statistical evidence for epistatic interactions. Other traits such as days to anthesis, anthesis-to-silking interval, barrenness, ears per plant, and yield per plant all showed statistical evidence for an epistatic interaction. Locus by density interactions are of critical importance for anthesis-to-silking interval, barrenness, and ears per plant. A second independent experiment to examine the stability of QTL for barrenness in a new environment clearly showed that the multilocus QTL were stable across environments in their differential response to density. In this verification experiment, the four-locus QTL was used to choose lines with the four unfavorable alleles and compare them with the lines with four favorable alleles and the effect was confirmed.}, number={6}, journal={HEREDITY}, author={Gonzalo, M. and Holland, J. B. and Vyn, T. J. and McIntyre, L. M.}, year={2010}, month={Jun}, pages={583–599} }
 @article{coles_mcmullen_balint-kurti_pratt_holland_2010, title={Genetic Control of Photoperiod Sensitivity in Maize Revealed by Joint Multiple Population Analysis}, volume={184}, ISSN={["1943-2631"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77950619493&partnerID=MN8TOARS}, DOI={10.1534/genetics.109.110304}, abstractNote={AbstractVariation in maize for response to photoperiod is related to geographical adaptation in the species. Maize possesses homologs of many genes identified as regulators of flowering time in other species, but their relation to the natural variation for photoperiod response in maize is unknown. Candidate gene sequences were mapped in four populations created by crossing two temperate inbred lines to two photoperiod-sensitive tropical inbreds. Whole-genome scans were conducted by high-density genotyping of the populations, which were phenotyped over 3 years in both short- and long-day environments. Joint multiple population analysis identified genomic regions controlling photoperiod responses in flowering time, plant height, and total leaf number. Four key genome regions controlling photoperiod response across populations were identified, referred to as ZmPR1–4. Functional allelic differences within these regions among phenotypically similar founders suggest distinct evolutionary trajectories for photoperiod adaptation in maize. These regions encompass candidate genes CCA/LHY, CONZ1, CRY2, ELF4, GHD7, VGT1, HY1/SE5, TOC1/PRR7/PPD-1, PIF3, ZCN8, and ZCN19.}, number={3}, journal={GENETICS}, publisher={Genetics Society of America}, author={Coles, Nathan D. and McMullen, Michael D. and Balint-Kurti, Peter J. and Pratt, Richard C. and Holland, James B.}, year={2010}, month={Mar}, pages={799–U301} }
 @article{mcmullen_kresovich_villeda_bradbury_li_sun_flint-garcia_thornsberry_acharya_bottoms_et al._2009, title={Genetic properties of the maize nested association mapping population}, volume={325}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-68449094455&partnerID=MN8TOARS}, DOI={10.1126/science.1174320}, abstractNote={Codifying Maize Modifications
          
            Maize, one of our most important crop species, has been the target of genetic investigation and experimentation for more than 100 years. Crossing two inbred lines tends to result in “better” offspring, in a process known as heterosis. Attempts to map the genetic loci that control traits important for farming have been made, but few have been successful (see the Perspective by
            
              Mackay
            
            ).
            
              Buckler
              et al.
            
            (p.
            714
            ) and
            
              McMullen
              et al.
            
            (p.
            737
            ) produced a genomic map of maize that relates recombination to genome structure. Even tremendous adaptations in very diverse species were produced by numerous, small additive steps. Differences in flowering time in maize among inbred lines were not caused by a few genes with large effects, but by the cumulative effects of numerous quantitative trait loci—each of which has only a small impact on the trait.
          }, number={5941}, journal={Science}, author={McMullen, M.D. and Kresovich, S. and Villeda, H.S. and Bradbury, P. and Li, H. and Sun, Q. and Flint-Garcia, S. and Thornsberry, J. and Acharya, C. and Bottoms, C. and et al.}, year={2009}, pages={737–740} }
 @inbook{holland_cardinal_2009, title={Harnessing quantitative genetics and genomics for understanding and improving complex traits in crops}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84970959798&partnerID=MN8TOARS}, DOI={10.1142/9789814280013_0008}, abstractNote={Drought Frontiers in Rice, pp. 123-136 (2009) No AccessHarnessing quantitative genetics and genomics for understanding and improving complex traits in cropsJames B. Holland and Andrea J. CardinalJames B. HollandUSDA-ARS Plant Science Research Unit, Raleigh, NC 27695, USADepartment of Crop Science, North Carolina State University, Raleigh, NC 27695, USA and Andrea J. CardinalDepartment of Crop Science, North Carolina State University, Raleigh, NC 27695, USAhttps://doi.org/10.1142/9789814280013_0008Cited by:0 PreviousNext AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack CitationsRecommend to Library ShareShare onFacebookTwitterLinked InRedditEmail Abstract: Classical quantitative genetics aids crop improvement by providing the means to estimate heritability, genetic correlations, and predicted responses to various selection schemes. Genomics has the potential to aid quantitative genetics and applied crop improvement programs via large-scale high-throughput DNA sequencing and fingerprinting, gene expression analyses, and reverse genetics methods. To date, these techniques have mainly been useful in the identification of genes with discrete or at least moderate effects on high-value traits. A practical result of this research is the development of allele-specific markers that tend to be useful across many breeding populations. For example, knowledge of the fatty acid biosynthesis pathway in plants and the sequencing of genes in that pathway is being exploited to produce DNA markers to aid selection for specific modified fatty acid traits in soybean. The application of large-scale gene mapping techniques to the improvement of highly quantitative traits (controlled by many genes of small effects) is not yet proven, however, and, even if useful, may not be highly cost-effective unless large-scale genomics infrastructure is already in place to aid breeding programs. An example of the application of genomics to large-scale genetic diversity studies is the large-scale maize QTL mapping study under way based on the development of 26 related RIL populations that capture a large portion of the genetic variation available worldwide among public lines. For genomics to be useful for the improvement of drought resistance in rice, the identification of component traits with relatively simpler architecture and/or a very large-scale investment in genomics-assisted breeding may be required. Some of the research described here was supported by grants from the U.S. National Science Foundation (DBI-0321467) to JBH and from U.S. Department of Agriculture National Research Initiative (Competitive Grants Program award numbers 2001-35301-10601 to JBH and 2003-00691 to AJC). FiguresReferencesRelatedDetails Drought Frontiers in RiceMetrics History PDF download}, booktitle={Drought Frontiers in Rice: Crop Improvement for Increased Rainfed Production}, author={Holland, J.B. and Cardinal, A.J.}, year={2009}, pages={123–136} }
 @article{zwonitzer_coles_krakowsky_arellano_holland_mcmullen_pratt_balint-kurti_2010, title={Mapping resistance quantitative trait loci for three foliar diseases in a maize recombinant inbred line population - Evidence for multiple disease resistance?}, volume={100}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-75649139868&partnerID=MN8TOARS}, DOI={10.1094/PHYTO-100-1-0072}, abstractNote={ Southern leaf blight (SLB), gray leaf spot (GLS), and northern leaf blight (NLB) are all important foliar diseases impacting maize production. The objectives of this study were to identify quantitative trait loci (QTL) for resistance to these diseases in a maize recombinant inbred line (RIL) population derived from a cross between maize lines Ki14 and B73, and to evaluate the evidence for the presence genes or loci conferring multiple disease resistance (MDR). Each disease was scored in multiple separate trials. Highly significant correlations between the resistances and the three diseases were found. The highest correlation was identified between SLB and GLS resistance (r = 0.62). Correlations between resistance to each of the diseases and time to flowering were also highly significant. Nine, eight, and six QTL were identified for SLB, GLS, and NLB resistance, respectively. QTL for all three diseases colocalized in bin 1.06, while QTL colocalizing for two of the three diseases were identified in bins 1.08 to 1.09, 2.02/2.03, 3.04/3.05, 8.05, and 10.05. QTL for time to flowering were also identified at four of these six loci (bins 1.06, 3.04/3.05, 8.05, and 10.05). No disease resistance QTL was identified at the largest-effect QTL for flowering time in bin 10.03. }, number={1}, journal={Phytopathology}, publisher={Scientific Societies}, author={Zwonitzer, John C. and Coles, Nathan D. and Krakowsky, Matthew D. and Arellano, Consuelo and Holland, James B. and McMullen, Michael D. and Pratt, Richard C. and Balint-Kurti, Peter J.}, year={2010}, pages={72–79} }
 @article{wooten_livingston_lyerly_holland_jellen_marshall_murphy_2009, title={Quantitative Trait Loci and Epistasis for Oat Winter-Hardiness Component Traits}, volume={49}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-70749094348&partnerID=MN8TOARS}, DOI={10.2135/cropsci2008.10.0612}, abstractNote={ABSTRACTWinter hardiness is a complex trait and poor winter hardiness limits commercial production of winter oat (Avena spp.). The objective of this study was to identify quantitative trait loci (QTL) for five winter‐hardiness component traits in a recombinant inbred line population derived from a cross between the winter‐tender cultivar Fulghum and the winter‐hardy cultivar Norline. Crown freezing tolerance, vernalization response, and photoperiod response were evaluated in controlled environment studies. Heading date and plant height were evaluated over two seasons in Kinston, NC, and winter field survival was evaluated in five environments over two seasons in the mountains of North Carolina and Virginia. A partial genetic linkage map of regions believed to affect winter hardiness was developed using restriction fragment length polymorphism and simple sequence repeat markers. Most QTL were located on linkage groups FN3, FN22, and FN24. Quantitative trait loci were identified for all traits except photoperiod response, and epistatic interactions were identified for winter field survival, crown freezing tolerance, vernalization response, and plant height. Major QTL for winter field survival (R 2 = 35%) and crown freezing tolerance (R 2 = 53%) were identified on linkage group FN3, which was associated with an intergenomic reciprocal translocation between chromosomes 7C and 17.}, number={6}, journal={CROP SCIENCE}, author={Wooten, D. R. and Livingston, D. P., III and Lyerly, H. J. and Holland, J. B. and Jellen, E. N. and Marshall, D. S. and Murphy, J. P.}, year={2009}, pages={1989–1998} }
 @article{buckler_holland_bradbury_acharya_brown_browne_ersoz_flint-garcia_garcia_glaubitz_et al._2009, title={The Genetic Architecture of Maize Flowering Time}, volume={325}, ISSN={["1095-9203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-68449083317&partnerID=MN8TOARS}, DOI={10.1126/science.1174276}, abstractNote={Codifying Maize Modifications
          
            Maize, one of our most important crop species, has been the target of genetic investigation and experimentation for more than 100 years. Crossing two inbred lines tends to result in “better” offspring, in a process known as heterosis. Attempts to map the genetic loci that control traits important for farming have been made, but few have been successful (see the Perspective by
            
              Mackay
            
            ).
            
              Buckler
              et al.
            
            (p.
            714
            ) and
            
              McMullen
              et al.
            
            (p.
            737
            ) produced a genomic map of maize that relates recombination to genome structure. Even tremendous adaptations in very diverse species were produced by numerous, small additive steps. Differences in flowering time in maize among inbred lines were not caused by a few genes with large effects, but by the cumulative effects of numerous quantitative trait loci—each of which has only a small impact on the trait.
          }, number={5941}, journal={SCIENCE}, author={Buckler, Edward S. and Holland, James B. and Bradbury, Peter J. and Acharya, Charlotte B. and Brown, Patrick J. and Browne, Chris and Ersoz, Elhan and Flint-Garcia, Sherry and Garcia, Arturo and Glaubitz, Jeffrey C. and et al.}, year={2009}, month={Aug}, pages={714–718} }
 @article{van esbroeck_corral_gonzalez_holland_2008, title={A Comparison of leaf appearance rates among teosinte, maize landraces and modern maize}, volume={53}, number={2}, journal={Maydica}, author={Van Esbroeck, G. A. and Corral, J. A. R. and Gonzalez, J. J. S. and Holland, J. B.}, year={2008}, pages={117–123} }
 @article{van esbroeck_ruiz corral_sanchez gonzalez_holland_2008, title={A comparison of leaf appearance rates among teosinte, maize landraces and modern maize}, volume={53}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-57849127135&partnerID=MN8TOARS}, number={2}, journal={Maydica}, author={Van Esbroeck, G.A. and Ruiz Corral, J.A. and Sanchez Gonzalez, J.J. and Holland, J.B.}, year={2008}, pages={117–123} }
 @article{eller_holland_payne_2008, title={BREEDING FOR IMPROVED RESISTANCE TO FUMONISIN CONTAMINATION IN MAIZE}, volume={27}, ISSN={["1556-9551"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77956939673&partnerID=MN8TOARS}, DOI={10.1080/15569540802450326}, abstractNote={Maize grain infected by Fusarium verticillioides may contain the mycotoxin fumonisin, which is associated with livestock and human diseases. To reduce levels of fumonisin in grain, efforts are under way to identify sources of maize with increased resistance to fungal infection and fumonisin contamination. Field and laboratory techniques have been developed to measure both Fusarium ear rot and fumonisin contamination. Application of these techniques has led to the identification of resistant maize lines and facilitated genetic analysis of resistance to ear rot and fumonisin accumulation. Maize genetics and breeding studies are guiding strategies to improve resistance to fumonisin accumulation.}, number={3-4}, journal={TOXIN REVIEWS}, author={Eller, Magen S. and Holland, James B. and Payne, Gary A.}, year={2008}, pages={371–389} }
 @article{ruiz corral_puga_sanchez gonzalez_parra_gonzalez eguiarte_holland_medina garcia_2008, title={Climatic adaptation and ecological descriptors of 42 Mexican maize races}, volume={48}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-49149121288&partnerID=MN8TOARS}, DOI={10.2135/cropsci2007.09.0518}, abstractNote={To better understand the range of adaptation of maize (Zea mays L.) landraces, climatic adaptation intervals of 42 Mexican maize races were determined. A database of 4161 maize accessions was used to characterize altitudinal and climatic conditions where the 42 maize races grow, yielding ecological descriptors for each race. Using the geographical coordinates of the collection sites of each accession, their climatic conditions were characterized using the geographic information system IDRISI and a national environmental information system. Analyses of variance and cluster analyses of the racial ecological descriptors were performed to determine possible environmental groupings of the races. We found a very high level of variation among and within Mexican maize races for climate adaptation and ecological descriptors. The general overall climatic ranges for maize were 0 to 2900 m of altitude, 11.3 to 26.6°C annual mean temperature, 12.0 to 29.1°C growing season mean temperature, 426 to 4245 mm annual rainfall, 400 to 3555 mm growing season rainfall, and 12.46 to 12.98 h mean growing season daylength. These climatic ranges of maize surpass those from its closest relative, teosinte (Z. mays ssp. parviglumis Iltis and Doebley), indicating that maize has evolved adaptability beyond the environmental range in which ancestral maize was first domesticated.}, number={4}, journal={CROP SCIENCE}, author={Ruiz Corral, Jose Ariel and Puga, Noe Duran and Sanchez Gonzalez, Jose de Jesus and Parra, Jose Ron and Gonzalez Eguiarte, Diego Raymundo and Holland, J. B. and Medina Garcia, Guillermo}, year={2008}, pages={1502–1512} }
 @article{yu_holland_mcmullen_buckler_2008, title={Genetic design and statistical power of nested association mapping in maize}, volume={178}, ISSN={["1943-2631"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-40849089396&partnerID=MN8TOARS}, DOI={10.1534/genetics.107.074245}, abstractNote={AbstractWe investigated the genetic and statistical properties of the nested association mapping (NAM) design currently being implemented in maize (26 diverse founders and 5000 distinct immortal genotypes) to dissect the genetic basis of complex quantitative traits. The NAM design simultaneously exploits the advantages of both linkage analysis and association mapping. We demonstrated the power of NAM for high-power cost-effective genome scans through computer simulations based on empirical marker data and simulated traits with different complexities. With common-parent-specific (CPS) markers genotyped for the founders and the progenies, the inheritance of chromosome segments nested within two adjacent CPS markers was inferred through linkage. Genotyping the founders with additional high-density markers enabled the projection of genetic information, capturing linkage disequilibrium information, from founders to progenies. With 5000 genotypes, 30–79% of the simulated quantitative trait loci (QTL) were precisely identified. By integrating genetic design, natural diversity, and genomics technologies, this new complex trait dissection strategy should greatly facilitate endeavors to link molecular variation with phenotypic variation for various complex traits.}, number={1}, journal={GENETICS}, author={Yu, Jianming and Holland, James B. and McMullen, Michael D. and Buckler, Edward S.}, year={2008}, month={Jan}, pages={539–551} }
 @article{eller_robertson-hoyt_payne_holland_2008, title={Grain yield and fusarium ear rot of maize hybrids developed from lines with varying levels of resistance}, volume={53}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77956931980&partnerID=MN8TOARS}, number={1-4}, journal={Maydica}, author={Eller, M.S. and Robertson-Hoyt, L.A. and Payne, G.A. and Holland, J.B.}, year={2008}, pages={231–237} }
 @article{nelson_coles_holland_bubeck_smith_goodman_2008, title={Molecular characterization of maize inbreds with expired US plant variety protection}, volume={48}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-54949106977&partnerID=MN8TOARS}, DOI={10.2135/cropsci2008.02.0092}, abstractNote={Maize inbred lines with expired Plant Variety Protection Act (PVPA) certificates are publicly available and potentially represent a new germplasm resource for many public and private breeding programs. However, accurate pedigree and genetic background information for ex‐PVPA maize inbreds is necessary if they are to be effectively utilized in breeding efforts. We have used single nucleotide polymorphism (SNP) markers to evaluate the relationships and population structure among 92 ex‐PVPA inbred lines in relation to 17 well‐known public inbreds. Based on unweighted pair group method with arithmetic mean clustering, principal components analysis, and model‐based clustering, we identified six primary genetic clusters represented by the prominent inbred lines B73, Mo17, PH207, A632, Oh43, and B37. We also determined the genetic background of ex‐PVPA inbreds with conflicting, ambiguous, or undisclosed pedigrees. We assessed genetic diversity across subsets of ex‐PVPA lines and concluded that the ex‐PVPA lines are no more diverse than the public set evaluated here. Additionally, all alleles present in the ex‐PVPA inbreds, for the 614 SNPs included in this study, are also found in public temperate maize germplasm.}, number={5}, journal={CROP SCIENCE}, author={Nelson, Paul T. and Coles, Nathan D. and Holland, James B. and Bubeck, David M. and Smith, Stephen and Goodman, Major M.}, year={2008}, pages={1673–1685} }
 @article{wooten_livingston_holland_marshall_murphy_2008, title={Quantitative trait loci and epistasis for crown freezing tolerance in the 'Kanota' x 'Ogle' hexaploid oat mapping population}, volume={48}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-35348818142&partnerID=MN8TOARS}, DOI={10.2135/cropsci2006.12.0793}, abstractNote={Crown freezing tolerance is the most important factor conferring oat (Avena spp.) winter hardiness. The objective of this study was to identify quantitative trait loci (QTL) for crown freezing tolerance in the ‘Kanota’ × ‘Ogle’ recombinant inbred line (RIL) mapping population and to examine their relationship with other winter hardiness traits. One hundred thirty‐five RILs were evaluated for crown freezing tolerance in a controlled environment. Previously published molecular marker and linkage map information was used for QTL detection. Seven QTL and four complementary epistatic interactions were identified that accounted for 56% of the phenotypic variation. Ogle contributed alleles for increased crown freezing tolerance at three loci, while Kanota contributed alleles for increased crown freezing tolerance at four loci. All loci where Kanota alleles increased crown freezing tolerance showed complementary epistasis for decreased crown freezing tolerance with the QTL near UMN13. Two of the major QTL identified were in the linkage groups (LG) associated with a reciprocal translocation between chromosomes 7C and 17, which was previously associated with spring growth habit in oat. The results confirm the importance of the chromosomes involved in the reciprocal 7C‐17 translocation in controlling winter hardiness component traits.}, number={1}, journal={CROP SCIENCE}, author={Wooten, David R. and Livingston, David P., III and Holland, James B. and Marshall, David S. and Murphy, J. Paul}, year={2008}, pages={149–157} }
 @misc{holland_2007, title={Genetic architecture of complex traits in plants}, volume={10}, ISSN={["1369-5266"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33847297054&partnerID=MN8TOARS}, DOI={10.1016/j.pbi.2007.01.003}, abstractNote={Genetic architecture refers to the numbers and genome locations of genes that affect a trait, the magnitude of their effects, and the relative contributions of additive, dominant, and epistatic gene effects. Quantitative trait locus (QTL) mapping techniques are commonly used to investigate genetic architectures, but the scope of inferences drawn from QTL studies are often restricted by the limitations of the experimental designs. Recent advances in experimental and statistical procedures, including the simultaneous analysis of QTL that segregate in diverse germplasm, should improve genetic architecture studies. High-resolution QTL mapping methods are being developed that may define the specific DNA sequence variants underlying QTL. Studies of genetic architecture, combined with improved knowledge of the structure of plant populations, will impact our understanding of plant evolution and the design of crop improvement strategies.}, number={2}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Holland, James B.}, year={2007}, month={Apr}, pages={156–161} }
 @article{krakowsky_lee_holland_2007, title={Genotypic correlation and multivariate QTL analyses for cell wall components and resistance to stalk tunneling by the European corn borer in maize}, volume={47}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-34247275826&partnerID=MN8TOARS}, DOI={10.2135/cropsci2006.05.0283}, abstractNote={ABSTRACTCorrelations between concentrations of cell wall components (CWCs) in the leaf sheath and stalk and resistance to stalk tunneling by the European corn borer (ECB) [Ostrinia nubilalis (Hübner)] have been reported in some maize (Zea mays L.) populations. Evaluations of resistance to ECB stalk tunneling (ECB‐ST) and concentrations of neutral detergent fiber (NDF), acid detergent fiber (ADF), and acid detergent lignin (ADL) have been performed on recombinant inbred lines (RILs) developed from the cross of maize inbred lines B73 (susceptible to ECB‐ST, low to moderate CWC concentrations) and DE811 (resistant to ECB‐ST, high CWC concentrations). The objective of this study was to estimate genotypic correlations between ECB‐ST and CWC concentrations and compare locations and effects of quantitative trait loci (QTL) for those traits. Genotypic correlations between ECB‐ST and CWCs were not significant, but clustering of QTL for ECB‐ST and CWCs was observed. Negative genotypic correlations between ECB‐ST and CWC concentrations were observed at some loci, and resistance to ECB‐ST may be associated with a subset of the QTL observed for CWCs and ADF in particular. Resistance to ECB‐ST may also be associated with starch concentration in the stalk, which could explain the detection of resistance alleles contributed by B73. Examination of temporal differences in CWC and starch concentrations, and marker‐assisted transfer of select alleles, could provide more information on mechanisms of resistance to ECB‐ST.}, number={2}, journal={CROP SCIENCE}, author={Krakowsky, M. D. and Lee, M. and Holland, J. B.}, year={2007}, pages={485–490} }
 @article{burke_holland_burton_york_wilcut_2007, title={Johnsongrass (Sorghum halepense) pollen expresses ACCase target-site resistance}, volume={21}, ISSN={["1550-2740"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-36448953142&partnerID=MN8TOARS}, DOI={10.1614/WT-06-061.1}, abstractNote={Three studies were conducted to develop pollen tests for the screening of acetyl coenzyme-A carboxylase (ACCase) target-site resistance in a biotype of johnsongrass. The assays were based on germination of johnsongrass pollen in media supplemented with clethodim. Two different methods were used to evaluate pollen germination—a visual assessment and a spectrophotometric assay. The response of pollen to the germination media was linear for 16 h. At 6 h after treatment, absorbance at 500 nm was nearly 0.5; consequently, 6 h was chosen to conduct the pollen assays using the spectrophotometer. Both assessment methods differentiated the susceptible (S) and resistant (R) biotypes. Pollen from the susceptible biotype of johnsongrass was strongly inhibited by increasing concentrations of clethodim, with a GR50 of 25.8 ± 0.6 (SE) µM and GR50 of 16.4 ± 1.7 (SE) µM clethodim by visual assessment and spectrophotometric assessment, respectively. Minimum R/S values were > 3.9 by visual assessment and > 6.1 by spectrophotometric assessment. ACCase target-site resistance is expressed in johnsongrass pollen. Nomenclature: johnsongrass, Sorghum halepense (L.) Pers. SORHA.}, number={2}, journal={WEED TECHNOLOGY}, author={Burke, Ian C. and Holland, James B. and Burton, James D. and York, Alan C. and Wilcut, John W.}, year={2007}, pages={384–388} }
 @article{gonzalo_vyn_holland_mcintyre_2007, title={Mapping reciprocal effects and interactions with plant density stress in Zea mays L.}, volume={99}, ISSN={["1365-2540"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-34347340535&partnerID=MN8TOARS}, DOI={10.1038/sj.hdy.6800955}, abstractNote={Reciprocal effects are due to genetic effects of the parents (i.e. maternal and paternal effects), cytoplasmic effects and parent-of-origin effects. However, in Zea mays L. the extent to which reciprocal effects exist, or can be attributed to specific underlying components, remains an area of interest and study. Reciprocal effects have been reported by several investigators for various agronomic characters in different types of maize materials for grain and silage usage. Maize geneticists and breeders have recognized reciprocal effects as one source of genetic variability, but the lack of consistency in the observation of these effects, particularly due to stress conditions, has prevented a systematic exploitation of these effects in practical breeding programs. There is mounting molecular evidence for underlying mechanisms in maize, which could be responsible for both the existence, and the instability of reciprocal effects. In this study, we developed population of reciprocal backcrosses based on an initial set of recombinant inbred lines. This population was used for dissecting reciprocal effects into the underlying components (maternal, cytoplasmic and parent-of-origin) effects. We also developed statistical framework to identify and map contributions of specific nuclear chromosomal regions to reciprocal effects. We showed that differences in maternal parents, endosperm DNA and maternally transmitted factors collectively influence reciprocal effects early during the season, and that their influence diluted at later stages. We also found evidence that parent-of-origin effects in the sporophyte DNA existed at all stages and played an important role in establishing differences between reciprocal backcrosses at later developmental stages.}, number={1}, journal={HEREDITY}, author={Gonzalo, M. and Vyn, T. J. and Holland, J. B. and McIntyre, L. M.}, year={2007}, month={Jul}, pages={14–30} }
 @article{balint-kurti_zwonitzer_wisser_carson_oropeza-rosas_holland_szalma_2007, title={Precise mapping of quantitative trait loci for resistance to southern leaf blight, caused by Cochliobolus heterostrophus race O, and flowering time using advanced intercross maize lines}, volume={176}, ISSN={["1943-2631"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-34548569322&partnerID=MN8TOARS}, DOI={10.1534/genetics.106.067892}, abstractNote={Abstract
               The intermated B73 × Mo17 (IBM) population, an advanced intercross recombinant inbred line population derived from a cross between the maize lines B73 (susceptible) and Mo17 (resistant), was evaluated in four environments for resistance to southern leaf blight (SLB) disease caused by Cochliobolus heterostrophus race O. Two environments were artificially inoculated, while two were not inoculated and consequently had substantially lower disease pressure. Four common SLB resistance quantitative trait loci (QTL) were identified in all environments, two in bin 3.04 and one each in bins 1.10 and 8.02/3. There was no significant correlation between disease resistance and days to anthesis. A direct comparison was made between SLB QTL detected in two populations, independently derived from the same parental cross: the IBM advanced intercross population and a conventional recombinant inbred line population. Several QTL for SLB resistance were detected in both populations, with the IBM providing between 5 and, in one case, 50 times greater mapping resolution.}, number={1}, journal={GENETICS}, author={Balint-Kurti, P. J. and Zwonitzer, J. C. and Wisser, R. J. and Carson, M. L. and Oropeza-Rosas, M. A. and Holland, J. B. and Szalma, S. J.}, year={2007}, month={May}, pages={645–657} }
 @article{szalma_hostert_ledeaux_stuber_holland_2007, title={QTL mapping with near-isogenic lines in maize}, volume={114}, ISSN={["1432-2242"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-34247847700&partnerID=MN8TOARS}, DOI={10.1007/s00122-007-0512-6}, abstractNote={A set of 89 near-isogenic lines (NILs) of maize was created using marker-assisted selection. Nineteen genomic regions, identified by restriction fragment length polymorphism loci and chosen to represent portions of all ten maize chromosomes, were introgressed by backcrossing three generations from donor line Tx303 into the B73 genetic background. NILs were genotyped at an additional 128 simple sequence repeat loci to estimate the size of introgressions and the amount of background introgression. Tx303 introgressions ranged in size from 10 to 150 cM, with an average of 60 cM. Across all NILs, 89% of the Tx303 genome is represented in targeted and background introgressions. The average proportion of background introgression was 2.5% (range 0-15%), significantly lower than the expected value of 9.4% for third backcross generation lines developed without marker-assisted selection. The NILs were grown in replicated field evaluations in two years to map QTLs for flowering time traits. A parallel experiment of testcrosses of each NIL to the unrelated inbred, Mo17, was conducted in the same environments to map QTLs in NIL testcross hybrids. QTLs affecting days to anthesis, days to silking, and anthesis-silk interval were detected in both inbreds and hybrids in both environments. The testing environments differed dramatically for drought stress, and different sets of QTLs were detected across environments. Furthermore, QTLs detected in inbreds were typically different from QTLs detected in hybrids, demonstrating the genetic complexity of flowering time. NILs can serve as a valuable genetic mapping resource for maize breeders and geneticists.}, number={7}, journal={THEORETICAL AND APPLIED GENETICS}, author={Szalma, S. J. and Hostert, B. M. and LeDeaux, J. R. and Stuber, C. W. and Holland, J. B.}, year={2007}, month={May}, pages={1211–1228} }
 @article{robertson-hoyt_betran_payne_white_isakeit_maragos_molnar_holland_2007, title={Relationships among resistances to Fusarium and Aspergillus ear rots and contamination by fumonisin and aflatoxin in maize}, volume={97}, ISSN={["1943-7684"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33847337945&partnerID=MN8TOARS}, DOI={10.1094/PHYTO-97-3-0311}, abstractNote={ Fusarium verticillioides, F. proliferatum, and Aspergillus flavus cause ear rots of maize and contaminate the grain with mycotoxins (fumonisin or aflatoxin). The objective of this study was to investigate the relationships between resistance to Fusarium and Aspergillus ear rots and fumonisin and aflatoxin contamination. Based on a previous study of 143 recombinant inbred lines from the cross NC300 × B104, 24 lines with the highest and 24 lines with the lowest mean fumonisin concentration were selected for further evaluation. Paired plots of each line were inoculated with F. verticillioides and F. proliferatum or with A. flavus in replicated trials in 2004 and 2005 in Clayton, NC, and College Station, TX. The low-fumonisin group had significantly lower levels of fumonisin, aflatoxin, and Fusarium and Aspergillus ear rots. Across year-location environments, all four traits were significantly correlated; the genotypic correlation (rG) ranged from rG = 0.88 (aflatoxin and Aspergillus ear rot) to rG = 0.99 (Fusarium and Aspergillus ear rots). Quantitative trait loci (QTLs) were identified and their effects estimated. Two QTLs affected both toxin concentrations, one QTL affected both ear rots, and one QTL affected Aspergillus and Fusarium rots and fumonisin. These results suggest that at least some of the genes involved in resistance to ear rots and mycotoxin contamination are identical or genetically linked. }, number={3}, journal={PHYTOPATHOLOGY}, author={Robertson-Hoyt, Leilani A. and Betran, Javier and Payne, Gary A. and White, Don G. and Isakeit, Thomas and Maragos, Chris M. and Molnar, Terence L. and Holland, James B.}, year={2007}, month={Mar}, pages={311–317} }
 @article{robertson-hoyt_kleinschmidt_white_payne_maragos_holland_2007, title={Relationships of resistance to Fusarium ear rot and fumonisin contamination with agronomic performance of maize}, volume={47}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-35348855713&partnerID=MN8TOARS}, DOI={10.2135/cropsci2006.10.0676}, abstractNote={Resistance to Fusarium ear rot [caused by Fusarium verticillioides (Sacc.) Nirenberg (synonym F. moniliforme Sheldon) (teleomorph: Gibberella moniliformis) and F. proliferatum (Matsushima) Nirenberg (teleomorph: G. intermedia)] and fumonisin contamination is heritable and controlled by at least 11 gene regions in a maize (Zea mays L.) population created by backcrossing the highly resistant donor line, GE440, to the susceptible but commercially successful recurrent parent line, FR1064. The relationship between resistances to Fusarium ear rot and fumonisin contamination and agronomic performance has not been reported. Therefore, the objective of this study was to examine the relationship between disease resistance and agronomic utility in this population by measuring resistances to Fusarium ear rot and fumonisin contamination in BC1F1:2 lines, and yield and agronomic performance in topcrosses of these lines. Fumonisin contamination was not correlated with yield, but two fumonisin quantitative trait loci (QTL) mapped to similar positions as yield QTL. Fusarium ear rot had a small positive correlation with topcross yield (r = 0.29), but QTL for the two traits mapped to distinct genomic positions. Similar results for other traits indicate that QTL can contribute in opposite directions to the overall genetic correlations between traits and that some trait correlations arise in the absence of detectable QTL effects on both traits. In general, no strong relationships were observed between disease resistance traits and agronomic traits, thus selection for increased resistance should not unduly affect agronomic performance.}, number={5}, journal={CROP SCIENCE}, author={Robertson-Hoyt, Leilani A. and Kleinschmidt, Craig E. and White, Don G. and Payne, Gary A. and Maragos, Chris M. and Holland, James B.}, year={2007}, pages={1770–1778} }
 @article{robertson_kleinschmidt_white_payne_maragos_holland_2006, title={Erratum: Heritabilities and correlations of fusarium ear rot resistance and fumonisin contamination resistance in two maize populations (Crop Science 46, 1 (353-361))}, volume={46}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33646459781&partnerID=MN8TOARS}, DOI={10.2135/cropsci2005.0139er}, abstractNote={In volume 46, issue 1, p. 353–361, the estimates of heritability for fumonisin concentration and Fusarium ear rot in the NC3003 B104 recombinant inbred population were computed incorrectly. The corrected estimates of heritability on an entry mean basis are 0.88 (SE 5 0.03) for fumonisin concentration and 0.86 (SE 5 0.03) for ear rot. The corrected estimates of heritability on a plot basis are 0.58 (SE 5 0.06) for fumonisin concentration and 0.55 (SE 5 0.07) for ear rot. The corrected estimate of heritability on an individual plant basis for ear rot is 0.22 (SE 5 0.03). The corrected estimate of the relative efficiency of indirect selection is 0.85. All of the corrected parameter estimates are higher than the original estimates reported, and the changes do not affect our conclusions.}, number={3}, journal={Crop Science}, author={Robertson, L.A. and Kleinschmidt, C.E. and White, D.G. and Payne, G.A. and Maragos, C.M. and Holland, J.B.}, year={2006} }
 @article{holland_2006, title={Estimating genotypic correlations and their standard errors using multivariate restricted maximum likelihood estimation with SAS Proc MIXED}, volume={46}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33644988886&partnerID=MN8TOARS}, DOI={10.2135/cropsci2005.0191}, abstractNote={Plant breeders traditionally have estimated genotypic and phenotypic correlations between traits using the method of moments on the basis of a multivariate analysis of variance (MANOVA). Drawbacks of using the method of moments to estimate variance and covariance components include the possibility of obtaining estimates outside of parameter bounds, reduced estimation efficiency, and ignorance of the estimators' distributional properties when data are missing. An alternative approach that does not suffer these problems, but depends on the assumption of normally distributed random effects and large sample sizes, is restricted maximum likelihood (REML). This paper illustrates the use of Proc MIXED of the SAS system to implement REML estimation of genotypic and phenotypic correlations. Additionally, a method to obtain approximate parametric estimates of the sampling variances of the correlation estimates is presented. MANOVA and REML methods were compared with a real data set and with simulated data. The simulation study examined the effects of different correlation parameter values, genotypic and environmental sample sizes, and proportion of missing data on Type I and Type II error rates and on accuracy of confidence intervals. The two methods provided similar results when data were balanced or only 5% of data were missing. However, when 15 or 25% data were missing, the REML method generally performed better, resulting in higher power of detection of correlations and more accurate 95% confidence intervals. Samples of at least 75 genotypes and two environments are recommended to obtain accurate confidence intervals using the proposed method.}, number={2}, journal={CROP SCIENCE}, author={Holland, JB}, year={2006}, pages={642–654} }
 @article{tarter_holland_2006, title={Gains from selection during the development of semiexotic inbred lines from Latin American maize accessions}, volume={51}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33646828357&partnerID=MN8TOARS}, number={1}, journal={Maydica}, author={Tarter, J.A. and Holland, J.B.}, year={2006}, pages={15–23} }
 @article{robertson_kleinschmidt_white_payne_maragos_holland_2006, title={Heritabilities and correlations of fusarium ear rot resistance and fumonisin contamination resistance in two maize populations}, volume={46}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-32344440659&partnerID=MN8TOARS}, DOI={10.2135/cropsci2005.0139}, abstractNote={Fusarium verticillioides (Sacc.) Nirenberg (synonym F. moniliforme Sheldon) (teleomorph: Gibberella moniliformis) and F. proliferatum (Matsushima) Nirenberg (teleomorph: G. intermedia) are fungal pathogens of maize (Zea mays L.) that cause ear rot and contaminate grain with fumonisins, a family of mycotoxins that adversely affect animal and human health. The objective of this study was to estimate heritabilities of and genotypic and phenotypic correlations between fumonisin concentration, ear rot, and flowering time in two maize populations. In the (GE440 × FR1064) × FR1064 backcross population, the genotypic and phenotypic correlations between ear rot and fumonisin concentration were 0.96 and 0.40, respectively. Heritability estimated on an entry mean basis was 0.75 for fumonisin concentration and 0.47 for ear rot resistance. In the NC300 × B104 recombinant inbred line population, the genotypic and phenotypic correlations between ear rot and fumonisin concentration were 0.87 and 0.64, respectively. Heritability estimated on an entry mean basis was 0.86 for fumonisin concentration and 0.80 for ear rot resistance. Correlations between fumonisin concentration and silking date were not significant in either population, and correlations between ear rot resistance and silking date were small (less than 0.30) in both populations. Moderate to high heritabilities and strong genetic correlations between ear rot and fumonisin concentration suggest that selection for reduced ear rot should frequently identify lines with reduced fumonisin concentration. Ear rot can be screened visually and so is less costly and less time‐consuming to evaluate than laboratory assays for fumonisin concentration.}, number={1}, journal={CROP SCIENCE}, author={Robertson, LA and Kleinschmidt, CE and White, DG and Payne, GA and Maragos, CM and Holland, JB}, year={2006}, pages={353–361} }
 @article{balint-kurti_krakowsky_jines_robertson_molnar_goodman_holland_2006, title={Identification of quantitative trait loci for resistance to southern leaf blight and days to anthesis in a maize recombinant inbred line population}, volume={96}, ISSN={["1943-7684"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33749262148&partnerID=MN8TOARS}, DOI={10.1094/PHYTO-96-1067}, abstractNote={ A recombinant inbred line population derived from a cross between the maize lines NC300 (resistant) and B104 (susceptible) was evaluated for resistance to southern leaf blight (SLB) disease caused by Cochliobolus heterostrophus race O and for days to anthesis in four environments (Clayton, NC, and Tifton, GA, in both 2004 and 2005). Entry mean and average genetic correlations between disease ratings in different environments were high (0.78 to 0.89 and 0.9, respectively) and the overall entry mean heritability for SLB resistance was 0.89. When weighted mean disease ratings were fitted to a model using multiple interval mapping, seven potential quantitative trait loci (QTL) were identified, the two strongest being on chromosomes 3 (bin 3.04) and 9 (bin 9.03–9.04). These QTL explained a combined 80% of the phenotypic variation for SLB resistance. Some time-point-specific SLB resistance QTL were also identified. There was no significant correlation between disease resistance and days to anthesis. Six putative QTL for time to anthesis were identified, none of which coincided with any SLB resistance QTL. }, number={10}, journal={PHYTOPATHOLOGY}, author={Balint-Kurti, P. J. and Krakowsky, M. D. and Jines, M. P. and Robertson, L. A. and Molnar, T. L. and Goodman, M. M. and Holland, J. B.}, year={2006}, month={Oct}, pages={1067–1071} }
 @article{gonzalo_vyn_holland_mcintyre_2006, title={Mapping density response in maize: A direct approach for testing genotype and treatment interactions}, volume={173}, ISSN={["1943-2631"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33744488041&partnerID=MN8TOARS}, DOI={10.1534/genetics.105.045757}, abstractNote={Abstract
               Maize yield improvement has been strongly linked to improvements in stress tolerance, particularly to increased interplant competition. As a result, modern hybrids are able to produce kernels at high plant population densities. Identification of the genetic factors responsible for density response in maize requires direct testing of interactions between genetic effects and density and evaluation of that response in multiple traits. In this article we take a broad view of the problem and use a general approach based upon mixed models to analyze data from eight segmental inbred lines in a B73 background and their crosses to the unrelated parent Mo17 (hybrids). We directly test for the interaction between treatment effects and genetic effects instead of the commonly used overlaying of results on a common map. Additionally, we demonstrate one way to handle heteroscedasticity of variances common in stress responses. We find that some SILs are consistently different from the recurrent parent regardless of the density, while others differ from the recurrent parent in one density level but not in the other. Thus, we find positive evidence for both main effects and interaction between genetic loci and density in cases where the approach of overlapping results fails to find significant results. Furthermore, our study clearly identifies segments that respond differently to density depending upon the inbreeding level (inbred/hybrid).}, number={1}, journal={GENETICS}, author={Gonzalo, Martin and Vyn, Tony J. and Holland, James B. and McIntyre, Lauren M.}, year={2006}, month={May}, pages={331–348} }
 @article{jines_balint-kurti_robertson-hoyt_molnar_holland_goodman_2007, title={Mapping resistance to Southern rust in a tropical by temperate maize recombinant inbred topcross population}, volume={114}, ISSN={["1432-2242"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33846813838&partnerID=MN8TOARS}, DOI={10.1007/s00122-006-0466-0}, abstractNote={Southern rust, caused by Puccinia polysora Underw, is a foliar disease that can severely reduce grain yield in maize (Zea mays L.). Major resistance genes exist, but their effectiveness can be limited in areas where P. polysora is multi-racial. General resistance could be achieved by combining quantitative and race-specific resistances. This would be desirable if the resistance alleles maintained resistance across environments while not increasing plant maturity. Recombinant inbred (RI) lines were derived from a cross between NC300, a temperate-adapted all-tropical line, and B104, an Iowa Stiff Stalk Synthetic line. The RI lines were topcrossed to the tester FR615 x FR697. The 143 topcrosses were scored for Southern rust in four environments. Time to flowering was measured in two environments. The RI lines were genotyped at 113 simple sequence repeat markers and quantitative trait loci (QTL) were mapped for both traits. The entry mean heritability estimate for Southern rust resistance was 0.93. A multiple interval mapping model, including four QTL, accounted for 88% of the variation among average disease ratings. A major QTL located on the short arm of chromosome 10, explained 83% of the phenotypic variation, with the NC300 allele carrying the resistance. Significant (P < 0.001), but relatively minor, topcross-by-environment interaction occurred for Southern rust, and resulted from the interaction of the major QTL with the environment. Maturity and Southern rust rating were slightly correlated, but QTL for the two traits did not co-localize. Resistance was simply inherited in this population and the major QTL is likely a dominant resistant gene that is independent of plant maturity.}, number={4}, journal={THEORETICAL AND APPLIED GENETICS}, author={Jines, M. P. and Balint-Kurti, P. and Robertson-Hoyt, L. A. and Molnar, T. and Holland, J. B. and Goodman, M. M.}, year={2007}, month={Feb}, pages={659–667} }
 @article{zhao_canaran_jurkuta_fulton_glaubitz_buckler_doebley_gaut_goodman_holland_et al._2006, title={Panzea: a database and resource for molecular and functional diversity in the maize genome.}, volume={34}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33644874840&partnerID=MN8TOARS}, number={Database issue}, journal={Nucleic acids research.}, author={Zhao, W. and Canaran, P. and Jurkuta, R. and Fulton, T. and Glaubitz, J. and Buckler, E. and Doebley, J. and Gaut, B. and Goodman, M. and Holland, J. and et al.}, year={2006} }
 @article{robertson-hoyt_jines_balint-kurti_kleinschmidt_white_payne_maragos_molnár_holland_2006, title={QTL mapping for fusarium ear rot and fumonisin contamination resistance in two maize populations}, volume={46}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33746069043&partnerID=MN8TOARS}, DOI={10.2135/cropsci2005.12-0450}, abstractNote={Fusarium verticillioides (Sacc.) Nirenberg (synonym F. moniliforme Sheldon) (teleomorph: Gibberella moniliformis) and F. proliferatum (Matsushima) Nirenberg (teleomorph: G. intermedia) are fungal pathogens of maize (Zea mays L.) that cause ear rot and contaminate grain with fumonisins, mycotoxins that can harm animals and humans. The objective of this study was to identify quantitative trait loci (QTL) for resistance to Fusarium ear rot and fumonisin contamination in two maize populations, comprised of 213 BC1F1:2 families from the first backcross of GE440 to FR1064 (GEFR) and 143 recombinant inbred lines from the cross of NC300 to B104 (NCB). QTL mapping was used to study the genetic relationships between resistances to ear rot and fumonisin contamination and to investigate consistency of QTL across populations. In the GEFR population, seven QTL explained 47% of the phenotypic variation for mean ear rot resistance and nine QTL with one epistatic interaction explained 67% of the variation for mean fumonisin concentration. In the NCB population, five QTL explained 31% of the phenotypic variation for mean ear rot resistance and six QTL and three epistatic interactions explained 81% of the phenotypic variation for mean fumonisin concentration. Eight QTL in the GEFR population and five QTL in the NCB population affected both disease traits. At least three ear rot and two fumonisin contamination resistance QTL mapped to similar positions in the two populations. Two QTL, localized to chromosomes four and five, appeared to be consistent for both traits across both populations.}, number={4}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Robertson-Hoyt, Leilani A. and Jines, Michael P. and Balint-Kurti, Peter J. and Kleinschmidt, Craig E. and White, Don G. and Payne, Gary A. and Maragos, Chris M. and Molnár, Terence L. and Holland, James B.}, year={2006}, pages={1734–1743} }
 @article{long_holland_munkvold_jannink_2006, title={Responses to selection for partial resistance to crown rust in oat}, volume={46}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33646438072&partnerID=MN8TOARS}, DOI={10.2135/cropsci2005.06-0169}, abstractNote={ABSTRACTCrown rust, caused by the fungal pathogen, Puccinia coronata Corda var. avenae W.P. Fraser Ledingham, reduces kernel quality and grain yield in oat (Avena sativa L.). Partial resistance is considered to be a durable form of rust resistance. This study sought to evaluate the feasibility of simultaneously improving partial resistance to crown rust, grain yield, and seed weight in an oat population, and to estimate predicted and realized heritabilities for area under disease progress curve (AUDPC) and genetic correlations between AUDPC and agronomic traits in both crown rust‐inoculated and fungicide‐treated plots. A single cycle of selection for partial resistance to crown rust was performed. The initial (C0) and selected (C1) generations were evaluated in a field experiment in 2001 and 2002 at two Iowa locations. Selection on an index increased the levels of crown rust resistance, grain yield, and seed weight in crown rust−inoculated plots, and seed weight in fungicide‐treated plots. However, the change for the grain yield in fungicide‐treated plots was not significant. In both C0 and C1 populations, AUDPC was highly heritable (H = 0.77 and 0.78 respectively), and was favorably correlated with grain yield, seed weight, and test weight measured in inoculated plots. Realized heritabilities for all traits except grain yield under fungicide treatment were consistent with predicted heritabilities. Our results suggested that index selection could increase levels of crown rust resistance, grain yield, and seed weight simultaneously.}, number={3}, journal={CROP SCIENCE}, author={Long, J and Holland, JB and Munkvold, GP and Jannink, JL}, year={2006}, pages={1260–1265} }
 @book{holland_2008, title={Theoretical and Biological Foundations of Plant Breeding}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84889265588&partnerID=MN8TOARS}, DOI={10.1002/9780470752708.ch9}, abstractNote={This chapter contains section titled: Of what use is theory for plant breeding? Current understanding of the regulation of gene function Reconciling the biological basis of gene expression and quantitative genetics theory Reconciling quantitative genetics theory and biological knowledge of gene expression The paradox of interactions at molecular level and additivity at the phenotypic level Conclusions Acknowledgments}, journal={Plant Breeding: The Arnel R. Hallauer International Symposium}, author={Holland, J.B.}, year={2008}, pages={127–140} }
 @article{yu_pressoir_briggs_vroh bi_yamasaki_doebley_mcmullen_gaut_nielsen_holland_et al._2006, title={A unified mixed-model method for association mapping that accounts for multiple levels of relatedness}, volume={38}, ISSN={1061-4036 1546-1718}, url={http://dx.doi.org/10.1038/ng1702}, DOI={10.1038/ng1702}, abstractNote={As population structure can result in spurious associations, it has constrained the use of association studies in human and plant genetics. Association mapping, however, holds great promise if true signals of functional association can be separated from the vast number of false signals generated by population structure. We have developed a unified mixed-model approach to account for multiple levels of relatedness simultaneously as detected by random genetic markers. We applied this new approach to two samples: a family-based sample of 14 human families, for quantitative gene expression dissection, and a sample of 277 diverse maize inbred lines with complex familial relationships and population structure, for quantitative trait dissection. Our method demonstrates improved control of both type I and type II error rates over other methods. As this new method crosses the boundary between family-based and structured association samples, it provides a powerful complement to currently available methods for association mapping.}, number={2}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={Yu, Jianming and Pressoir, Gael and Briggs, William H and Vroh Bi, Irie and Yamasaki, Masanori and Doebley, John F and McMullen, Michael D and Gaut, Brandon S and Nielsen, Dahlia M and Holland, James B and et al.}, year={2006}, pages={203–208} }
 @article{tarter_goodman_holland_2004, title={Recovery of exotic alleles in semiexotic maize inbreds derived from crosses between Latin American accessions and a temperate line}, volume={109}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-4344701300&partnerID=MN8TOARS}, number={3}, journal={Theoretical and Applied Genetics}, author={Tarter, J.A. and Goodman, M.M. and Holland, J.B.}, year={2004}, pages={609–617} }
 @article{holland_goodman_2003, title={Combining ability of a tropical-derived maize population with isogenic BT and conventional testers}, volume={48}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0038419797&partnerID=MN8TOARS}, number={1}, journal={Maydica}, author={Holland, J.B. and Goodman, M.M.}, year={2003}, pages={1–8} }
 @article{helland_holland_2003, title={Genome-wide genetic diversity among components does not cause cultivar blend responses}, volume={43}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0141459295&partnerID=MN8TOARS}, number={5}, journal={Crop Science}, author={Helland, S.J. and Holland, J.B.}, year={2003}, pages={1618–1627} }
 @article{tarter_goodman_holland_2003, title={Testcross Performance of Semiexotic Inbred Lines Derived from Latin American Maize Accessions}, volume={43}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0242653940&partnerID=MN8TOARS}, number={6}, journal={Crop Science}, author={Tarter, J.A. and Goodman, M.M. and Holland, J.B.}, year={2003}, pages={2272–2278} }
 @article{cox_bender_picone_van tassel_holland_brummer_zoeller_paterson_jackson_2002, title={Breeding perennial grain crops}, volume={21}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0036216289&partnerID=MN8TOARS}, number={2}, journal={Critical Reviews in Plant Sciences}, author={Cox, T.S. and Bender, M. and Picone, C. and Van Tassel, D.L. and Holland, J.B. and Brummer, E.C. and Zoeller, B.E. and Paterson, A.H. and Jackson, W.}, year={2002}, pages={59–91} }
 @article{cervantes-martinez_frey_white_wesenberg_holland_2002, title={Correlated responses to selection for greater β-glucan content in two oat populations}, volume={42}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0036235335&partnerID=MN8TOARS}, number={3}, journal={Crop Science}, author={Cervantes-Martinez, C.T. and Frey, K.J. and White, P.J. and Wesenberg, D.M. and Holland, J.B.}, year={2002}, pages={730–738} }
 @article{holland_portyanko_hoffman_lee_2002, title={Genomic regions controlling vernalization and photoperiod responses in oat}, volume={105}, ISSN={["0040-5752"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0036923983&partnerID=MN8TOARS}, DOI={10.1007/s00122-001-0845-5}, abstractNote={Oat genotypes vary for photoperiod and vernalization responses. Vernalization often promotes earlier flowering in fall-sown but not spring-sown cultivars. Longer photoperiods also promote earlier flowering, and the response to longer photoperiods tends to be greater in cultivars from higher latitudes. To investigate the genetic basis of photoperiod and vernalization responses in oat, we mapped QTLs for flowering time under four combinations of photoperiod and vernalization treatments in the Ogle x TAM O-301 mapping population in growth chambers. We also mapped QTLs for flowering time in early spring and late-spring field plantings to determine the genetic basis of response to early spring planting in oat. Three major flowering-time QTLs (on linkage groups OT8, OT31 and OT32) were detected in most conditions. QTLs with smaller effects on flowering were less-consistently observed among treatments. Both vernalization-sensitive and insensitive QTLs were discovered. Longer photoperiod or vernalization alone tended to decrease the effects of flowering-time QTLs. Applied together, longer photoperiod and vernalization interacted synergistically, often on the same genomic regions. Earlier spring planting conferred an attenuated vernalization treatment on seeds. The major flowering-time QTLs mapped in this study matched those mapped previously in the Kanota x Ogle oat mapping population. Between these two studies, we found a concordance of flowering-time QTLs, segregation distortion, and complex genetic linkages. These effects may all be related to chromosomal rearrangements in hexaploid oat. Comparative mapping between oat and other grasses will facilitate molecular analysis of vernalization response in oat.}, number={1}, journal={THEORETICAL AND APPLIED GENETICS}, author={Holland, JB and Portyanko, VA and Hoffman, DL and Lee, M}, year={2002}, month={Jul}, pages={113–126} }
 @article{portyanko_hoffman_lee_holland_2001, title={A linkage map of hexaploid oat based on grass anchor DNA clones and its relationship to other oat maps}, volume={44}, ISSN={["0831-2796"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0035055426&partnerID=MN8TOARS}, DOI={10.1139/gen-44-2-249}, abstractNote={A cultivated oat linkage map was developed using a recombinant inbred population of 136 F6:7 lines from the cross 'Ogle' × 'TAM O-301'. A total of 441 marker loci, including 355 restriction fragment length polymorphism (RFLP) markers, 40 amplified fragment length polymorphisms (AFLPs), 22 random amplified polymorphic DNAs (RAPDs), 7 sequence-tagged sites (STSs), 1 simple sequence repeat (SSR), 12 isozyme loci, and 4 discrete morphological traits, was mapped. Fifteen loci remained unlinked, and 426 loci produced 34 linkage groups (with 2–43 loci each) spanning 2049 cM of the oat genome (from 4.2 to 174.0 cM per group). Comparisons with other Avena maps revealed 35 genome regions syntenic between hexaploid maps and 16–34 regions conserved between diploid and hexaploid maps. Those portions of hexaploid oat maps that could be compared were completely conserved. Considerable conservation of diploid genome regions on the hexaploid map also was observed (89–95%); however, at the whole-chromosome level, colinearity was much lower. Comparisons among linkage groups, both within and among Avena mapping populations, revealed several putative homoeologous linkage group sets as well as some linkage groups composed of segments from different homoeologous groups. The relationships between many Avena linkage groups remain uncertain, however, due to incomplete coverage by comparative markers and to complications introduced by genomic duplications and rearrangements.Key words: Avena, linkage map, comparative mapping, homoeology.}, number={2}, journal={GENOME}, author={Portyanko, VA and Hoffman, DL and Lee, M and Holland, JB}, year={2001}, month={Apr}, pages={249–265} }
 @article{kremer_lee_holland_2001, title={A restriction fragment length polymorphism based linkage map of a diploid Avena recombinant inbred line population}, volume={44}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0035055506&partnerID=MN8TOARS}, DOI={10.1139/gen-44-2-192}, number={2}, journal={Genome}, author={Kremer, C.A. and Lee, M. and Holland, J.B.}, year={2001}, pages={192–204} }
 @article{helland_holland_2001, title={Blend response and stability and cultivar blending ability in oat}, volume={41}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0035656793&partnerID=MN8TOARS}, number={6}, journal={Crop Science}, author={Helland, S.J. and Holland, J.B.}, year={2001}, pages={1689–1696} }
 @article{holland_frey_hammond_2001, title={Correlated responses of fatty acid composition, grain quality, and agronomic traits to nine cycles of recurrent selection for increased oil content in oat}, volume={122}, ISSN={["1573-5060"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0043198664&partnerID=MN8TOARS}, DOI={10.1023/A:1012639821332}, number={1}, journal={EUPHYTICA}, author={Holland, JB and Frey, KJ and Hammond, EG}, year={2001}, pages={69–79} }
 @article{holland_munkvold_2001, title={Genetic relationships of crown rust resistance, grain yield, test weight, and seed weight in oat}, volume={41}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0034891094&partnerID=MN8TOARS}, number={4}, journal={Crop Science}, author={Holland, J.B. and Munkvold, G.P.}, year={2001}, pages={1041–1050} }
 @article{holland_helland_sharopova_rhyne_2001, title={Polymorphism of PCR-based markers targeting exons, introns, promoter regions, and SSRs in maize and introns and repeat sequences in oat}, volume={44}, ISSN={["1480-3321"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0035543144&partnerID=MN8TOARS}, DOI={10.1139/gen-44-6-1065}, number={6}, journal={GENOME}, author={Holland, JB and Helland, SJ and Sharopova, N and Rhyne, DC}, year={2001}, month={Dec}, pages={1065–1076} }
 @article{holland_helland_sharopova_rhyne_2001, title={Polymorphism of PCR-based markers targeting exons, introns, promoter regions, and SSRs in maize and introns and repeat sequences in oat}, volume={44}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85047681394&partnerID=MN8TOARS}, DOI={10.1139/g01-110}, abstractNote={Sequence databases could be efficiently exploited for development of DNA markers if it were known which gene regions reveal the most polymorphism when amplified by PCR. We developed PCR primer pairs that target specific regions of previously sequenced genes from Avena and Zea species. Primers were targeted to amplify 40 introns, 24 exons, and 23 promoter regions within 54 maize genes. We surveyed 48 maize inbred lines (previously assayed for simple-sequence repeat (SSR) polymorphism) for amplification-product polymorphism. We also developed primers to target 14 SSRs and 12 introns within 18 Avena genes, and surveyed 22 hexaploid oat cultivars and 2 diploid Avena species for amplification-product polymorphism. In maize, 67% of promoter markers, 58% of intron markers, and 13% of exon markers exhibited amplification-product polymorphisms. Among polymorphic primer pairs in maize, genotype diversity was highest for SSR markers (0.60) followed by intron markers (0.46), exon markers (0.42), and promoter markers (0.28). Among all Avena genotypes, 64% of SSR markers and 58% of intron markers revealed polymorphisms, but among the cultivars only, 21% of SSR markers and 50% of intron markers were polymorphic. Polymorphic-sequence-tagged sites for plant-breeding applications can be created easily by targeting noncoding gene regions.Key words: Avena, Zea, genetic diversity, DNA sequence.}, number={6}, journal={Genome}, author={Holland, J.B. and Helland, S.J. and Sharopova, N. and Rhyne, D.C.}, year={2001}, pages={1065–1076} }
 @article{cervantes-martinez_frey_white_wesenberg_holland_2001, title={Selection for greater β-glucan content in oat grain}, volume={41}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0034890343&partnerID=MN8TOARS}, number={4}, journal={Crop Science}, author={Cervantes-Martinez, C.T. and Frey, K.J. and White, P.J. and Wesenberg, D.M. and Holland, J.B.}, year={2001}, pages={1085–1091} }
 @article{holland_bjornstad_frey_gullord_wesenberg_buraas_2000, title={Recurrent selection in oat for adaptation to diverse environments}, volume={113}, ISSN={["0014-2336"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0034076602&partnerID=MN8TOARS}, DOI={10.1023/A:1003933421378}, number={3}, journal={EUPHYTICA}, author={Holland, JB and Bjornstad, A and Frey, KJ and Gullord, M and Wesenberg, DM and Buraas, T}, year={2000}, pages={195–205} }
 @article{holland_brummer_1999, title={Cultivar effects on oat-berseem clover intercrops}, volume={91}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0032772190&partnerID=MN8TOARS}, number={2}, journal={Agronomy Journal}, author={Holland, J.B. and Brummer, E.C.}, year={1999}, pages={321–329} }
 @article{hoi_holland_hammond_1999, title={Heritability of lipase activity of oat caryopses}, volume={39}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0032770550&partnerID=MN8TOARS}, number={4}, journal={Crop Science}, author={Hoi, S.W. and Holland, J.B. and Hammond, E.G.}, year={1999}, pages={1055–1059} }
 @article{frey_holland_1999, title={Nine cycles of recurrent selection for increased groat-oil content in oat}, volume={39}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0033374759&partnerID=MN8TOARS}, number={6}, journal={Crop Science}, author={Frey, K.J. and Holland, J.B.}, year={1999}, pages={1636–1641} }
 @article{holland_1998, title={EPISTACY: A SAS program for detecting two-locus epistatic interactions using genetic marker information}, volume={89}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0031817262&partnerID=MN8TOARS}, DOI={10.1093/jhered/89.4.374}, number={4}, journal={Journal of Heredity}, author={Holland, J.B.}, year={1998}, pages={374–375} }
 @article{holland_uhr_jeffers_goodman_1998, title={Inheritance of resistance to southern corn rust in tropical by corn-belt maize populations}, volume={96}, ISSN={["0040-5752"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0031956880&partnerID=MN8TOARS}, DOI={10.1007/s001220050732}, number={2}, journal={THEORETICAL AND APPLIED GENETICS}, author={Holland, JB and Uhr, DV and Jeffers, D and Goodman, MM}, year={1998}, month={Feb}, pages={232–241} }
 @article{palmer_holland_lewers_1998, title={Recombination values for the Ms6-W1 chromosome region in different genetic backgrounds in soybean}, volume={38}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0031811862&partnerID=MN8TOARS}, number={2}, journal={Crop Science}, author={Palmer, R.G. and Holland, J.B. and Lewers, K.S.}, year={1998}, pages={293–296} }
 @article{qtls and epistasis associated with vernalization responses in oat_1997, volume={37}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0030822104&partnerID=MN8TOARS}, number={4}, journal={Crop Science}, year={1997}, pages={1306–1316} }
 @article{holland_goodman_castillo-gonzalez_1996, title={Identification of agronomically superior Latin American maize accessions via multi-stage evaluations}, volume={36}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0029832942&partnerID=MN8TOARS}, number={3}, journal={Crop Science}, author={Holland, J.B. and Goodman, M.M. and Castillo-Gonzalez, F.}, year={1996}, pages={778–784} }
 @article{holthaus_holland_white_frey_1996, title={Inheritance of β-glucan content of oat grain}, volume={36}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0029789190&partnerID=MN8TOARS}, number={3}, journal={Crop Science}, author={Holthaus, J.F. and Holland, J.B. and White, P.J. and Frey, K.J.}, year={1996}, pages={567–572} }
 @article{holland_goodman_1995, title={Combining ability of tropical maize accessions with U.S. germplasm}, volume={35}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0029165570&partnerID=MN8TOARS}, number={3}, journal={Crop Science}, author={Holland, J.B. and Goodman, M.M.}, year={1995}, pages={767–773} }
 @article{holland_bingham_1994, title={Genetic improvement for yield and fertility of alfalfa cultivars representing different eras of breeding}, volume={34}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0027995637&partnerID=MN8TOARS}, number={4}, journal={Crop Science}, author={Holland, J.B. and Bingham, E.T.}, year={1994}, pages={953–957} }