@article{fraher_schwarz_heim_gesteira_mollinari_pereira_zeng_brown-guedira_gorny_yencho_2024, title={Discovery of a major QTL for resistance to the guava root-knot nematode (<i>Meloidogyne enterolobii</i>) in 'Tanzania', an African landrace sweetpotato (<i>Ipomoea batatas</i>)}, volume={137}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-024-04739-1}, abstractNote={Sweetpotato, Ipomoea batatas (L.) Lam. (2n = 6x = 90), is among the world's most important food crops and is North Carolina's most important vegetable crop. The recent introduction of Meloidogyne enterolobii poses a significant economic threat to North Carolina's sweetpotato industry and breeding resistance into new varieties has become a high priority for the US sweetpotato industry. Previous studies have shown that 'Tanzania', a released African landrace, is resistant to M. enterolobii. We screened the biparental sweetpotato mapping population, 'Tanzania' x 'Beauregard', for resistance to M. enterolobii by inoculating 246 full-sibs with 10,000 eggs each under greenhouse conditions. 'Tanzania', the female parent, was highly resistant, while 'Beauregard' was highly susceptible. Our bioassays exhibited strong skewing toward resistance for three measures of resistance: reproductive factor, eggs per gram of root tissue, and root gall severity ratings. A 1:1 segregation for resistance suggested a major gene conferred M. enterolobii resistance. Using a random-effect multiple interval mapping model, we identified a single major QTL, herein designated as qIbMe-4.1, on linkage group 4 that explained 70% of variation in resistance to M. enterolobii. This study provides a new understanding of the genetic basis of M. enterolobii resistance in sweetpotato and represents a major step towards the identification of selectable markers for nematode resistance breeding.}, number={10}, journal={THEORETICAL AND APPLIED GENETICS}, author={Fraher, Simon and Schwarz, Tanner and Heim, Chris and Gesteira, Gabriel De Siqueira and Mollinari, Marcelo and Pereira, Guilherme Da Silva and Zeng, Zhao-Bang and Brown-Guedira, Gina and Gorny, Adrienne and Yencho, G. Craig}, year={2024}, month={Oct} }
 @article{rivera-burgos_vangessel_guedira_smith_marshall_jin_rouse_brown-guedira_2024, title={Fine mapping of stem rust resistance derived from soft red winter wheat cultivar AGS2000 to an NLR gene cluster on chromosome 6D}, volume={137}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-024-04702-0}, abstractNote={Abstract The Puccinia graminis f. sp. tritici ( Pgt ) Ug99-emerging virulent races present a major challenge to global wheat production. To meet present and future needs, new sources of resistance must be found. Identification of markers that allow tracking of resistance genes is needed for deployment strategies to combat highly virulent pathogen races. Field evaluation of a DH population located a QTL for stem rust (Sr) resistance, QSr.nc-6D from the breeding line MD01W28-08-11 to the distal region of chromosome arm 6DS where Sr resistance genes Sr42 , SrCad , and SrTmp have been identified. A locus for seedling resistance to Pgt race TTKSK was identified in a DH population and an RIL population derived from the cross AGS2000 × LA95135. The resistant cultivar AGS2000 is in the pedigree of MD01W28-08-11 and our results suggest that it is the source of Sr resistance in this breeding line. We exploited published markers and exome capture data to enrich marker density in a 10 Mb region flanking QSr.nc-6D . Our fine mapping in heterozygous inbred families identified three markers co-segregating with resistance and delimited QSr.nc-6D to a 1.3 Mb region. We further exploited information from other genome assemblies and identified collinear regions of 6DS harboring clusters of NLR genes. Evaluation of KASP assays corresponding to our co-segregating SNP suggests that they can be used to track this Sr resistance in breeding programs. However, our results also underscore the challenges posed in identifying genes underlying resistance in such complex regions in the absence of genome sequence from the resistant genotypes.}, number={9}, journal={THEORETICAL AND APPLIED GENETICS}, author={Rivera-Burgos, L. and VanGessel, C. and Guedira, M. and Smith, J. and Marshall, D. and Jin, Y. and Rouse, M. and Brown-Guedira, G.}, year={2024}, month={Sep} }
 @article{babar_khan_blount_barnett_harrison_dewitt_johnson_mergoum_boyles_murphy_et al._2024, title={Registration of 'FL16045-25': An early-maturing, high-yielding, disease-resistant soft red facultative wheat cultivar for the southern United States}, volume={4}, ISSN={["1940-3496"]}, DOI={10.1002/plr2.20343}, abstractNote={Abstract‘FL16045‐25’ (Reg. no. CV‐1207, PI 704484), a soft red, facultative doubled‐haploid wheat (Triticum aestivum L.) cultivar, was developed and tested as FL16045DH‐25 by the University of Florida and released in October 2022. FL16045‐25 was derived from the cross MD07W478‐14‐5/GA06112‐13EE16. It is well adapted from Texas to Virginia and provides producers with an early‐season, facultative (Vrn‐A1_short), medium‐height, awned, semi‐dwarf (Rht2) cultivar that has high yield potential, good straw strength, good grain volume weight, and good end‐use quality. It expresses moderate‐to‐high levels of resistance to most diseases prevalent in the southern United States. Molecular marker analysis confirms the presence of Sbm1, Yr17/Lr37/Sr38, Lr18, Sr36/Pm6, Pm54, and Pm1a‐linked disease‐resistant genes. The yield average of FL16045‐25 from 41 environments during 2020–2022 ranged from 4211 to 5782 kg ha−1, which is competitive with check cultivars that are widely used in the southern part of the United States. The grain volume weight of FL16045‐25 ranged from 749 to 785 kg m−3 (32 environments), which was higher than most of the checks. FL16045‐25 has soft grain texture with softness equivalence varying from 51.3% to 59.3% and sodium carbonate solvent retention capacity (SRC) ranging from 66.8% to 68.5%. Flour yields on a Quadrumat Senior milling system varied from 68.7% to 69.5%. Flour protein content varied from 8.9% to 9.1%. Cookie spread diameter varied from 19.4 to 19.5 cm. The presence of TaSus2‐2B, Sucrose Synthase2 gene on 2B or 2G:2B, was confirmed by marker analysis.}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Babar, Md Ali and Khan, Naeem and Blount, Ann and Barnett, Ronald D. and Harrison, Stephen A. and Dewitt, Noah and Johnson, Jerry and Mergoum, Mohamed and Boyles, Rick and Murphy, Paul and et al.}, year={2024}, month={Apr} }
 @article{boyles_ballen-taborda_brown-guedira_costa_cowger_dewitt_griffey_harrison_ibrahim_johnson_et al._2023, title={Approaching 25 years of progress towards Fusarium head blight resistance in southern soft red winter wheat (Triticum aestivum L.)}, volume={8}, ISSN={["1439-0523"]}, DOI={10.1111/pbr.13137}, abstractNote={AbstractTremendous progress has been made in variety development and host plant resistance to mitigate the impact of Fusarium head blight (FHB) since the disease manifested in the southeastern United States in the early 2000s. Much of this improvement was made possible through the establishment of and recurring support from the US Wheat & Barley Scab Initiative (USWBSI). Since its inception in 1997, the USWBSI has enabled land‐grant institutions to make advances in reducing the annual threat of devastating FHB epidemics. A coordinated field phenotyping effort for annual germplasm screening has become a staple tool for selection in public and private soft red winter wheat (SRWW) breeding programmes. Dedicated efforts of many SRWW breeders to identify and utilize resistance genes from both native and exotic sources provided a strong foundation for improvement. In recent years, implementation of genomics‐enabled breeding has further accelerated genetic gains in FHB resistance. This article reflects on the improvement of FHB resistance in southern SRWW and contextualizes the monumental progress made by collaborative, persistent, and good old‐fashioned cultivar development.}, journal={PLANT BREEDING}, author={Boyles, Richard E. and Ballen-Taborda, Carolina and Brown-Guedira, Gina and Costa, Jose and Cowger, Christina and DeWitt, Noah and Griffey, Carl A. and Harrison, Stephen A. and Ibrahim, Amir and Johnson, Jerry and et al.}, year={2023}, month={Aug} }
 @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{pettit_gowda_shrestha_harris_bart_bourland_brown-guedira_jones_kuraparthy_2023, title={Development and validation of Kompetitive allele-specific PCR (KASP) markers for bacterial blight resistant locus BB-13 in Upland cotton (Gossypium hirsutum L.)}, volume={8}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.21072}, abstractNote={AbstractCotton bacterial blight (CBB), caused by the pathogen Xanthomonas citri subsp. malvacearum (Xcm), can inflict significant damage to cotton (Gossypium hirsutum L.) production. Previously, we identified and mapped the broad‐spectrum CBB‐resistant locus BB‐13 on the long arm of chromosome D02 using array‐based single nucleotide polymorphisms (SNPs). In the current study, linked SNPs were converted into easily assayable Kompetitive Allele‐Specific PCR (KASP) markers to enable efficient detection and marker‐assisted selection of alleles at the BB‐13 locus. The KASP marker's efficiency in detecting the BB‐13 resistant gene was validated using an Upland cotton diversity panel of 72 accessions phenotyped with Xcm race 18. The KASP marker NCBB‐KASP4, derived from the CottonSNP63K array‐based marker i25755Gh that is closely associated with BB‐13, predicted the CBB response phenotypes with an error rate of 4.17% in the diversity panel. Additionally, two independent biparental recombinant inbred line populations segregating for resistance to Xcm race 18 were used for KASP marker validation and to test their utility in detecting the presence of the BB‐13 locus in the resistant accession CABD3CABCH‐1‐89. NCBB‐KASP4, validated across breeding populations and broad germplasm, is a reliable KASP marker for detection and testing of BB‐13 locus in cotton. Further, diagnostic array‐based SNP marker i25755Gh's allele pattern and the potential CBB response is described for 875 Gossypium accessions. These SNP‐based phenotypic predictions for 875 accessions along with disease response phenotypes to Xcm race 18 for 253 accessions provide a reference for CBB resistance in diverse cotton germplasm in the United States.}, journal={CROP SCIENCE}, author={Pettit, Nicole and Gowda, Satyanarayna Anjan and Shrestha, Navin and Harris, Taylor and Bart, Rebecca and Bourland, Fred and Brown-Guedira, Gina and Jones, Don C. and Kuraparthy, Vasu}, year={2023}, month={Aug} }
 @article{wu_jia_qiao_fu_brown-guedira_nagarajan_yan_2023, title={Genetic basis of resistance against powdery mildew in the wheat cultivar "Tabasco"}, volume={43}, ISSN={["1572-9788"]}, DOI={10.1007/s11032-023-01402-3}, abstractNote={{"Label"=>"UNLABELLED"} European winter wheat cultivar "Tabasco" was reported to have resistance to powdery mildew disease caused by  {"i"=>"Blumeria graminis"}  f. sp.  {"i"=>"tritici"}  ( {"i"=>"Bgt"} ) in China. In previous studies, Tabasco was reported to have the resistance gene designated as  {"i"=>"Pm48"}  on the short arm of chromosome 5D when a mapping population was phenotyped with pathogen isolate  {"i"=>"Bgt19"}  collected in China and was genotyped with simple sequence repeat (SSR) markers. In this study, single-nucleotide polymorphism (SNP) chips were used to rapidly determine the resistance gene by mapping a new F {"sub"=>"2"}  population that was developed from Tabasco and a susceptible cultivar "Ningmaizi119" and inoculated with pathogen isolate NCF-D-1-1 that was collected in the USA. The segregation of resistance in the population was found to link with  {"i"=>"Pm2"}  which was identified in Tabasco. Therefore, it was concluded that the previously reported  {"i"=>"Pm48"}  on chromosome arm 5DS in Tabasco should be the  {"i"=>"Pm2"}  gene on the same chromosome. The  {"i"=>"Pm2"}  was also found in European cultivars "Mattis" and "Claire" but not in any of the accessions from diploid wheat  {"i"=>"Aegilops tauschii"}  or modern cultivars such as "Gallagher," "Smith's Gold," and "OK Corral" being used in the Great Plains in the USA. A KASP marker was developed to track the resistance allele  {"i"=>"Pm2"}  in wheat breeding. {"Label"=>"SUPPLEMENTARY INFORMATION", "NlmCategory"=>"UNASSIGNED"} The online version contains supplementary material available at 10.1007/s11032-023-01402-3.}, number={7}, journal={MOLECULAR BREEDING}, author={Wu, Jizhong and Jia, Haiyan and Qiao, Linyi and Fu, Bisheng and Brown-Guedira, Gina and Nagarajan, Ragupathi and Yan, Liuling}, year={2023}, month={Jul} }
 @article{winn_acharya_merrill_lyerly_brown-guedira_cambron_harrison_reisig_murphy_2023, title={Mapping of a novel major effect Hessian fly field partial-resistance locus in southern soft red winter wheat line LA03136E71 (vol 134, pg 3911, 2021)}, volume={136}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-023-04304-2}, abstractNote={At the time of publication, it appears that there was scientific literature which was contradictory to a statement made in the abstract.The contradictory statement is that "This locus was identified on a chromosome where no other Hessian fly resistance/tolerance QTL has been previously identified."}, number={4}, journal={THEORETICAL AND APPLIED GENETICS}, author={Winn, Z. J. and Acharya, R. and Merrill, K. and Lyerly, J. and Brown-Guedira, G. and Cambron, S. and Harrison, S. H. and Reisig, D. and Murphy, J. P.}, year={2023}, month={Apr} }
 @article{winn_larkin_lozada_dewitt_brown-guedira_mason_2023, title={Multivariate genomic selection models improve prediction accuracy of agronomic traits in soft red winter wheat}, volume={5}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.20994}, abstractNote={AbstractUnivariate genomic selection (UVGS) is an important tool for increasing genetic gain and multivariate GS (MVGS), where correlated traits are included in genomic selection, which can improve genomic prediction accuracy. The objectives for this study were to evaluate MVGS approaches to improve prediction accuracy for four agronomic traits using a training population of 351 soft red winter wheat (Triticum aestivum L.) genotypes, evaluated over six site‐years in Arkansas from 2014 to 2017. Genotypes were phenotyped for grain yield, heading date, plant height, and test weight in both the training and test populations. In cross‐validations, various combinations of traits in MVGS models significantly improved prediction accuracy for test weight in comparison to a UVGS model. Marginal increases in predictive accuracy were also observed for grain yield, plant height, and heading date. Multivariate models which were identified as superior to the univariate case in cross‐validations were forward validated by predicting the advanced breeding nurseries of 2018 and 2020. In forward validation, consistent increases in accuracy were observed for test weight, plant height, and heading date using MVGS instead of UVGS. Overall, MVGS models improved prediction accuracies when correlated traits were included with the predicted response. The methods outlined in this study may be used to achieve higher prediction accuracies in unbalanced datasets over multiple environments.}, journal={CROP SCIENCE}, author={Winn, Zachary J. and Larkin, Dylan L. and Lozada, Dennis N. and DeWitt, Noah and Brown-Guedira, Gina and Mason, Richard Esten}, year={2023}, month={May} }
 @article{schoen_wallace_holbert_brown-guidera_harrison_murphy_sanantonio_van sanford_boyles_mergoum_et al._2023, title={Reducing the generation time in winter wheat cultivars using speed breeding}, volume={6}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.20989}, abstractNote={AbstractReducing generation time is critical to achieving the goals of genetic gain in important crops like wheat (Triticum aestivum). Speed breeding (SB) has been shown to considerably reduce generation times in crop plants. Unlike spring wheat cultivars, winter wheat varieties require typically 6–9 weeks of cold treatment, called vernalization, for flowering which extends the generation time for the development of improved winter wheat cultivars. Here, we optimized the SB method using a set of 48 diverse soft red winter wheat (SRWW) cultivars by testing vernalization duration, light and temperature requirements, and the viability of seeds harvested after different durations post‐anthesis under extended daylight conditions. We have found that using a 22‐h setting (22 h day/2 h night, 25°C/22°C) in high‐density 50‐cell trays results in rapid generation advancement. We used genotypic data for a panel of soft red winter wheat varieties from the regional programs to determine the impact of photoperiod and vernalization alleles on the efficiency of the SB approach. Using a set of 48 SRWW cultivars and germplasm from Maryland and four other public breeding programs, we establish that this protocol can allow for the advancement of four generations per year in controlled conditions for winter wheat varieties, experimental lines, or emerging cultivars. Our work shows the potential to reduce generation time by ∼30 days per generation faster than what had been reported in the SB strategies for winter wheat, thus allowing for a quicker turnaround time from original cross to genetically stable experimental genotypes that can be tested in field settings.}, journal={CROP SCIENCE}, author={Schoen, Adam and Wallace, Sydney and Holbert, Meghan Fisher and Brown-Guidera, Gina and Harrison, Stephen and Murphy, Paul and Sanantonio, Nicholas and Van Sanford, David and Boyles, Richard and Mergoum, Mohamed and et al.}, year={2023}, month={Jun} }
 @article{boden_mcintosh_uauy_krattinger_dubcovsky_rogers_xia_badaeva_bentley_brown-guedira_et al._2023, title={Updated guidelines for gene nomenclature in wheat}, volume={136}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-023-04253-w}, abstractNote={Abstract
                Key message
                Here, we provide an updated set of guidelines for naming genes in wheat that has been endorsed by the wheat research community.
              
                Abstract
                The last decade has seen a proliferation in genomic resources for wheat, including reference- and pan-genome assemblies with gene annotations, which provide new opportunities to detect, characterise, and describe genes that influence traits of interest. The expansion of genetic information has supported growth of the wheat research community and catalysed strong interest in the genes that control agronomically important traits, such as yield, pathogen resistance, grain quality, and abiotic stress tolerance. To accommodate these developments, we present an updated set of guidelines for gene nomenclature in wheat. These guidelines can be used to describe loci identified based on morphological or phenotypic features or to name genes based on sequence information, such as similarity to genes characterised in other species or the biochemical properties of the encoded protein. The updated guidelines provide a flexible system that is not overly prescriptive but provides structure and a common framework for naming genes in wheat, which may be extended to related cereal species. We propose these guidelines be used henceforth by the wheat research community to facilitate integration of data from independent studies and allow broader and more efficient use of text and data mining approaches, which will ultimately help further accelerate wheat research and breeding.
              }, number={4}, journal={THEORETICAL AND APPLIED GENETICS}, author={Boden, S. A. and McIntosh, R. A. and Uauy, C. and Krattinger, S. G. and Dubcovsky, J. and Rogers, W. J. and Xia, X. C. and Badaeva, E. D. and Bentley, A. R. and Brown-Guedira, G. and et al.}, year={2023}, month={Apr} }
 @article{winn_lyerly_brown-guedira_murphy_mason_2023, title={Utilization of a publicly available diversity panel in genomic prediction of Fusarium head blight resistance traits in wheat}, volume={5}, ISSN={["1940-3372"]}, DOI={10.1002/tpg2.20353}, abstractNote={AbstractFusarium head blight (FHB) is an economically and environmentally concerning disease of wheat (Triticum aestivum L). A two‐pronged approach of marker‐assisted selection coupled with genomic selection has been suggested when breeding for FHB resistance. A historical dataset comprised of entries in the Southern Uniform Winter Wheat Scab Nursery (SUWWSN) from 2011 to 2021 was partitioned and used in genomic prediction. Two traits were curated from 2011 to 2021 in the SUWWSN: percent Fusarium damaged kernels (FDK) and deoxynivalenol (DON) content. Heritability was estimated for each trait‐by‐environment combination. A consistent set of check lines was drawn from each year in the SUWWSN, and k‐means clustering was performed across environments to assign environments into clusters. Two clusters were identified as FDK and three for DON. Cross‐validation on SUWWSN data from 2011 to 2019 indicated no outperforming training population in comparison to the combined dataset. Forward validation for FDK on the SUWWSN 2020 and 2021 data indicated a predictive accuracy  and , respectively. Forward validation for DON indicated a predictive accuracy of  and , respectively. Forward validation using environments in cluster one for FDK indicated a predictive accuracy of  and , respectively. Forward validation using environments in cluster one for DON indicated a predictive accuracy of  and , respectively. These results indicated that selecting environments based on check performance may produce higher forward prediction accuracies. This work may be used as a model for utilizing public resources for genomic prediction of FHB resistance traits across public wheat breeding programs.}, journal={PLANT GENOME}, author={Winn, Zachary J. J. and Lyerly, Jeanette H. H. and Brown-Guedira, Gina and Murphy, Joseph P. P. and Mason, Richard Esten}, year={2023}, month={May} }
 @article{dewitt_guedira_murphy_marshall_mergoum_maltecca_brown-guedira_2022, title={A network modeling approach provides insights into the environment-specific yield architecture of wheat}, volume={5}, ISSN={["1943-2631"]}, url={https://doi.org/10.1093/genetics/iyac076}, DOI={10.1093/genetics/iyac076}, abstractNote={Abstract
               Wheat (Triticum aestivum) yield is impacted by a diversity of developmental processes which interact with the environment during plant growth. This complex genetic architecture complicates identifying quantitative trait loci that can be used to improve yield. Trait data collected on individual processes or components of yield have simpler genetic bases and can be used to model how quantitative trait loci generate yield variation. The objectives of this experiment were to identify quantitative trait loci affecting spike yield, evaluate how their effects on spike yield proceed from effects on component phenotypes, and to understand how the genetic basis of spike yield variation changes between environments. A 358 F5:6 recombinant inbred line population developed from the cross of LA-95135 and SS-MPV-57 was evaluated in 2 replications at 5 locations over the 2018 and 2019 seasons. The parents were 2 soft red winter wheat cultivars differing in flowering, plant height, and yield component characters. Data on yield components and plant growth were used to assemble a structural equation model to characterize the relationships between quantitative trait loci, yield components, and overall spike yield. The effects of major quantitative trait loci on spike yield varied by environment, and their effects on total spike yield were proportionally smaller than their effects on component traits. This typically resulted from contrasting effects on component traits, where an increase in traits associated with kernel number was generally associated with a decrease in traits related to kernel size. In all, the complete set of identified quantitative trait loci was sufficient to explain most of the spike yield variation observed within each environment. Still, the relative importance of individual quantitative trait loci varied dramatically. Path analysis based on coefficients estimated through structural equation model demonstrated that these variations in effects resulted from both different effects of quantitative trait loci on phenotypes and environment-by-environment differences in the effects of phenotypes on one another, providing a conceptual model for yield genotype-by-environment interactions in wheat.}, number={3}, journal={GENETICS}, author={DeWitt, Noah and Guedira, Mohammed and Murphy, Joseph Paul and Marshall, David and Mergoum, Mohamed and Maltecca, Christian and Brown-Guedira, Gina}, editor={Juenger, TEditor}, year={2022}, month={May} }
 @article{mergoum_johnson_buck_buntin_sutton_lopez_mailhot_chen_bland_harrison_et al._2022, title={A new soft red winter wheat cultivar 'GA 08535-15LE29' adapted to Georgia and the US southeast region}, volume={5}, ISSN={["1940-3496"]}, DOI={10.1002/plr2.20235}, abstractNote={AbstractSoft red winter wheat (SRWW) (Triticum aestivum L.) production in the southeastern United States is affected by biotic and abiotic stresses that can result in yield losses and reduced acreage. Developing new cultivars with high yield, good resistance to predominant pests, and acceptable quality to maximize value in regional markets is needed. The University of Georgia (UGA) SRWW breeding program, in collaboration with institutions in the region including the Southern UNiversities GRAINS (SUNGRAINS) programs, is responding to these challenges by developing and releasing superior cultivars adapted to the region. ‘GA 08535‐15LE29’ (Reg. no. CV‐1191, PI 693269) SRWW cultivar was developed and released by the UGA College of Agricultural and Environmental Sciences and licensed to Uni South Genetics seed company in 2018 as USG 3640. GA 08535‐15LE29 is well adapted to Georgia and the U.S. southeast region with high yield and good resistance to leaf (Puccinia triticina Erikss.) and stripe (P. striiformis Westend.) rusts, Fusarium head blight (caused by Fusarium graminearum Schwabe), powdery mildew (Erisyphe graminis), and Soil‐borne wheat mosaic virus (SBWMV) diseases. GA 08535‐15LE29 showed moderate field resistance to Hessian fly [Mayetiola destructor (Say)]. GA 08535‐15LE29 has Sbm1 and Yr17/Lr37/Sr38 for resistance to SBWMV and rust diseases and has good grain volume weight and acceptable milling and baking qualities.}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Mergoum, Mohamed and Johnson, Jerry and Buck, James and Buntin, G. David and Sutton, Steve and Lopez, Benjamin and Mailhot, Daniel and Chen, Zhenbang and Bland, Dan and Harrison, Stephen and et al.}, year={2022}, month={May} }
 @article{ma_brown-guedira_kang_baik_2022, title={Allelic Variations in Phenology Genes of Eastern U.S. Soft Winter and Korean Winter Wheat and Their Associations with Heading Date}, url={https://www.mdpi.com/2223-7747/11/22/3116}, DOI={10.3390/plants11223116}, abstractNote={Wheat heading time is genetically controlled by phenology genes including vernalization (Vrn), photoperiod (Ppd) and earliness per se (Eps) genes. Characterization of the existing genetic variation in the phenology genes of wheat would provide breeding programs with valuable genetic resources necessary for the development of wheat varieties well-adapted to the local environment and early-maturing traits suitable for double-cropping system. One hundred forty-nine eastern U.S. soft winter (ESW) and 32 Korean winter (KW) wheat genotypes were characterized using molecular markers for Vrn, Ppd, Eps and reduced-height (Rht) genes, and phenotyped for heading date (HD) in the eastern U.S. region. The Ppd-D1 and Rht-D1 genes exhibited the highest genetic diversity in ESW and KW wheat, respectively. The genetic variations for HD of ESW wheat were largely contributed by Ppd-B1, Ppd-D1 and Vrn-D3 genes. The Rht-D1 gene largely contributed to the genetic variation for HD of KW wheat. KW wheat headed on average 14 days earlier than ESW wheat in each crop year, largely due to the presence of the one-copy vrn-A1 allele in the former. The development of early-maturing ESW wheat varieties could be achieved by selecting for the one-copy vrn-A1 and vrn-D3a alleles in combination with Ppd-B1a and Ppd-D1a photoperiod insensitive alleles.}, journal={Plants}, author={Ma, Fengyun and Brown-Guedira, Gina and Kang, Moonseok and Baik, Byung-Kee}, year={2022}, month={Nov} }
 @article{he_wang_rutter_jordan_ren_taagen_dewitt_sehgal_sukumaran_dreisigacker_et al._2022, title={Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat}, volume={13}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-022-28453-y}, abstractNote={AbstractAllopolyploidy greatly expands the range of possible regulatory interactions among functionally redundant homoeologous genes. However, connection between the emerging regulatory complexity and expression and phenotypic diversity in polyploid crops remains elusive. Here, we use diverse wheat accessions to map expression quantitative trait loci (eQTL) and evaluate their effects on the population-scale variation in homoeolog expression dosage. The relative contribution of cis- and trans-eQTL to homoeolog expression variation is strongly affected by both selection and demographic events. Though trans-acting effects play major role in expression regulation, the expression dosage of homoeologs is largely influenced by cis-acting variants, which appear to be subjected to selection. The frequency and expression of homoeologous gene alleles showing strong expression dosage bias are predictive of variation in yield-related traits, and have likely been impacted by breeding for increased productivity. Our study highlights the importance of genomic variants affecting homoeolog expression dosage in shaping agronomic phenotypes and points at their potential utility for improving yield in polyploid crops.}, number={1}, journal={NATURE COMMUNICATIONS}, author={He, Fei and Wang, Wei and Rutter, William B. and Jordan, Katherine W. and Ren, Jie and Taagen, Ellie and DeWitt, Noah and Sehgal, Deepmala and Sukumaran, Sivakumar and Dreisigacker, Susanne and et al.}, year={2022}, month={Feb} }
 @article{langridge_alaux_almeida_ammar_baum_bekkaoui_bentley_beres_berger_braun_et al._2022, title={Meeting the Challenges Facing Wheat Production: The Strategic Research Agenda of the Global Wheat Initiative}, url={https://www.mdpi.com/2073-4395/12/11/2767}, DOI={10.3390/agronomy12112767}, abstractNote={Wheat occupies a special role in global food security since, in addition to providing 20% of our carbohydrates and protein, almost 25% of the global production is traded internationally. The importance of wheat for food security was recognised by the Chief Agricultural Scientists of the G20 group of countries when they endorsed the establishment of the Wheat Initiative in 2011. The Wheat Initiative was tasked with supporting the wheat research community by facilitating collaboration, information and resource sharing and helping to build the capacity to address challenges facing production in an increasingly variable environment. Many countries invest in wheat research. Innovations in wheat breeding and agronomy have delivered enormous gains over the past few decades, with the average global yield increasing from just over 1 tonne per hectare in the early 1960s to around 3.5 tonnes in the past decade. These gains are threatened by climate change, the rapidly rising financial and environmental costs of fertilizer, and pesticides, combined with declines in water availability for irrigation in many regions. The international wheat research community has worked to identify major opportunities to help ensure that global wheat production can meet demand. The outcomes of these discussions are presented in this paper.}, journal={Agronomy}, author={Langridge, Peter and Alaux, Michael and Almeida, Nuno Felipe and Ammar, Karim and Baum, Michael and Bekkaoui, Faouzi and Bentley, Alison and Beres, Brian and Berger, Bettina and Braun, Hans-Joachim and et al.}, year={2022}, month={Nov} }
 @article{gaire_arruda_mohammadi_brown-guedira_kolb_rutkoski_2022, title={Multi-trait genomic selection can increase selection accuracy for deoxynivalenol accumulation resulting from fusarium head blight in wheat}, volume={1}, ISSN={["1940-3372"]}, DOI={10.1002/tpg2.20188}, abstractNote={AbstractMulti‐trait genomic prediction (MTGP) can improve selection accuracy for economically valuable ‘primary’ traits by incorporating data on correlated secondary traits. Resistance to Fusarium head blight (FHB), a fungal disease of wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), is evaluated using four genetically correlated traits: incidence (INC), severity (SEV), Fusarium damaged kernels (FDK), and deoxynivalenol content (DON). Both FDK and DON are primary traits; DON evaluation is expensive and usually requires several months for wheat breeders to get results from service laboratories performing the evaluations. We evaluated MTGP for DON using three soft red winter wheat breeding datasets: two diversity panels from the University of Illinois (IL) and Purdue University (PU) and a dataset consisting of 2019–2020 University of Illinois breeding cohorts. For DON, relative to single‐trait (ST) genomic prediction, MTGP including phenotypic data for secondary traits on both validation and training sets, resulted in 23.4 and 10.6% higher predictive abilities in IL and PU panels, respectively. The MTGP models were advantageous only when secondary traits were included in both training and validation sets. In addition, MTGP models were more accurate than ST models only when FDK was included, and once FDK was included in the model, adding additional traits hardly improved accuracy. Evaluation of MTGP models across testing cohorts indicated that MTGP could increase accuracy by more than twofold in the early stages. Overall, we show that MTGP can increase selection accuracy for resistance to DON accumulation in wheat provided FDK is evaluated on the selection candidates.}, journal={PLANT GENOME}, author={Gaire, Rupesh and Arruda, Marcio Pais and Mohammadi, Mohsen and Brown-Guedira, Gina and Kolb, Frederic L. and Rutkoski, Jessica}, year={2022}, month={Jan} }
 @article{winn_lyerly_ward_brown-guedira_boyles_mergoum_johnson_harrison_babar_mason_et al._2022, title={Profiling of Fusarium head blight resistance QTL haplotypes through molecular markers, genotyping-by-sequencing, and machine learning}, volume={7}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-022-04178-w}, abstractNote={Marker-assisted selection is important for cultivar development. We propose a system where a training population genotyped for QTL and genome-wide markers may predict QTL haplotypes in early development germplasm. Breeders screen germplasm with molecular markers to identify and select individuals that have desirable haplotypes. The objective of this research was to investigate whether QTL haplotypes can be accurately predicted using SNPs derived by genotyping-by-sequencing (GBS). In the SunGrains program during 2020 (SG20) and 2021 (SG21), 1,536 and 2,352 lines submitted for GBS were genotyped with markers linked to the Fusarium head blight QTL: Qfhb.nc-1A, Qfhb.vt-1B, Fhb1, and Qfhb.nc-4A. In parallel, data were compiled from the 2011-2020 Southern Uniform Winter Wheat Scab Nursery (SUWWSN), which had been screened for the same QTL, sequenced via GBS, and phenotyped for: visual Fusarium severity rating (SEV), percent Fusarium damaged kernels (FDK), deoxynivalenol content (DON), plant height, and heading date. Three machine learning models were evaluated: random forest, k-nearest neighbors, and gradient boosting machine. Data were randomly partitioned into training-testing splits. The QTL haplotype and 100 most correlated GBS SNPs were used for training and tuning of each model. Trained machine learning models were used to predict QTL haplotypes in the testing partition of SG20, SG21, and the total SUWWSN. Mean disease ratings for the observed and predicted QTL haplotypes were compared in the SUWWSN. For all models trained using the SG20 and SG21, the observed Fhb1 haplotype estimated group means for SEV, FDK, DON, plant height, and heading date in the SUWWSN were not significantly different from any of the predicted Fhb1 calls. This indicated that machine learning may be utilized in breeding programs to accurately predict QTL haplotypes in earlier generations.}, journal={THEORETICAL AND APPLIED GENETICS}, author={Winn, Zachary J. and Lyerly, Jeanette and Ward, Brian and Brown-Guedira, Gina and Boyles, Richard E. and Mergoum, Mohamed and Johnson, Jerry and Harrison, Stephen and Babar, Ali and Mason, Richard E. and et al.}, year={2022}, month={Jul} }
 @article{olson_brown-guedira_noble_smith_forsberg_brisco_brown_2022, title={The 'Minibulk' system for advancing winter cereal breeding populations}, volume={3}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.20718}, abstractNote={AbstractConventional selected‐bulk breeding is a low cost means of advancing populations but requires years of selection in the field to generate fixed lines. Doubled haploid (DH) methods produce fixed lines quickly but without selection and at high cost. The ‘Minibulk’ system was developed to combine the speed of DHs with the population size and crossover opportunities of selected‐bulk breeding. Breeding populations of winter wheat (Triticum aestivum L.) were vernalized and advanced at high density in the greenhouse from the F2 to the F4 generation. F4 populations underwent visual selection in the field, and derived lines were genotyped for variants at photoperiod and vernalization alleles and across the genome using genotyping‐by‐sequencing. The number of crossover events and parental genome contributions were determined for recombinant inbred lines (RILs) within populations and among RILs across populations. During vernalization, seeds in all populations germinated and underwent vegetative growth, forming a dense seed mat that was transplanted directly into greenhouse pots. A 22‐h photoperiod accelerated development, and many populations reached physiological maturity as soon as five weeks after transplanting. Increasing the number of seeds planted from 300 in the F2 to 500 in the F3 increased the number of fertile spikes produced, thereby maintaining a larger population size. The number of crossovers detected differed significantly between populations and chromosomes, while the number of crossovers detected in each population was related to marker density. Adoption of the minibulk system by winter cereal breeding programs can lead to significant cost savings and acceleration of the breeding cycle.}, journal={CROP SCIENCE}, author={Olson, Eric and Brown-Guedira, Gina and Noble, Amanda and Smith, Jared and Forsberg, Lance and Brisco, Elizabeth and Brown, Linda}, year={2022}, month={Mar} }
 @article{ballen-taborda_lyerly_smith_howell_brown-guedira_babar_harrison_mason_mergoum_murphy_et al._2022, title={Utilizing genomics and historical data to optimize gene pools for new breeding programs: A case study in winter wheat}, volume={13}, ISSN={["1664-8021"]}, DOI={10.3389/fgene.2022.964684}, abstractNote={With the rapid generation and preservation of both genomic and phenotypic information for many genotypes within crops and across locations, emerging breeding programs have a valuable opportunity to leverage these resources to 1) establish the most appropriate genetic foundation at program inception and 2) implement robust genomic prediction platforms that can effectively select future breeding lines. Integrating genomics-enabled1 breeding into cultivar development can save costs and allow resources to be reallocated towards advanced (i.e., later) stages of field evaluation, which can facilitate an increased number of testing locations and replicates within locations. In this context, a reestablished winter wheat breeding program was used as a case study to understand best practices to leverage and tailor existing genomic and phenotypic resources to determine optimal genetics for a specific target population of environments. First, historical multi-environment phenotype data, representing 1,285 advanced breeding lines, were compiled from multi-institutional testing as part of the SunGrains cooperative and used to produce GGE biplots and PCA for yield. Locations were clustered based on highly correlated line performance among the target population of environments into 22 subsets. For each of the subsets generated, EMMs and BLUPs were calculated using linear models with the ‘lme4’ R package. Second, for each subset, TPs representative of the new SC breeding lines were determined based on genetic relatedness using the ‘STPGA’ R package. Third, for each TP, phenotypic values and SNP data were incorporated into the ‘rrBLUP’ mixed models for generation of GEBVs of YLD, TW, HD and PH. Using a five-fold cross-validation strategy, an average accuracy of r = 0.42 was obtained for yield between all TPs. The validation performed with 58 SC elite breeding lines resulted in an accuracy of r = 0.62 when the TP included complete historical data. Lastly, QTL-by-environment interaction for 18 major effect genes across three geographic regions was examined. Lines harboring major QTL in the absence of disease could potentially underperform (e.g., Fhb1 R-gene), whereas it is advantageous to express a major QTL under biotic pressure (e.g., stripe rust R-gene). This study highlights the importance of genomics-enabled breeding and multi-institutional partnerships to accelerate cultivar development.}, journal={FRONTIERS IN GENETICS}, author={Ballen-Taborda, Carolina and Lyerly, Jeanette and Smith, Jared and Howell, Kimberly and Brown-Guedira, Gina and Babar, Md. Ali and Harrison, Stephen A. A. and Mason, Richard E. E. and Mergoum, Mohamed and Murphy, J. Paul and et al.}, year={2022}, month={Oct} }
 @article{mergoum_johnson_buck_sutton_lopez_bland_chen_buntin_mailhot_babar_et al._2021, title={'GA JT141-14E45': A new soft red winter wheat cultivar adapted to Georgia and the US Southeast region}, volume={8}, ISSN={["1940-3496"]}, DOI={10.1002/plr2.20070}, abstractNote={AbstractIn Georgia and the southeast region of the United States, acreage of soft red winter wheat (SRWW) (Triticum aestivum L.) has decreased in recent years. There is an urgent need to release new cultivars with high yield potential, resistance to yield‐limiting diseases and insects, and good baking quality to maximize value in regional markets. To address this, the SRWW breeding program at the University of Georgia (UGA), in collaboration with the SUNGRAINS breeding programs, developed ‘GA JT141‐14E45’ (Reg. no. CV‐1183, PI 689519), a SRWW cultivar released by the UGA College of Agricultural and Environmental Sciences and licensed to AGSouth (AGS) Genetics as AGS 3030. GA JT141‐14E45 is widely adapted to the U.S. Southeast, having high yield, good resistance to diseases such as leaf rust, stripe rust, powdery mildew, and Soil‐borne wheat mosaic virus (SBWMV) and to current biotypes of Hessian fly (Mayetiola destructor Say). It has good resistance to Fusarium head blight (FHB) or scab. GA JT141‐14E45 has good grain volume weight and acceptable milling and baking quality. GA JT141‐14E45 was derived from the cross of ‘AGS 2026’/‘Jamestown’. Jamestown was used in the cross mainly for its resistance to FHB (FHB QTL 1A‐Neuse and 1B‐Jamestown). AGS 2026 is a UGA cultivar released in 2007 with very good disease resistance to rusts (Yr17/Lr37/Sr38), Hessian fly resistance (H13), and excellent yield.}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Mergoum, Mohamed and Johnson, Jerry W. and Buck, James W. and Sutton, Steve and Lopez, Benjamin and Bland, Daniel and Chen, Z. and Buntin, G. D. and Mailhot, Daniel J. and Babar, Md A. and et al.}, year={2021}, month={Aug} }
 @article{mergoum_johnson_buck_sutton_lopez_bland_chen_buntin_mailhot_babar_et al._2021, title={A new soft red winter wheat cultivar, 'GA 07353-14E19', adapted to Georgia and the US Southeast environments}, volume={15}, ISSN={["1940-3496"]}, DOI={10.1002/plr2.20113}, abstractNote={AbstractSoft red winter wheat (SRWW) (Triticum aestivum L.), historically a major crop in Georgia and the U.S. Southeast (SE) region, has been challenged by numerous biotic and abiotic constraints resulting in decreased hectarage in recent years. Hence, an urgent need exists to release new cultivars with high yield potential, good resistance to predominant diseases and insects, and acceptable quality attributes to capture and maximize value in regional markets. The SRWW breeding program at the University of Georgia (UGA), in collaboration with the Southeastern University GRAINS (SUNGRAINS) breeding programs, is responding to these challenges by developing and releasing superior SRWW cultivars adapted to Georgia and the SE wheat region. ‘GA 07353‐14E19’ (Reg. no. CV‐1179, PI 689520), a SRWW cultivar developed by the UGA small grains breeding program, was released by the UGA College of Agricultural and Environmental Sciences and licensed to Stratton Seed Company in 2017 as GO WHEAT 2032. GA 07353‐14E19 is adapted to the SE region with high yield, good resistance to prevalent diseases, including leaf and stripe rusts, Fusarium head blight, powdery mildew, and Soil‐borne wheat mosaic virus. GA 07353‐14E19 also showed good resistance to current biotypes of Hessian fly. GA 07353‐14E19 possesses the H13, Sbm1, and Yr17–Lr37–Sr38 genes that protect it against the above pests. It has very good grain volume weight and good milling and baking quality as a SRWW.}, number={2}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Mergoum, Mohamed and Johnson, Jerry W. and Buck, James W. and Sutton, Steve and Lopez, Benjamin and Bland, Daniel and Chen, Z. and Buntin, G. D. and Mailhot, Daniel J. and Babar, Md A. and et al.}, year={2021}, month={May}, pages={337–344} }
 @article{ward_merrill_bulli_pumphrey_mason_mergoum_johnson_sapkota_lopez_marshall_et al._2021, title={Analysis of the primary sources of quantitative adult plant resistance to stripe rust in US soft red winter wheat germplasm}, volume={14}, ISSN={["1940-3372"]}, DOI={10.1002/tpg2.20082}, abstractNote={AbstractStripe rust, or yellow rust (Puccinia striiformis Westend. f. sp. tritic), is a disease of wheat (Triticum aestivum L.) historically causing significant economic losses in cooler growing regions. Novel isolates of stripe rust with increased tolerance for high temperatures were detected in the United States circa 2000. This increased heat tolerance puts geographic regions, such as the soft red winter wheat (SRWW) growing region of the southeastern United States, at greater risk of stripe rust induced losses. In order to identify sources of stripe rust resistance in contemporary germplasm, we conducted genome‐wide association (GWA) studies on stripe rust severity measured in two panels. The first consisted of 273 older varieties, landraces, and some modern elite breeding lines and was evaluated in environments in the U.S. Pacific Northwest and the southeastern United States. The second panel consisted of 588 modern, elite SRWW breeding lines and was evaluated in four environments in Arkansas and Georgia. The analyses identified three major resistance loci on chromosomes: 2AS (presumably the 2NS:2AS alien introgression from Aegilops ventricosa Tausch; syn. Ae. caudata L.), 3BS, and 4BL. The 4BL locus explained a greater portion of variance in resistance than either the 2AS or 3BS loci in southeastern environments. However, its effects were unstable across different environments and sets of germplasm, possibly a result of its involvement in epistatic interactions. Relatively few lines carry resistance alleles at all three loci, suggesting that there is a pre‐existing reservoir of enhanced stripe rust resistance that may be further exploited by regional breeding programs.}, number={1}, journal={PLANT GENOME}, author={Ward, Brian P. and Merrill, Keith and Bulli, Peter and Pumphrey, Mike and Mason, Richard Esten and Mergoum, Mohamed and Johnson, Jerry and Sapkota, Suraj and Lopez, Benjamin and Marshall, David and et al.}, year={2021}, month={Mar} }
 @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{hawkes_kjoller_raaijmakers_riber_christensen_rasmussen_christensen_dahl_westergaard_nielsen_et al._2021, title={Extension of Plant Phenotypes by the Foliar Microbiome}, volume={72}, ISSN={["1545-2123"]}, DOI={10.1146/annurev-arplant-080620-114342}, abstractNote={ The foliar microbiome can extend the host plant phenotype by expanding its genomic and metabolic capabilities. Despite increasing recognition of the importance of the foliar microbiome for plant fitness, stress physiology, and yield, the diversity, function, and contribution of foliar microbiomes to plant phenotypic traits remain largely elusive. The recent adoption of high-throughput technologies is helping to unravel the diversityand spatiotemporal dynamics of foliar microbiomes, but we have yet to resolve their functional importance for plant growth, development, and ecology. Here, we focus on the processes that govern the assembly of the foliar microbiome and the potential mechanisms involved in extended plant phenotypes. We highlight knowledge gaps and provide suggestions for new research directions that can propel the field forward. These efforts will be instrumental in maximizing the functional potential of the foliar microbiome for sustainable crop production. }, journal={ANNUAL REVIEW OF PLANT BIOLOGY, VOL 72, 2021}, author={Hawkes, Christine V. and Kjoller, Rasmus and Raaijmakers, Jos M. and Riber, Leise and Christensen, Svend and Rasmussen, Simon and Christensen, Jan H. and Dahl, Anders Bjorholm and Westergaard, Jesper Cairo and Nielsen, Mads and et al.}, year={2021}, pages={823–846} }
 @article{gaire_brown-guedira_dong_ohm_mohammadi_2021, title={Genome-Wide Association Studies for Fusarium Head Blight Resistance and Its Trade-Off With Grain Yield in Soft Red Winter Wheat}, volume={105}, ISSN={["1943-7692"]}, DOI={10.1094/PDIS-06-20-1361-RE}, abstractNote={ Identification of quantitative trait loci for Fusarium head blight (FHB) resistance from different sources and pyramiding them into cultivars could provide effective protection against FHB. The objective of this study was to characterize a soft red winter wheat (SRWW) breeding population that has been subjected to intense germplasm introduction and alien introgression for FHB resistance in the past. The population was evaluated under misted FHB nurseries inoculated with Fusarium graminearum-infested corn spawn for two years. Phenotypic data included disease incidence (INC), disease severity (SEV), Fusarium damaged kernels (FDK), FHB index (FHBdx), and deoxynivalenol concentration (DON). Genome-wide association studies using 13,784 SNP markers identified 25 genomic regions at -logP ≥ 4.0 that were associated with five FHB-related traits. Of these 25, the marker trait associations that explained more than 5% phenotypic variation were localized on chromosomes 1A, 2B, 3B, 5A, 7A, 7B, and 7D, and from diverse sources including adapted SRWW lines such as Truman and Bess, and unadapted common wheat lines such as Ning7840 and Fundulea 201R. Furthermore, individuals with favorable alleles at the four loci Fhb1, Qfhb.nc-2B.1 (Q2B.1), Q7D.1, and Q7D.2 showed better FDK and DON scores (but not INC, SEV, and FHBdx) compared with other allelic combinations. Our data also showed while pyramiding multiple loci provides protection against FHB disease, it has a significant trade-off with grain yield. }, number={9}, journal={PLANT DISEASE}, author={Gaire, Rupesh and Brown-Guedira, Gina and Dong, Yanhong and Ohm, Herbert and Mohammadi, Mohsen}, year={2021}, month={Sep}, pages={2435–2444} }
 @article{glenn_zhang_brown-guedira_dewitt_cook_li_akhunov_dubcovsky_2021, title={Identification and characterization of a natural polymorphism in FT-A2 associated with increased number of grains per spike in wheat}, volume={11}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-021-03992-y}, abstractNote={Abstract
                Key message
                We discovered a natural FT-A2 allele that increases grain number per spike in both pasta and bread wheat with limited effect on heading time.
              
                Abstract
                Increases in wheat grain yield are necessary to meet future global food demands. A previous study showed that loss-of-function mutations in FLOWERING LOCUS T2 (FT2) increase spikelet number per spike (SNS), an important grain yield component. However, these mutations were also associated with reduced fertility, offsetting the beneficial effect of the increases in SNS on grain number. Here, we report a natural mutation resulting in an aspartic acid to alanine change at position 10 (D10A) associated with significant increases in SNS and no negative effects on fertility. Using a high-density genetic map, we delimited the SNS candidate region to a 5.2-Mb region on chromosome 3AS including 28 genes. Among them, only FT-A2 showed a non-synonymous polymorphism (D10A) present in two different populations segregating for the SNS QTL on chromosome arm 3AS. These results, together with the known effect of the ft-A2 mutations on SNS, suggest that variation in FT-A2 is the most likely cause of the observed differences in SNS. We validated the positive effects of the A10 allele on SNS, grain number, and grain yield per spike in near-isogenic tetraploid wheat lines and in an hexaploid winter wheat population. The A10 allele is present at very low frequency in durum wheat and at much higher frequency in hexaploid wheat, particularly in winter and fall-planted spring varieties. These results suggest that the FT-A2 A10 allele may be particularly useful for improving grain yield in durum wheat and fall-planted common wheat varieties.
              }, journal={THEORETICAL AND APPLIED GENETICS}, author={Glenn, Priscilla and Zhang, Junli and Brown-Guedira, Gina and DeWitt, Noah and Cook, Jason P. and Li, Kun and Akhunov, Eduard and Dubcovsky, Jorge}, year={2021}, month={Nov} }
 @article{winn_acharya_merrill_lyerly_brown-guedira_cambron_harrison_reisig_murphy_2021, title={Mapping of a novel major effect Hessian fly field partial-resistance locus in southern soft red winter wheat line LA03136E71}, volume={8}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-021-03936-6}, abstractNote={Hessian fly resistance has centralized around resistance loci that are biotype specific. We show that field resistance is evident and controlled by a single locus on chromosome 7D. Hessian flies (Mayetiola destructor Say) infest and feed upon wheat (Triticum aestivum L) resulting in significant yield loss. Genetically resistant cultivars are the most effective method of Hessian fly management. Wheat breeders in the southern USA have observed cultivars exhibiting a "field resistance" to Hessian fly that is not detectable by greenhouse assay. The resistant breeding line "LA03136E71" and susceptible cultivar "Shirley" were crossed to develop a population of 200 random F 4:5  lines using single seed descent. The population was evaluated in a total of five locations in North Carolina during the 2019, 2020, and 2021 seasons. A subsample of each plot was evaluated for the total number of tillers, number of infested tillers, and total number of larvae/pupae. From these data, the percent infested tillers, number of larvae/pupae per tiller, and the number of larvae/pupae per infested tiller were estimated. In all within and across environment combinations for all traits recorded, the genotype effect was significant (p < 0.05). Interval mapping identified a single large effect QTL distally on the short arm of chromosome 7D for all environment-trait combinations. This locus was identified on a chromosome where no other Hessian fly resistance/tolerance QTL has been previously identified. This novel Hessian fly partial-resistance QTL is termed QHft.nc-7D. Fine mapping must be conducted in this region to narrow down the causal agents responsible for this trait, and investigation into the mode of action is highly suggested.}, journal={THEORETICAL AND APPLIED GENETICS}, author={Winn, Z. J. and Acharya, R. and Merrill, K. and Lyerly, J. and Brown-Guedira, G. and Cambron, S. and Harrison, S. H. and Reisig, D. and Murphy, J. P.}, year={2021}, month={Aug} }
 @article{carmack_clark_lyerly_dong_brown-guedira_van sanford_2021, title={Optical sorter-augmented genomic selection lowers deoxynivalenol accumulation in wheat}, volume={6}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.20494}, abstractNote={AbstractPrevious results from our laboratory have shown that optical sorter–based indirect selection reduced deoxynivalenol (DON) accumulation in soft red winter wheat (SRWW). In this paper we evaluate the efficacy of optical sorter–augmented genomic selection (OSA‐GS) for lowering DON accumulation at three selection intensities across 2 yr. In total, 758 SRWW breeding lines were genotyped and then phenotyped in an inoculated Fusarium head blight (FHB) nursery. Accumulation of DON was measured on all breeding lines. The proportion of Fusarium‐damaged kernels estimated using an optical sorter (FDKos) was measured on 120 lines; these data were used to train a genomic prediction model. Genomic estimated breeding values (GEBVs) for FDKos were computed for all lines without actual FDKos data. The top 20, 30, and 40% of lines without actual FDKos data were selected based on FDKos GEBVs. The same was done using actual measured DON values. Both strategies lowered DON, but traditional direct phenotypic selection based on actual DON values outperformed OSA‐GS. In other words, phenotypic selection was necessary to achieve the greatest reductions in DON. However, using previously published cost estimates for the price of an optical sorter, DON analysis, and genotyping, we determined that OSA‐GS required less financial investment than phenotypic selection based on measured DON. Taken together, our findings indicate that OSA‐GS is a cost‐effective method for lowering DON accumulation and support the usefulness of an optical sorter as a tool for FHB resistance breeding in SRWW.}, journal={CROP SCIENCE}, author={Carmack, W. Jesse and Clark, Anthony J. and Lyerly, H. Jeanette and Dong, Yanhong and Brown-Guedira, Gina and Van Sanford, David Anthony}, year={2021}, month={Jun} }
 @article{larkin_mason_moon_holder_ward_brown-guedira_2021, title={Predicting Fusarium Head Blight Resistance for Advanced Trials in a Soft Red Winter Wheat Breeding Program With Genomic Selection}, volume={12}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2021.715314}, abstractNote={Many studies have evaluated the effectiveness of genomic selection (GS) using cross-validation within training populations; however, few have looked at its performance for forward prediction within a breeding program. The objectives for this study were to compare the performance of naïve GS (NGS) models without covariates and multi-trait GS (MTGS) models by predicting two years of F4:7 advanced breeding lines for three Fusarium head blight (FHB) resistance traits, deoxynivalenol (DON) accumulation, Fusarium damaged kernels (FDK), and severity (SEV) in soft red winter wheat and comparing predictions with phenotypic performance over two years of selection based on selection accuracy and response to selection. On average, for DON, the NGS model correctly selected 69.2% of elite genotypes, while the MTGS model correctly selected 70.1% of elite genotypes compared with 33.0% based on phenotypic selection from the advanced generation. During the 2018 breeding cycle, GS models had the greatest response to selection for DON, FDK, and SEV compared with phenotypic selection. The MTGS model performed better than NGS during the 2019 breeding cycle for all three traits, whereas NGS outperformed MTGS during the 2018 breeding cycle for all traits except for SEV. Overall, GS models were comparable, if not better than phenotypic selection for FHB resistance traits. This is particularly helpful when adverse environmental conditions prohibit accurate phenotyping. This study also shows that MTGS models can be effective for forward prediction when there are strong correlations between traits of interest and covariates in both training and validation populations.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Larkin, Dylan L. and Mason, Richard Esten and Moon, David E. and Holder, Amanda L. and Ward, Brian P. and Brown-Guedira, Gina}, year={2021}, month={Oct} }
 @article{ibrahim_sutton_johnson_mergoum_simoneaux_harrison_murphy_mason_babar_neely_et al._2021, title={Registration of 'GA06343-13E2 (TX-EL2)' soft red winter wheat}, volume={15}, ISBN={1940-3496}, DOI={10.1002/plr2.20031}, abstractNote={Abstract‘GA06343‐13E2 (TX‐EL2)’ (Reg. no. CV‐1172, PI 695071), a medium‐height, medium‐maturing soft red winter wheat (Triticum aestivum L.) (SRWW), was jointly released by Texas A&M AgriLife Research and the University of Georgia Agricultural Experiment Station in 2019. GA06343‐13E2 (TX‐EL2) was released based on merits of its wide area of adaptation and above‐average grain yield in Texas in particular and the Gulf Atlantic SRWW growing areas in general, in addition to average grain volume weight, good leaf rust and stripe rust resistance, and good end‐use quality characteristics. GA06343‐13E2 (TX‐EL2) was derived from the cross GA011638‐G1/GA961592‐8//GA991336‐47 made at the University of Georgia. The pedigree of GA011638‐G1 is GA01034 (‘AGS 2000’*3/96667)/AGS 2000. The pedigrees of GA961592‐8 and GA991336‐47 are GA951329 (GA88129‐32‐3‐5/GA87467‐14‐1‐14‐1)/GA88127‐1‐3‐3 and GA92432‐21‐5‐2/GA981622 [AGS 2000/Pioneer ‘26R61’ (XW663)], respectively. Authorized seed classes of GA06343‐13E2 (TX‐EL2) in the United States will be breeder, foundation, registered, and certified. We will submit GA06343‐13E2 (TX‐EL2) for U.S. Plant Variety Protection with the certification option.}, number={1}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Ibrahim, Amir M. H. and Sutton, Russell and Johnson, Jerry W. and Mergoum, Mohamed and Simoneaux, Bryan and Harrison, Stephen A. and Murphy, J. Paul and Mason, R. Esten and Babar, Md A. and Neely, Clark and et al.}, year={2021}, month={Jan}, pages={107–112} }
 @article{mergoum_johnson_buck_sutton_lopez_bland_chen_buntin_mailhot_babar_et al._2021, title={Soft red winter wheat 'GA 051207-14E53': Adapted cultivar to Georgia and the US Southeast region}, volume={15}, ISSN={["1940-3496"]}, DOI={10.1002/plr2.20102}, abstractNote={AbstractSoft red winter wheat (SRWW) (Triticum aestivum L.) is a major crop in Georgia and the U.S. Southeast (SE) region. Hence, new cultivars with high yield potential, high resistance levels to predominant pests, and adequate quality parameters are required to capture and maximize regional market values. Therefore, the University of Georgia SRWW breeding program in collaboration with the SUNGRAINS breeding programs, aims to develop and release SRWW cultivars adapted to Georgia and the SE wheat region with high yield, quality, and pest resistance. ‘GA 051207‐14E53’ SRWW (Reg. no. CV‐1168, PI 689518) was developed and released by the University of Georgia and licensed to AGSouth Genetics Company in 2017 under the name AGS 3040. GA 051207‐14E53 is well adapted to Georgia and the SE region. It has high yield and high resistance to leaf rust, stripe rust, and Soil‐borne wheat mosaic virus. It has medium resistance to powdery mildew and to biotypes C and O of Hessian fly and is resistant to biotypes B and L. GA 051207‐14E53 has good Fusarium head blight resistance. GA 051207‐14E53 possesses H9, Sbm1, and the 2NS:2AS alien introgression from Aegilops ventricosa Tausch, having the Yr17/Lr37/Sr38 genes that protect it against these pests. Grain volume weight and milling and baking qualities of GA 051207‐14E53 are good and meet the SRWW grade standards.}, number={1}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Mergoum, Mohamed and Johnson, Jerry W. and Buck, James W. and Sutton, Steve and Lopez, Benjamin and Bland, Daniel and Chen, Z. and Buntin, G. D. and Mailhot, Daniel J. and Babar, Md A. and et al.}, year={2021}, month={Jan}, pages={132–139} }
 @article{larkin_holder_mason_moon_brown-guedira_price_harrison_dong_2020, title={Genome-wide analysis and prediction of Fusarium head blight resistance in soft red winter wheat}, volume={60}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.20273}, abstractNote={AbstractFusarium head blight (FHB) is a disease in wheat (Triticum aestivum L.) caused by the fungal pathogen Fusarium graminearum Schwabe. Fusarium head blight poses potential economic losses and health risks due to the accumulation of the mycotoxin deoxynivalenol (DON) on infected seed heads. The objectives of this study were to identify novel FHB resistance loci using a genome‐wide association study (GWAS) approach and to evaluate two genomic selection (GS) approaches to improve prediction accuracies for FHB traits in a population of 354 soft red winter wheat (SRWW) genotypes. The GS approaches included GS+GWAS, where markers associated with a trait were used as fixed effects, and multivariate GS (MVGS), where correlated traits were used as covariates. The population was evaluated in FHB nurseries in Fayetteville and Newport, AR, and Winnsboro, LA, from 2014 to 2017. Genotypes were phenotyped for DON, Fusarium‐damaged kernels (FDK), incidence (INC), and severity (SEV). Forty‐two single nucleotide polymorphism (SNP) markers were significantly (false discovery rate, q [FDRq] ≤ .10) associated with resistance traits across 17 chromosomes. Ten significant SNPs were identified for DON, notably on chromosomes 2BL and 3BL. Eleven were identified for FDK, notably on chromosomes 4BL, 3AL, 1BL, 5BL, and 5DL. Nine were identified for INC, notably on chromosomes 2BS, 2BL, 7BL, 5DL, 6AS, and 5DS. Twelve were identified for SEV, notably on chromosomes 3BL, 4AL, and 4BL. The naïve GS models significantly outperformed the GS+GWAS model for all traits, whereas MVGS models significantly outperformed the naïve GS models for all traits. Results from this study will facilitate the development of SRWW cultivars with improved FHB resistance.}, number={6}, journal={CROP SCIENCE}, author={Larkin, Dylan L. and Holder, Amanda L. and Mason, R. Esten and Moon, David E. and Brown-Guedira, Gina and Price, Paul P. and Harrison, Stephen A. and Dong, Yanhong}, year={2020}, pages={2882–2900} }
 @article{carpenter_wright_malla_singh_van sanford_clark_harrison_murphy_costa_chao_et al._2020, title={Identification and validation of Fusarium head blight resistance QTL in the US soft red winter wheat cultivar 'Jamestown'}, volume={60}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.20307}, abstractNote={AbstractUse of genetic resistance is one of the most important strategies to manage the devastating disease Fusarium head blight (FHB) in wheat. Numerous quantitative trait loci (QTL) having varying effects on reducing FHB and the mycotoxin deoxynivalenol (DON) accumulation have been reported from Asian, European, or distant sources such as wild relatives of wheat (Triticum aestivum L.). However, coming from nonadapted backgrounds, the incorporation of such QTL into regional breeding programs has often resulted in the simultaneous transfer of other undesirable traits. Therefore, it is important to identify, characterize, and deploy sources of genetic resistance that do not suffer from poor adaptability and/or linkage drag. In the present work, QTL associated with FHB resistance in a high‐yielding, moderately resistant soft red winter wheat cultivar ‘Jamestown’ were mapped and validated. The QTL mapping was done using a recombinant inbred line (RIL) population of Pioneer ‘25R47’ × Jamestown having 186 individuals. Phenotyping over 2 yr at three locations, and genotyping using the 90K single nucleotide polymorphism (SNP) platform identified two new QTL, named QFHB.vt‐1B.1 and QFHB.vt‐1B.2, on the chromosome 1B long arm. The QTL contributed to FHB incidence, FHB severity, Fusarium‐damaged kernels, and DON content. Independent mapping of these QTL using two additional RIL populations of FG95195 × Jamestown (170 RILs) and Jamestown × LA97113UC‐124 (77 RILs) validated their stability and effectiveness in different genetic backgrounds. Kompetitive allele specific polymerase chain reaction (KASP) assays were developed using linked SNPs for marker‐assisted selection of the QTL. These QTL are being used in breeding programs to develop FHB‐resistant, high‐yielding varieties.}, number={6}, journal={CROP SCIENCE}, author={Carpenter, Neal R. and Wright, Emily and Malla, Subas and Singh, Lovepreet and Van Sanford, David and Clark, Anthony and Harrison, Stephen and Murphy, J. Paul and Costa, Jose and Chao, Shiaoman and et al.}, year={2020}, pages={2919–2930} }
 @article{gaire_ohm_brown-guedira_mohammadi_2020, title={Identification of regions under selection and loci controlling agronomic traits in a soft red winter wheat population}, volume={13}, ISSN={["1940-3372"]}, DOI={10.1002/tpg2.20031}, abstractNote={AbstractComprehensive information of a breeding population is a necessity to design promising crosses. This study was conducted to characterize a soft red winter wheat breeding population that was subject of intensive germplasm introductions and introgression from exotic germplasm. We used genome‐wide markers and phenotypic assessment to identify signatures of selection and loci controlling agronomic traits in a soft red winter wheat population. The study of linkage disequilibrium (LD) revealed that the extent of LD and its decay varied among chromosomes with chromosomes 2B and 7D showing the most extended islands of high‐LD with slow rates of decay. Four sub‐populations, two with North American origin and two with Australian and Chinese origins, were identified. Genome‐wide scans for selection signatures using FST and hapFLK identified 13 genomic regions under selection, of which five loci (LT, Fr‐A2, Vrn‐A1, Vrn‐B1, Vrn3) were associated with environmental adaptation and two loci were associated with disease resistance genes (Sr36 and Fhb1). Genome‐wide association studies identified major loci controlling yield and yield related traits. For days to heading and plant height, major loci with effects sizes of 2.2 days and 5 cm were identified on chromosomes 7B and 6A respectively. For test weight, number of spikes per square meter, and number of kernels per square meter, large effect loci were identified on chromosomes 1A, 4B, and 5A, respectively. However, for yield alone, no major loci were detected. A combination of selection for large effect loci for yield components and genomic selection could be a promising approach for yield improvement.}, number={2}, journal={PLANT GENOME}, author={Gaire, Rupesh and Ohm, Herbert and Brown-Guedira, Gina and Mohammadi, Mohsen}, year={2020}, month={Jul} }
 @article{rehman_gale_brown-guedira_jin_marshall_whitcher_williamson_rouse_ahmad_ahmad_et al._2020, title={Identification of seedling resistance to stem rust in advanced wheat lines and varieties from Pakistan}, volume={60}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.20056}, abstractNote={AbstractStem rust is a major disease of wheat (Triticum aestivum L.) worldwide and new Puccinia graminis f. sp. tritici (Pgt) races including TTKSK (Ug99) pose a serious threat to wheat production. The protection of new varieties against Pgt races can be increased by identifying and combining several types of stem rust resistance genes (Sr). We screened a set of 707 wheat lines and cultivars against 11 Pgt races under glass house conditions. Of the tested lines, groups of 99, 513, 289, and 515 exhibited low infection type (IT < 3) to races TTKSK, TRTTF, TTTTF, and RRTTF, respectively. Screening against Pgt races (QFCSC, QTHJC, MCCFC, RCRSC, RKRQC, TPMKC, and QCCSM) showed that most of the tested lines were resistant. These lines were screened with eight DNA markers for the presence of Sr2, Sr9a, Sr24, Sr25, Sr31, Sr36, Sr38, and Sr57 genes. Sr36 was absent from all the tested lines, whereas Sr9a was detected in four lines. The marker Sr2_ger93p predicted the presence of Sr2 in 40 lines, and marker barc71 suggested the presence of Sr24 in 12 lines. Sr25 and Sr38 were present in 13 and 54 lines, respectively. The highest frequency of Sr genes was observed for Sr57 (199 lines) and Sr31 (177 lines). Except for lines carrying Sr25 and/or Sr24 genes, most lines were susceptible to Pgt race TTKSK. Since Ug99 is overcoming Sr genes worldwide, including Sr24 and Sr36, a strategy to pyramid multiple Sr genes in new cultivars should be pursued to achieve a durable control of stem rust. The effectiveness of lines such as NRL0902, 11050, B‐2(RF)‐11, and CCRI‐6, found in the current study and featuring other Sr genes, warrants further investigation to identify the source of their resistance and use it in Pakistan wheat breeding programs.}, number={2}, journal={CROP SCIENCE}, author={Rehman, Monsif Ur and Gale, Sam and Brown-Guedira, Gina and Jin, Yue and Marshall, David and Whitcher, Lynda and Williamson, Sharon and Rouse, Matthew and Ahmad, Javed and Ahmad, Gulzar and et al.}, year={2020}, pages={804–811} }
 @article{guo_khan_pradhan_shahi_khan_avci_mcbreen_harrison_brown-guedira_murphy_et al._2020, title={Multi-Trait Genomic Prediction of Yield-Related Traits in US Soft Wheat under Variable Water Regimes}, volume={11}, ISSN={["2073-4425"]}, DOI={10.3390/genes11111270}, abstractNote={The performance of genomic prediction (GP) on genetically correlated traits can be improved through an interdependence multi-trait model under a multi-environment context. In this study, a panel of 237 soft facultative wheat (Triticum aestivum L.) lines was evaluated to compare single- and multi-trait models for predicting grain yield (GY), harvest index (HI), spike fertility (SF), and thousand grain weight (TGW). The panel was phenotyped in two locations and two years in Florida under drought and moderately drought stress conditions, while the genotyping was performed using 27,957 genotyping-by-sequencing (GBS) single nucleotide polymorphism (SNP) makers. Five predictive models including Multi-environment Genomic Best Linear Unbiased Predictor (MGBLUP), Bayesian Multi-trait Multi-environment (BMTME), Bayesian Multi-output Regressor Stacking (BMORS), Single-trait Multi-environment Deep Learning (SMDL), and Multi-trait Multi-environment Deep Learning (MMDL) were compared. Across environments, the multi-trait statistical model (BMTME) was superior to the multi-trait DL model for prediction accuracy in most scenarios, but the DL models were comparable to the statistical models for response to selection. The multi-trait model also showed 5 to 22% more genetic gain compared to the single-trait model across environment reflected by the response to selection. Overall, these results suggest that multi-trait genomic prediction can be an efficient strategy for economically important yield component related traits in soft wheat.}, number={11}, journal={GENES}, author={Guo, Jia and Khan, Jahangir and Pradhan, Sumit and Shahi, Dipendra and Khan, Naeem and Avci, Muhsin and Mcbreen, Jordan and Harrison, Stephen and Brown-Guedira, Gina and Murphy, Joseph Paul and et al.}, year={2020}, month={Nov} }
 @article{cowger_ward_brown-guedira_brown_2020, title={Role of Effector-Sensitivity Gene Interactions and Durability of Quantitative Resistance to Septoria Nodorum Blotch in Eastern US Wheat}, volume={11}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2020.00155}, abstractNote={Important advances have been made in understanding the relationship of necrotrophic effectors (NE) and host sensitivity (Snn) genes in the Parastagonospora nodorum-wheat pathosystem. Yet much remains to be learned about the role of these interactions in determining wheat resistance levels in the field, and there is mixed evidence on whether breeding programs have selected against Snn genes due to their role in conferring susceptibility. SNB occurs ubiquitously in the U.S. Atlantic seaboard, and the environment is especially well suited to field studies of resistance to natural P. nodorum populations, as there are no other important wheat leaf blights. Insights into the nature of SNB resistance have been gleaned from multi-year data on phenotypes and markers in cultivars representative of the region’s germplasm. In this perspective article, we review the evidence that in this eastern region of the U.S., wheat cultivars have durable quantitative SNB resistance and Snn–NE interactions are of limited importance. This conclusion is discussed in light of the relevant available information from other parts of the world.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Cowger, Christina and Ward, Brian and Brown-Guedira, Gina and Brown, James K. M.}, year={2020}, month={Mar} }
 @article{lozada_mason_sarinelli_brown-guedira_2019, title={Accuracy of genomic selection for grain yield and agronomic traits in soft red winter wheat}, volume={20}, ISSN={["1471-2156"]}, DOI={10.1186/s12863-019-0785-1}, abstractNote={AbstractBackgroundGenomic selection has the potential to increase genetic gains by using molecular markers as predictors of breeding values of individuals. This study evaluated the accuracy of predictions for grain yield, heading date, plant height, and yield components in soft red winter wheat under different prediction scenarios. Response to selection for grain yield was also compared across different selection strategies- phenotypic, marker-based, genomic, combination of phenotypic and genomic, and random selections.ResultsGenomic selection was implemented through a ridge regression best linear unbiased prediction model in two scenarios- cross-validations and independent predictions. Accuracy for cross-validations was assessed using a diverse panel under different marker number, training population size, relatedness between training and validation populations, and inclusion of fixed effect in the model. The population in the first scenario was then trained and used to predict grain yield of biparental populations for independent validations. Using subsets of significant markers from association mapping increased accuracy by 64–70% for grain yield but resulted in lower accuracy for traits with high heritability such as plant height. Increasing size of training population resulted in an increase in accuracy,with maximum values reached when ~ 60% of the lines were used as a training panel. Predictions using related subpopulations also resulted in higher accuracies. Inclusion of major growth habit genes as fixed effect in the model caused increase in grain yield accuracy under a cross-validation procedure. Independent predictions resulted in accuracy ranging between − 0.14 and 0.43, dependent on the grouping of site-year data for the training and validation populations. Genomic selection was “superior” to marker-based selection in terms of response to selection for yield. Supplementing phenotypic with genomic selection resulted in approximately 10% gain in response compared to using phenotypic selection alone.ConclusionsOur results showed the effects of different factors on accuracy for yield and agronomic traits. Among the factors studied, training population size and relatedness between training and validation population had the greatest impact on accuracy. Ultimately, combining phenotypic with genomic selection would be relevant for accelerating genetic gains for yield in winter wheat.}, number={1}, journal={BMC GENETICS}, author={Lozada, Dennis N. and Mason, R. Esten and Sarinelli, Jose Martin and Brown-Guedira, Gina}, year={2019}, month={Nov} }
 @article{gaire_huang_sneller_griffey_brown-guedira_mohammadi_2019, title={Association Analysis of Baking and Milling Quality Traits in an Elite Soft Red Winter Wheat Population}, volume={59}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2018.12.0751}, abstractNote={Although grain yield is the most important trait for growers, milling and baking industries demand high‐quality and scab‐free grains for various end products. To accelerate breeding of wheat (Triticum aestivum L.) cultivars with high grain quality, genetic dissection of quality traits is necessary. Genome‐wide association studies (GWAS) were conducted to identify genomic regions responsible for milling and baking quality traits in soft red winter wheat (SRWW). Seven quality traits were evaluated in two locations and 2 yr for 270 elite SRWW lines. These traits include flour yield, softness equivalent, flour protein, and four solvent (lactose, sodium carbonate, sucrose, and water) retention capacity measurements. In this study, 27,449 single nucleotide polymorphism (SNP) markers were developed by using both genotyping‐by‐sequencing and 90K SNP array technologies. A linear mixed model in GWAS, accounting for population structure and kinship, was fitted to identify 18 [−log(P) ≥ 4.0] genomic regions on 12 different chromosomes associated with the quality traits. Only one of these associations seems to be a previously identified quantitative trait locus, whereas others are novel associations. The most significant associations for quality traits were identified on chromosomes 1B, 2A, 2B, 4B, 5A, 7A, and 7D. Candidate gene searches, facilitated by the wheat genome assembly, led us to the identification of putative genes related to SRWW quality traits including fasciclin‐like arabinogalactan. The results of this study can be used in developing high‐quality SRWW varieties for the eastern region of the United States.}, number={3}, journal={CROP SCIENCE}, author={Gaire, Rupesh and Huang, Mao and Sneller, Clay and Griffey, Carl and Brown-Guedira, Gina and Mohammadi, Mohsen}, year={2019}, pages={1085–1094} }
 @article{hemshrot_poets_tyagi_lei_carter_hirsch_li_brown-guedira_morrell_muehlbauer_et al._2019, title={Development of a Multiparent Population for Genetic Mapping and Allele Discovery in Six-Row Barley}, volume={213}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.119.302046}, abstractNote={Abstract
               Germplasm collections hold valuable allelic diversity for crop improvement and genetic mapping of complex traits. To gain access to the genetic diversity within the USDA National Small Grain Collection (NSGC), we developed the Barley Recombinant Inbred Diverse Germplasm Population (BRIDG6), a six-row spring barley multiparent population (MPP) with 88 cultivated accessions crossed to a common parent (Rasmusson). The parents were randomly selected from a core subset of the NSGC that represents the genetic diversity of landrace and breeding accessions. In total, we generated 6160 F5 recombinant inbred lines (RILs), with an average of 69 and a range of 37–168 RILs per family, that were genotyped with 7773 SNPs, with an average of 3889 SNPs segregating per family. We detected 23 quantitative trait loci (QTL) associated with flowering time with five QTL found coincident with previously described flowering time genes. A major QTL was detected near the flowering time gene, HvPpd-H1 which affects photoperiod. Haplotype-based analysis of HvPpd-H1 identified private alleles to families of Asian origin conferring both positive and negative effects, providing the first observation of flowering time-related alleles private to Asian accessions. We evaluated several subsampling strategies to determine the effect of sample size on the power of QTL detection, and found that, for flowering time in barley, a sample size >50 families or 3000 individuals results in the highest power for QTL detection. This MPP will be useful for uncovering large and small effect QTL for traits of interest, and identifying and utilizing valuable alleles from the NSGC for barley improvement.}, number={2}, journal={GENETICS}, author={Hemshrot, Alex and Poets, Ana M. and Tyagi, Priyanka and Lei, Li and Carter, Corey K. and Hirsch, Candice N. and Li, Lin and Brown-Guedira, Gina and Morrell, Peter L. and Muehlbauer, Gary J. and et al.}, year={2019}, month={Oct}, pages={595–613} }
 @article{ward_brown-guedira_kolb_van sanford_tyagi_sneller_griffey_2019, title={Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia}, volume={14}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0208217}, abstractNote={Grain yield is a trait of paramount importance in the breeding of all cereals. In wheat (Triticum aestivum L.), yield has steadily increased since the Green Revolution, though the current rate of increase is not forecasted to keep pace with demand due to growing world population and increasing affluence. While several genome-wide association studies (GWAS) on yield and related component traits have been performed in wheat, the previous lack of a reference genome has made comparisons between studies difficult. In this study, a GWAS for yield and yield-related traits was carried out on a population of 322 soft red winter wheat lines across a total of four rain-fed environments in the state of Virginia using single-nucleotide polymorphism (SNP) marker data generated by a genotyping-by-sequencing (GBS) protocol. Two separate mixed linear models were used to identify significant marker-trait associations (MTAs). The first was a single-locus model utilizing a leave-one-chromosome-out approach to estimating kinship. The second was a sub-setting kinship estimation multi-locus method (FarmCPU). The single-locus model identified nine significant MTAs for various yield-related traits, while the FarmCPU model identified 74 significant MTAs. The availability of the wheat reference genome allowed for the description of MTAs in terms of both genetic and physical positions, and enabled more extensive post-GWAS characterization of significant MTAs. The results indicate a number of promising candidate genes contributing to grain yield, including an ortholog of the rice aberrant panicle organization (APO1) protein and a gibberellin oxidase protein (GA2ox-A1) affecting the trait grains per square meter, an ortholog of the Arabidopsis thaliana mother of flowering time and terminal flowering 1 (MFT) gene affecting the trait seeds per square meter, and a B2 heat stress response protein affecting the trait seeds per head.}, number={2}, journal={PLOS ONE}, author={Ward, Brian P. and Brown-Guedira, Gina and Kolb, Frederic L. and Van Sanford, David A. and Tyagi, Priyanka and Sneller, Clay H. and Griffey, Carl A.}, year={2019}, month={Feb} }
 @article{daba_tyagi_brown-guedira_mohammadi_2020, title={Genome-wide association study in historical and contemporary U.S. winter wheats identifies height-reducing loci}, volume={8}, ISSN={["2214-5141"]}, DOI={10.1016/j.cj.2019.09.005}, abstractNote={Plant height has been a major target for selection of high-yielding varieties in wheat. Two height-reducing loci (Rht-B1 and Rht-D1) have been widely used since the Green Revolution. However, these genes also negatively affect other agronomic traits such as kernel weight. Identifying alternative height-reducing loci could benefit wheat improvement. This study focused on the genetics of plant height in 260 historical and contemporary winter wheat accessions via genome-wide association studies using 38,693 single nucleotide polymorphism (SNP) markers generated through genotyping by sequencing, two Kompetitive Allele Specific Polymorphism markers, and phenotypic data recorded in two seasons (2016 and 2018). The 260 accessions showed wide variation in plant height. Most accessions developed after 1960 were shorter than earlier accessions. The broad-sense heritability for plant height was high (H2 = 0.82), which was also supported by a high correlation (r = 0.82, P < 0.0001) between heights from the two years. We detected a total of 16 marker–trait associations (MTAs) for plant height at –lg (P) ≥ 4.0 on chromosomes 1A, 2B, 2D, 3B, 4D, 5A, 5D, 6A, 6B, 7A, and 7D. We detected three of the MTAs (QPLH-2D, QPLH-4B.2, and QPLH-4D) consistently in individual-year and combined-year analyses. These MTAs individually explained 10%–16% of phenotypic variation. The height-reducing alleles at these three MTAs appeared after 1960 and increased in frequency thereafter. Among the genes near these loci were gibberellic acid insensitive (GAI) and GRAS transcription factor (GIBBERELLIC-ACID INSENSITIVE (GAI), REPRESSOR of GAI (RGA), and SCARECROW (SCR)). The evidence from this study and previous reports suggests that QPLH-2D is Rht8. A gene encoding a GRAS transcription factor is located near QPLH-2D. Validation of the QPLH-2D locus and associated candidate genes awaits further study.}, number={2}, journal={CROP JOURNAL}, author={Daba, Sintayehu D. and Tyagi, Priyanka and Brown-Guedira, Gina and Mohammadi, Mohsen}, year={2020}, month={Apr}, pages={243–251} }
 @article{kuzay_xu_zhang_katz_pearce_su_fraser_anderson_brown-guedira_dewitt_et al._2019, title={Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping}, volume={132}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-019-03382-5}, abstractNote={A high-resolution genetic map combined with haplotype analyses identified a wheat ortholog of rice gene APO1 as the best candidate gene for a 7AL locus affecting spikelet number per spike. A better understanding of the genes controlling differences in wheat grain yield components can accelerate the improvements required to satisfy future food demands. In this study, we identified a promising candidate gene underlying a quantitative trait locus (QTL) on wheat chromosome arm 7AL regulating spikelet number per spike (SNS). We used large heterogeneous inbred families ( > 10,000 plants) from two crosses to map the 7AL QTL to an 87-kb region (674,019,191-674,106,327 bp, RefSeq v1.0) containing two complete and two partial genes. In this region, we found three major haplotypes that were designated as H1, H2 and H3. The H2 haplotype contributed the high-SNS allele in both H1 × H2 and H2 × H3 segregating populations. The ancestral H3 haplotype is frequent in wild emmer (48%) but rare (~ 1%) in cultivated wheats. By contrast, the H1 and H2 haplotypes became predominant in modern cultivated durum and common wheat, respectively. Among the four candidate genes, only TraesCS7A02G481600 showed a non-synonymous polymorphism that differentiated H2 from the other two haplotypes. This gene, designated here as WHEAT ORTHOLOG OF APO1 (WAPO1), is an ortholog of the rice gene ABERRANT PANICLE ORGANIZATION 1 (APO1), which affects spikelet number. Taken together, the high-resolution genetic map, the association between polymorphisms in the different mapping populations with differences in SNS, and the known role of orthologous genes in other grass species suggest that WAPO-A1 is the most likely candidate gene for the 7AL SNS QTL among the four genes identified in the candidate gene region.}, number={9}, journal={THEORETICAL AND APPLIED GENETICS}, author={Kuzay, Saarah and Xu, Yunfeng and Zhang, Junli and Katz, Andrew and Pearce, Stephen and Su, Zhenqi and Fraser, Max and Anderson, James A. and Brown-Guedira, Gina and DeWitt, Noah and et al.}, year={2019}, month={Sep}, pages={2689–2705} }
 @article{ward_brown-guedira_tyagi_kolb_van sanford_sneller_griffey_2019, title={Multienvironment and Multitrait Genomic Selection Models in Unbalanced Early-Generation Wheat Yield Trials}, volume={59}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2018.03.0189}, abstractNote={The majority of studies evaluating genomic selection (GS) for plant breeding have used single‐trait, single‐site models that ignore genotype × environment interaction (GEI) effects. However, such studies do not accurately reflect the complexities of many applied breeding programs, and previous papers have found that models that incorporate GEI effects and multiple traits can increase the accuracy of genomic estimated breeding values (GEBVs). This study's goal was to test GS methods for prediction in scenarios that simulate early‐generation yield testing by correcting for field spatial variation, and fitting multienvironment and multitrait models on data for 14 traits of varying heritability evaluated in unbalanced designs across four environments. Corrections for spatial variation increased across‐environment trait heritability by 25%, on average, but had little effect on model predictive ability. Results between all models were generally equivalent when predicting the performance of newly introduced genotypes. However, models incorporating GEI information and multiple traits increased prediction accuracy by up to 9.6% for low‐heritability traits when phenotypic data were sparsely collected across environments. The results suggest that GS models using multiple traits and incorporating GEI effects may best be suited to predicting line performance in new environments when phenotypic data have already been collected across a subset of the total testing environments.}, number={2}, journal={CROP SCIENCE}, author={Ward, Brian P. and Brown-Guedira, Gina and Tyagi, Priyanka and Kolb, Frederic L. and Van Sanford, David A. and Sneller, Clay H. and Griffey, Carl A.}, year={2019}, pages={491–507} }
 @article{dewitt_guedira_lauer_sarinelli_tyagi_fu_hao_murphy_marshall_akhunova_et al._2020, title={Sequence-based mapping identifies a candidate transcription repressor underlying awn suppression at the B1 locus in wheat}, volume={225}, ISSN={["1469-8137"]}, DOI={10.1111/nph.16152}, abstractNote={Summary


Awns are stiff, hair‐like structures which grow from the lemmas of wheat (Triticum aestivum) and other grasses that contribute to photosynthesis and play a role in seed dispersal. Variation in awn length in domesticated wheat is controlled primarily by three major genes, most commonly the dominant awn suppressor Tipped1 (B1). This study identifies a transcription repressor responsible for awn inhibition at the B1 locus.

Association mapping was combined with analysis in biparental populations to delimit B1 to a distal region of 5AL colocalized with QTL for number of spikelets per spike, kernel weight, kernel length, and test weight.

Fine‐mapping located B1 to a region containing only two predicted genes, including C2H2 zinc finger transcriptional repressor TraesCS5A02G542800 upregulated in developing spikes of awnless individuals. Deletions encompassing this candidate gene were present in awned mutants of an awnless wheat. Sequence polymorphisms in the B1 coding region were not observed in diverse wheat germplasm whereas a nearby polymorphism was highly predictive of awn suppression.

Transcriptional repression by B1 is the major determinant of awn suppression in global wheat germplasm. It is associated with increased number of spikelets per spike and decreased kernel size.

}, number={1}, journal={NEW PHYTOLOGIST}, author={DeWitt, Noah and Guedira, Mohammed and Lauer, Edwin and Sarinelli, Martin and Tyagi, Priyanka and Fu, Daolin and Hao, QunQun and Murphy, J. Paul and Marshall, David and Akhunova, Alina and et al.}, year={2020}, month={Jan}, pages={326–339} }
 @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{beyer_daba_tyagi_bockelman_brown-guedira_mohammadi_2019, title={Loci and candidate genes controlling root traits in wheat seedlingsa wheat root GWAS}, volume={19}, ISSN={["1438-7948"]}, DOI={10.1007/s10142-018-0630-z}, abstractNote={Two hundred one hexaploid wheat accessions, representing 200 years of selection and breeding history, were sampled from the National Small Grains Collection in Aberdeen, ID, and evaluated for five root traits at the seedling stage. A paper roll-supported hydroponic system was used for seedling growth. Replicated roots samples were analyzed by WinRHIZO. We observed accessions with nearly no branching and accessions with up to 132 cm of branching. Total seminal root length ranged from 70 to 248 cm, a 3.5-fold difference. Next-generation sequencing was used to produce single-nucleotide polymorphism (SNP) markers and genomic libraries that were aligned to the wheat reference genome IWGSCv1 and were called single-nucleotide polymorphism (SNP) markers. After filtering and imputation, a total of 20,881 polymorphic sites were used to perform association mapping in TASSEL. Gene annotations were conducted for identified marker-trait associations (MTAs) with - log 10 P > 3.5 (p value < 0.003). In total, we identified 63 MTAs with seven for seminal axis root length (SAR), 24 for branching (BR), four for total seminal root length (TSR), eight for root dry matter (RDM), and 20 for root diameter (RD). Putative proteins of interest that we identified include chalcone synthase, aquaporin, and chymotrypsin inhibitor for SAR, MYB transcription factor and peroxidase for BR, zinc fingers and amino acid transporters for RDM, and cinnamoyl-CoA reductase for RD. We evaluated the effects of height-reducing Rht alleles and the 1B/1R translocation event on root traits and found presence of the Rht-B1b allele decreased RDM, while presence of the Rht-D1b allele increased TSR and decreased RD.}, number={1}, journal={FUNCTIONAL & INTEGRATIVE GENOMICS}, author={Beyer, Savannah and Daba, Sintayehu and Tyagi, Priyanka and Bockelman, Harold and Brown-Guedira, Gina and Mohammadi, Mohsen}, year={2019}, month={Jan}, pages={91–107} }
 @article{case_bhavani_macharia_pretorius_coetzee_kloppers_tyagi_brown-guedira_steffenson_2018, title={Mapping adult plant stem rust resistance in barley accessions Hietpas-5 and GAW-79}, volume={131}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-018-3149-8}, abstractNote={Key message Major stem rust resistance QTLs proposed to be Rpg2 from Hietpas-5 and Rpg3 from GAW-79 were identified in chromosomes 2H and 5H, respectively, and will enhance the diversity of stem rust resistance in barley improvement programs. Stem rust is a devastating disease of cereal crops worldwide. In barley (Hordeum vulgare ssp. vulgare), the disease is caused by two pathogens: Puccinia graminis f. sp. secalis (Pgs) and Puccinia graminis f. sp. tritici (Pgt). In North America, the stem rust resistance gene Rpg1 has protected barley from serious losses for more than 60 years; however, widely virulent Pgt races from Africa in the Ug99 group threaten the crop. The accessions Hietpas-5 (CIho 7124) and GAW-79 (PI 382313) both possess moderate-to-high levels of adult plant resistance to stem rust and are the sources of the resistance genes Rpg2 and Rpg3, respectively. To identify quantitative trait loci (QTL) for stem rust resistance in Hietpas-5 and GAW-79, two biparental populations were developed with Hiproly (PI 60693), a stem rust-susceptible accession. Both populations were phenotyped to the North American Pgt races of MCCFC, QCCJB, and HKHJC in St. Paul, Minnesota, and to African Pgt races (predominately TTKSK in the Ug99 group) in Njoro, Kenya. In the Hietpas-5/Hiproly population, a major effect QTL was identified in chromosome 2H, which is proposed as the location for Rpg2. In the GAW-79/Hiproly population, a major effect QTL was identified in chromosome 5H and is the proposed location for Rpg3. These QTLs will enhance the diversity of stem rust resistance in barley improvement programs.}, number={10}, journal={THEORETICAL AND APPLIED GENETICS}, author={Case, Austin J. and Bhavani, Sridhar and Macharia, Godwin and Pretorius, Zacharias and Coetzee, Vicky and Kloppers, Frederik and Tyagi, Priyanka and Brown-Guedira, Gina and Steffenson, Brian J.}, year={2018}, month={Oct}, pages={2245–2266} }
 @article{case_bhavani_macharia_pretorius_coetzee_kloppers_tyagi_brown-guedira_steffenson_2018, title={Mapping adult plant stem rust resistance in barley accessions Hietpas-5 and GAW-79 (vol 131, pg 2245, 2018)}, volume={131}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-018-3170-y}, abstractNote={Unfortunately, one co-author name was incorrectly published in the original publication. The complete correct name should read as follows.}, number={10}, journal={THEORETICAL AND APPLIED GENETICS}, author={Case, Austin J. and Bhavani, Sridhar and Macharia, Godwin and Pretorius, Zacharias and Coetzee, Vicky and Kloppers, Frederik and Tyagi, Priyanka and Brown-Guedira, Gina and Steffenson, Brian J.}, year={2018}, month={Oct}, pages={2267–2267} }
 @article{kippes_guedira_lin_alvarez_brown-guedira_dubcovsky_2018, title={Single nucleotide polymorphisms in a regulatory site of VRN-A1 first intron are associated with differences in vernalization requirement in winter wheat}, volume={293}, ISSN={["1617-4623"]}, DOI={10.1007/s00438-018-1455-0}, abstractNote={Winter wheats require a long exposure to cold temperatures (vernalization) to accelerate flowering. However, varieties differ in the length of the period of cold required to saturate the vernalization response. Here we show that single nucleotide polymorphisms (SNP) at the binding site of the GRP2 protein in the VRN-A1 first intron (henceforth, RIP3) are associated with significant differences in heading time after a partial vernalization treatment. The ancestral winter VRN-A1 allele in 'Triple Dirk C' has one SNP in the RIP3 region (1_SNP) relative to the canonical RIP3 sequence, whereas the derived 'Jagger' allele has three SNPs (3_SNPs). Both varieties have a single VRN-A1 copy encoding identical proteins. In an F2 population generated from a cross between these two varieties, plants with the 3_SNPs haplotype headed significantly earlier (P < 0.001) than those with the 1_SNP haplotype, both in the absence of vernalization (17 days difference) and after 3-weeks of vernalization (11 days difference). Plants with the 3_SNPs haplotype showed higher VRN-A1 transcript levels than those with the 1_SNP haplotype. The 3_SNPs haplotype was also associated with early heading in a panel of 127 winter wheat varieties grown in three separate controlled-environment experiments under partial vernalization (36 to 54 days, P < 0.001) and one experiment under field conditions (21 d, P < 0.0001). The RIP3 polymorphisms can be used by wheat breeders to develop winter wheat varieties adapted to regions with different duration or intensity of the cold season.}, number={5}, journal={MOLECULAR GENETICS AND GENOMICS}, author={Kippes, Nestor and Guedira, Mohammed and Lin, Lijuan and Alvarez, Maria A. and Brown-Guedira, Gina L. and Dubcovsky, Jorge}, year={2018}, month={Oct}, pages={1231–1243} }
 @article{huang_ward_griffey_van sanford_mckendry_brown-guedira_tyagi_sneller_2018, title={The Accuracy of Genomic Prediction between Environments and Populations for Soft Wheat Traits}, volume={58}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2017.10.0638}, abstractNote={Genomic selection (GS) uses training population (TP) data to estimate the value of lines in a selection population. In breeding, the TP and selection population are often grown in different environments, which can cause low prediction accuracy when the correlation of genetic effects between the environments is low. Subsets of TP data may be more predictive than using all TP data. Our objectives were (i) to evaluate the effect of using subsets of TP data on GS accuracy between environments, and (ii) to assess the accuracy of models incorporating marker × environment interaction (MEI). Two wheat (Triticum aestivum L.) populations were phenotyped for 11 traits in independent environments and genotyped with single‐nucleotide polymorphism markers. Within each population–trait combination, environments were clustered. Data from one cluster were used as the TP to predict the value of the same lines in the other cluster(s) of environments. Models were built using all TP data or subsets of markers selected for their effect and stability. The GS accuracy using all TP data was >0.25 for 9 of 11 traits. The between‐environment accuracy was generally greatest using a subset of stable and significant markers; accuracy increased up to 48% relative to using all TP data. We also assessed accuracy using each population as the TP and the other as the selection population. Using subsets of TP data or the MEI models did not improve accuracy between populations. Using optimized subsets of markers within a population can improve GS accuracy by reducing noise in the prediction data set.}, number={6}, journal={CROP SCIENCE}, author={Huang, Mao and Ward, Brian and Griffey, Carl and Van Sanford, David and McKendry, Anne and Brown-Guedira, Gina and Tyagi, Priyanka and Sneller, Clay}, year={2018}, pages={2274–2288} }
 @article{mason_addison_babar_acuna_lozada_subramanian_arguello_miller_brown-guedira_guedira_et al._2018, title={Diagnostic Markers for Vernalization and Photoperiod Loci Improve Genomic Selection for Grain Yield and Spectral Reflectance in Wheat}, volume={58}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2017.06.0348}, abstractNote={ABSTRACTThe objective of this study was to identify quantitative trait loci (QTL) associated with normalized difference vegetation index (NDVI) measured across different growth stages in a wheat (Triticum aestivum L.) recombinant inbred line (RIL) population and to determine the predictability of NDVI and grain yield (GY) using a genomic selection (GS) approach. The RILs were grown over three seasons in 12 total site‐years and NDVI was measured in seven site‐years. Measurements of NDVI from tillering to physiological maturity showed low to moderate heritability (h2 = 0.06–0.68). Positive correlations were observed among NDVI, GY, and biomass, particularly in low‐yielding site‐years. Quantitative trait loci analysis found 18 genomic regions associated with NDVI, with most pleiotropic across multiple growth stages. The QTL were detected near markers for Ppd‐B1, Ppd‐D1, vrn‐A1, and vrn‐B1, with Ppd‐D1 having the largest effect. Multiple QTL models showed that epistatic interactions between Ppd and Vrn loci also significantly influenced NDVI. Genomic selection accuracy ranged from r = −0.10 to 0.54 for NDVI across growth stages. However, the inclusion of Vrn and Ppd loci as fixed effect covariates increased GS accuracy for NDVI and GY in site‐year groupings with the lowest heritability. The highest accuracy for GY (r = 0.58–0.59) was observed in the site‐year grouping with the highest heritability (h2 = 0.85). Overall, these results will aid in future selection of optimal plant growth for target environments using both phenotypic and GS approaches.}, number={1}, journal={CROP SCIENCE}, author={Mason, R. Esten and Addison, Christopher K. and Babar, Ali and Acuna, Andrea and Lozada, Dennis and Subramanian, Nithya and Arguello, Maria Nelly and Miller, Randall G. and Brown-Guedira, Gina and Guedira, Mohammed and et al.}, year={2018}, pages={242–252} }
 @article{yada_brown-guedira_alajo_ssemakula_owusu-mensah_carey_mwanga_yencho_2017, title={Genetic analysis and association of simple sequence repeat markers with storage root yield, dry matter, starch and β-carotene content in sweetpotato}, volume={67}, ISSN={1344-7610 1347-3735}, url={http://dx.doi.org/10.1270/jsbbs.16089}, DOI={10.1270/jsbbs.16089}, abstractNote={Molecular markers are needed for enhancing the development of elite sweetpotato (Ipomoea batatas (L.) Lam) cultivars with a wide range of commercially important traits in sub-Saharan Africa. This study was conducted to estimate the heritability and determine trait correlations of storage root yield, dry matter, starch and β-carotene content in a cross between ‘New Kawogo’ × ‘Beauregard’. The study was also conducted to identify simple sequence repeat (SSR) markers associated with these traits. A total of 287 progeny and the parents were evaluated for two seasons at three sites in Uganda and genotyped with 250 SSR markers. Broad sense heritability (H2) for storage root yield, dry matter, starch and β-carotene content were 0.24, 0.68, 0.70 and 0.90, respectively. Storage root β-carotene content was negatively correlated with dry matter (r = −0.59, P < 0.001) and starch (r = −0.93, P < 0.001) content, while storage root yield was positively correlated with dry matter (r = 0.57, P = 0.029) and starch (r = 0.41, P = 0.008) content. Through logistic regression, a total of 12, 4, 6 and 8 SSR markers were associated with storage root yield, dry matter, starch and β-carotene content, respectively. The SSR markers used in this study may be useful for quantitative trait loci analysis and selection for these traits in future.}, number={2}, journal={Breeding Science}, publisher={Japanese Society of Breeding}, author={Yada, Benard and Brown-Guedira, Gina and Alajo, Agnes and Ssemakula, Gorrettie N. and Owusu-Mensah, Eric and Carey, Edward E. and Mwanga, Robert O.M. and Yencho, G. Craig}, year={2017}, pages={140–150} }
 @article{yada_alajo_ssemakula_brown-guedira_otema_stevenson_mwanga_yencho_2017, title={Identification of simple sequence repeat markers for sweetpotato weevil resistance}, volume={213}, ISSN={["1573-5060"]}, DOI={10.1007/s10681-017-1917-1}, abstractNote={AbstractThe development of sweetpotato [Ipomoea batatas (L.) Lam] germplasm with resistance to sweetpotato weevil (SPW) requires an understanding of the biochemical and genetic mechanisms of resistance to optimize crop resistance. The African sweetpotato landrace, ‘New Kawogo’, was reported to be moderately resistant to two species of SPW, Cylas puncticollis and Cylas brunneus. Resistance has been associated with the presence of hydroxycinnamic acids esters (HCAs), but the underlying genetic basis remains unknown. To determine the genetic basis of this resistance, a bi-parental sweetpotato population from a cross between the moderately resistant, white-fleshed ‘New Kawogo’ and the highly susceptible, orange-fleshed North American variety ‘Beauregard’ was evaluated for SPW resistance and genotyped with simple sequence repeat (SSR) markers to identify weevil resistance loci. SPW resistance was measured on the basis of field storage root SPW damage severity and total HCA ester concentrations. Moderate broad sense heritability (H2 = 0.49) was observed for weevil resistance in the population. Mean genotype SPW severity scores ranged from 1.0 to 9.0 and 25 progeny exhibited transgressive segregation for SPW resistance. Mean genotype total HCA ester concentrations were significantly different (P < 0.0001). A weak but significant correlation (r = 0.103, P = 0.015) was observed between total HCA ester concentration and SPW severity. A total of five and seven SSR markers were associated with field SPW severity and total HCA ester concentration, respectively. Markers IBS11, IbE5 and IbJ544b showed significant association with both field and HCA-based resistance, representing potential markers for the development of SPW resistant sweetpotato cultivars.}, number={6}, journal={Euphytica}, publisher={Springer Nature}, author={Yada, B. and Alajo, A. and Ssemakula, G. N. and Brown-Guedira, G. and Otema, M. A. and Stevenson, P. C. and Mwanga, R. O. M. and Yencho, G. C.}, year={2017}, pages={129} }
 @article{yada_alajo_ssemakula_mwanga_brown-guedira_yencho_2017, title={Selection of simple sequence repeat markers associated with inheritance of sweetpotato virus disease resistance in sweetpotato}, volume={57}, DOI={10.2135/cropsci2016.08.0695}, abstractNote={Sweetpotato virus disease (SPVD), a complex of Sweet potato chlorotic stunt virus (SPCSV; Crinivirus) and Sweet potato feathery mottle virus (SPFMV; Potyvirus) causes high yield losses in sub‐Saharan Africa (SSA). The development of resistant cultivars to SPVD has been limited by the complex sweetpotato [Ipomoea batatas (L.) Lam. var. batatas] genetics and high levels of mutations in the causal viruses. The objectives of this study were to understand the inheritance of SPVD resistance and identify simple‐sequence repeat (SSR) markers associated with its resistance in a biparental sweetpotato mapping population. A total of 287 progeny and parents of the ‘New Kawogo’ × ‘Beauregard’ population were genotyped with 250 SSR markers and phenotyped for SPVD resistance at three sites and two seasons in Uganda. The broad‐sense heritability for SPVD resistance was 0.51. Two progeny showed positive transgressive segregation for overall genotype mean SPVD severity across sites and seasons. A total of seven SSR markers were significantly associated with SPVD resistance in this population. These markers and other SSRs need to be used to fine map the quantitative trait loci (QTL) of SPVD resistance for future implementation of marker‐assisted selection (MAS) for SPVD resistance in sweetpotato.}, number={3}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Yada, B. and Alajo, A. and Ssemakula, G. N. and Mwanga, R. O. M. and Brown-Guedira, G. and Yencho, G. C.}, year={2017}, pages={1421–1430} }
 @article{nice_steffenson_brown-guedira_akhunov_liu_kono_morrell_blake_horsley_smith_et al._2016, title={Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild x Cultivated Barley}, volume={203}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.116.190736}, abstractNote={Abstract
               The ability to access alleles from unadapted germplasm collections is a long-standing problem for geneticists and breeders. Here we developed, characterized, and demonstrated the utility of a wild barley advanced backcross-nested association mapping (AB-NAM) population. We developed this population by backcrossing 25 wild barley accessions to the six-rowed malting barley cultivar Rasmusson. The 25 wild barley parents were selected from the 318 accession Wild Barley Diversity Collection (WBDC) to maximize allelic diversity. The resulting 796 BC2F4:6 lines were genotyped with 384 SNP markers, and an additional 4022 SNPs and 263,531 sequence variants were imputed onto the population using 9K iSelect SNP genotypes and exome capture sequence of the parents, respectively. On average, 96% of each wild parent was introgressed into the Rasmusson background, and the population exhibited low population structure. While linkage disequilibrium (LD) decay (r2 = 0.2) was lowest in the WBDC (0.36 cM), the AB-NAM (9.2 cM) exhibited more rapid LD decay than comparable advanced backcross (28.6 cM) and recombinant inbred line (32.3 cM) populations. Three qualitative traits: glossy spike, glossy sheath, and black hull color were mapped with high resolution to loci corresponding to known barley mutants for these traits. Additionally, a total of 10 QTL were identified for grain protein content. The combination of low LD, negligible population structure, and high diversity in an adapted background make the AB-NAM an important tool for high-resolution gene mapping and discovery of novel allelic variation using wild barley germplasm.}, number={3}, journal={GENETICS}, author={Nice, Liana M. and Steffenson, Brian J. and Brown-Guedira, Gina L. and Akhunov, Eduard D. and Liu, Chaochih and Kono, Thomas J. Y. and Morrell, Peter L. and Blake, Thomas K. and Horsley, Richard D. and Smith, Kevin P. and et al.}, year={2016}, month={Jul}, pages={1453-+} }
 @article{guedira_xiong_hao_johnson_harrison_marshall_brown-guedira_2016, title={Heading Date QTL in Winter Wheat (Triticum aestivum L.) Coincide with Major Developmental Genes VERNALIZATION1 and PHOTOPERIOD1}, volume={11}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0154242}, abstractNote={In wheat (Triticum aestivum L.), time from planting to spike emergence is influenced by genes controlling vernalization requirement and photoperiod response. Characterizing the available genetic diversity of known and novel alleles of VERNALIZATION1 (VRN1) and PHOTOPERIOD1 (PPD1) in winter wheat can inform approaches for breeding climate resilient cultivars. This study identified QTL for heading date (HD) associated with multiple VRN1 and PPD1 loci in a population developed from a cross between two early flowering winter wheat cultivars. When the population was grown in the greenhouse after partial vernalization treatment, major heading date QTLs co-located with the VRN-A1 and VRN-B1 loci. Copy number variation at the VRN-A1 locus influenced HD such that RIL having three copies required longer cold exposure to transition to flowering than RIL having two VRN-A1 copies. Sequencing vrn-B1 winter alleles of the parents revealed multiple polymorphisms in the first intron that were the basis of mapping a major HD QTL coinciding with VRN-B1. A 36 bp deletion in the first intron of VRN-B1 was associated with earlier HD after partial vernalization in lines having either two or three haploid copies of VRN-A1. The VRN1 loci interacted significantly and influenced time to heading in field experiments in Louisiana, Georgia and North Carolina. The PPD1 loci were significant determinants of heading date in the fully vernalized treatment in the greenhouse and in all field environments. Heading date QTL were associated with alleles having large deletions in the upstream regions of PPD-A1 and PPD-D1 and with copy number variants at the PPD-B1 locus. The PPD-D1 locus was determined to have the largest genetic effect, followed by PPD-A1 and PPD-B1. Our results demonstrate that VRN1 and PPD1 alleles of varying strength allow fine tuning of flowering time in diverse winter wheat growing environments.}, number={5}, journal={PLOS ONE}, author={Guedira, Mohammed and Xiong, Mai and Hao, Yuan Feng and Johnson, Jerry and Harrison, Steve and Marshall, David and Brown-Guedira, Gina}, year={2016}, month={May} }
 @article{petersen_lyerly_maloney_brown-guedira_cowger_costa_dong_murphy_2016, title={Mapping of Fusarium Head Blight Resistance Quantitative Trait Loci in Winter Wheat Cultivar NC-Neuse}, volume={56}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2015.05.0312}, abstractNote={Fusarium head blight (FHB), primarily caused by Fusarium graminearum, can significantly reduce the grain quality of wheat (Triticum aestivum L.) due to mycotoxin contamination. The objective of this study was to identify quantitative trait loci (QTL) for FHB resistance in the moderately resistant soft red winter wheat cultivar NC‐Neuse. A total of 170 recombinant inbred lines (RILs) from a cross between NC‐Neuse and the susceptible cultivar AGS 2000 were evaluated in inoculated, mist‐irrigated field nurseries. The lines were evaluated for FHB incidence (INC), severity (SEV), Fusarium‐damaged kernels (FDK), and deoxynivalenol (DON) content in seven environments between 2011 and 2014. A 3,419 cM linkage map was developed based on 1839 simple sequence repeat (SSR), diversity array technology (DArT), and single nucleotide polymorphism (SNP) markers. Seven FHB resistance QTL on chromosomes 1A, 1B, 1D, 2A, 4A, 5B, and 6A were mapped. The QTL alleles conferring resistance on 1A, 1B, 2A, 4A, and 6A originated from NC‐Neuse, while the alleles associated with resistance on 1D and 5B originated from AGS 2000. Quantitative trait loci effects ranged from 9 to 12% for INC, from 6 to 11% for SEV, from 8 to 20% for FDK, and from 6 to 18% for DON. The QTL on 5B co‐localized with the Vrn‐B1 locus. Kompetitive Allele‐Specific PCR (KASP) assays were developed for each NC‐Neuse QTL region. A preliminary test using these assays on recent Uniform Southern Winter Wheat Nursery (USWWN) entries indicated Qfhb.nc‐1A, Qfhb.nc‐1B, and Qfhb.nc‐6A as likely the best candidates for use in marker‐assisted selection.}, number={4}, journal={CROP SCIENCE}, author={Petersen, Stine and Lyerly, Jeanette H. and Maloney, Peter V. and Brown-Guedira, Gina and Cowger, Christina and Costa, Jose M. and Dong, Yanhong and Murphy, J. Paul}, year={2016}, pages={1473–1483} }
 @article{addison_mason_brown-guedira_guedira_hao_miller_subramanian_lozada_acuna_arguello_et al._2016, title={QTL and major genes influencing grain yield potential in soft red winter wheat adapted to the southern United States}, volume={209}, ISSN={["1573-5060"]}, DOI={10.1007/s10681-016-1650-1}, number={3}, journal={EUPHYTICA}, author={Addison, Christopher K. and Mason, R. Esten and Brown-Guedira, Gina and Guedira, Mohammed and Hao, Yuanfeng and Miller, Randall G. and Subramanian, Nithya and Lozada, Dennis N. and Acuna, Andrea and Arguello, Maria N. and et al.}, year={2016}, month={Jun}, pages={665–677} }
 @article{petersen_lyerly_mckendry_islam_brown-guedira_cowger_dong_murphy_2017, title={Validation of Fusarium Head Blight Resistance QTL in US Winter Wheat}, volume={57}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2015.07.0415}, abstractNote={Fusarium head blight (FHB), primarily caused by Fusarium graminearum Schwabe [telemorph: Gibberella zeae Schw. (Petch)], can significantly reduce the grain quality of wheat (Triticum aestivum L.) due to mycotoxin contamination. Two US soft red winter wheat cultivars, Bess and NC‐Neuse, have moderate resistance to FHB. The objective of this study was to validate genomic regions associated with FHB resistance identified in previous studies involving NC‐Neuse and the cultivar Truman, a full‐sib of Bess. A total of 98 doubled haploid lines derived from the cross Bess × NC‐Neuse were evaluated in inoculated, mist‐irrigated field nurseries. The lines were evaluated for FHB incidence, severity, Fusarium‐damaged kernels, and deoxynivalenol content in seven environments between 2011 and 2014. A 3338‐cM linkage map was developed based on 4014 simple sequence repeat and single nucleotide polymorphism markers. Twelve quantitative trait loci (QTL) associated with FHB resistance were identified. NC‐Neuse alleles provided resistance at QTL on five chromosomes and Bess alleles provided resistance at QTL on five other chromosomes. Alignment of linkage maps revealed that five of these QTL were overlapping with previously identified regions. Quantitative trait loci on chromosomes 1A, 4A, and 6A identified in this study overlapped with QTL regions identified in NC‐Neuse, and QTL identified on chromosomes 2B and 3B overlapped with QTL regions identified in Truman. A preliminary test using Kompetitive Allele‐Specific polymerase chain reaction assays on recent Uniform Southern Winter Wheat Scab Nursery entries showed that the assays developed for Qfhb.nc‐2B.1 may be good candidates for use in marker‐assisted selection.}, number={1}, journal={CROP SCIENCE}, author={Petersen, Stine and Lyerly, Jeanette H. and McKendry, Anne L. and Islam, M. Sariful and Brown-Guedira, Gina and Cowger, Christina and Dong, Yanhong and Murphy, J. Paul}, year={2017}, pages={1–12} }
 @article{milus_lee_brown-guedira_2015, title={Characterization of Stripe Rust Resistance in Wheat Lines with Resistance Gene Yr17 and Implications for Evaluating Resistance and Virulence}, volume={105}, ISSN={["1943-7684"]}, DOI={10.1094/phyto-11-14-0304-r}, abstractNote={ Stripe rust, caused by Puccinia striiformis f. sp. tritici, has been the most important foliar wheat disease in south central United States since 2000 when a new strain of the pathogen emerged. The resistance gene Yr17 was used by many breeding programs to develop resistant cultivars. Although Yr17 was classified as a seedling (all-stage) resistance gene conferring a low infection type, seedlings with Yr17 frequently had intermediate to high infection types when inoculated with isolates that caused little or no disease on adult plants of the same wheat lines. The objectives of this study were to determine how to best evaluate Yr17 resistance in wheat lines and to determine which factors made seedling tests involving Yr17 so variable. Stripe rust reactions on wheat seedlings with Yr17 were influenced by temperature, wheat genotype, pathogen isolate, and the leaf (first or second) used to assess the seedling reaction. The most critical factors for accurately evaluating Yr17 reactions at the seedling stage were to avoid night temperatures below 12°C, to use the first leaf to assess the seedling reaction, to use multiple differentials with Yr17 and known avirulent, partially virulent and virulent isolates as controls, and to recognize that intermediate infection types likely represent a level of partial virulence in the pathogen that is insufficient to cause disease on adult plants in the field. }, number={8}, journal={PHYTOPATHOLOGY}, author={Milus, Eugene A. and Lee, Kevin D. and Brown-Guedira, Gina}, year={2015}, month={Aug}, pages={1123–1130} }
 @article{subramanian_mason_milus_moon_brown-guedira_2016, title={Characterization of Two Adult-Plant Stripe Rust Resistance Genes on Chromosomes 3BS and 4BL in Soft Red Winter Wheat}, volume={56}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2015.01.0043}, abstractNote={ABSTRACTStripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst), is an important foliar disease of soft red winter wheat (SRWW) (Triticum aestivum L.) in the eastern United States. However, very few resistance genes have been characterized in the SRWW germplasm pool. The SRWW line VA96W‐270 is known to be resistant to stripe rust race PST‐100, which was the predominant race in the United States from 2003 to 2006. To elucidate the genetic basis of resistance, a recombinant inbred line (RIL) population developed from a cross between VA96W‐270 and the susceptible cultivar Coker 9835 was evaluated for response to stripe rust infection in inoculated field nurseries over a 3‐yr period. The RIL population was then genotyped with stripe rust‐linked simple sequence repeat (SSR) markers and 90K single‐nucleotide polymorphism (SNP) markers. Two major quantitative trait loci (QTL) were identified, located on chromosomes 3BS and 4BL, both contributed by VA96W‐270. The 3BS and 4BL QTL explained up to 28 and 25% of the phenotypic variation for area under disease pressure curve (AUDPC), respectively. Recombinant inbred lines containing both QTL had average disease severity of 6%, compared with 38 to 45% for lines containing one of the two QTL and 69% for those containing neither QTL. Based on susceptibility of VA96W‐270 to infection at the seedling stage, the two genes appear to be associated with adult‐plant resistance. Markers associated with the two QTL were polymorphic in various wheat genotypes, suggesting they could be useful in marker‐assisted selection (MAS) to develop wheat cultivars with improved stripe rust resistance.}, number={1}, journal={CROP SCIENCE}, author={Subramanian, Nithya K. and Mason, Richard Esten and Milus, Eugene A. and Moon, David E. and Brown-Guedira, Gina}, year={2016}, pages={143–153} }
 @article{kumssa_baenziger_rouse_guttieri_dweikat_brown-guedira_williamson_graybosch_wegulo_lorenz_et al._2015, title={Characterization of stem rust resistance in wheat cultivar gage}, volume={55}, number={1}, journal={Crop Science}, author={Kumssa, T. T. and Baenziger, P. S. and Rouse, M. N. and Guttieri, M. and Dweikat, I. and Brown-Guedira, G. and Williamson, S. and Graybosch, R. A. and Wegulo, S. N. and Lorenz, A. J. and et al.}, year={2015}, pages={229–239} }
 @article{bonman_babiker_cuesta-marcos_esvelt-klos_brown-guedira_chao_see_chen_akhunov_zhang_et al._2015, title={Genetic Diversity among Wheat Accessions from the USDA National Small Grains Collection}, volume={55}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2014.09.0621}, abstractNote={ABSTRACTAccessions of common wheat (Triticum aestivum L. subsp. aestivum) from the USDA–ARS National Small Grains Collection (NSGC) are a resource for wheat scientists worldwide. The genetic diversity of the wheat core subset, representing approximately 10% of the collection's 42,138 T. aestivum accessions, was examined using 390 diversity arrays technology (DArT) markers, 4941 single nucleotide polymorphisms (SNPs), and descriptor data. The marker profiles revealed duplicates, which were excluded to form an informative core (iCore) of 3230 accessions. The iCore population structure and diversity within various subgroups were examined with analysis of molecular variance, principal coordinate analysis, cluster analysis, and by ranking the contribution of individual accessions to overall diversity. Accession groups based on molecular marker data corresponded well to their geographic origin, and population structure was accounted for primarily by differences between Iranian landrace accessions and the rest of the accessions. Accessions classified as breeding lines were overrepresented among those ranked as most diverse based on SNP data, whereas Iranian landraces were underrepresented. Although less diverse as a group, Iranian landrace accessions had a higher frequency of resistance to bunt diseases and Russian wheat aphid compared with the iCore as a whole. The present study provides support for establishing core subsets based on geographic origin of accessions and will be a basis for further study of diversity among NSGC wheats.}, number={3}, journal={CROP SCIENCE}, author={Bonman, J. Michael and Babiker, Ebrahiem M. and Cuesta-Marcos, Alfonso and Esvelt-Klos, Kathy and Brown-Guedira, Gina and Chao, Shiaoman and See, Deven and Chen, Jianli and Akhunov, Eduard and Zhang, Junli and et al.}, year={2015}, pages={1243–1253} }
 @article{pauli_brown-guedira_blake_2015, title={Identification of Malting Quality QTLs in Advanced Generation Breeding Germplasm}, volume={73}, ISSN={["1943-7854"]}, DOI={10.1094/asbcj-2015-0129-01}, abstractNote={Malting quality has been one of the primary foci in barley (Hordeum vulgare L.) breeding programs but has been difficult for breeders to manipulate due to the quantitative nature of the traits involved and the cost of trait measurement. To assist in breeding for malt quality traits, identifying the genomic regions that affect these traits is essential. Two populations were used to conduct genome-wide association studies in order to elucidate the alleles responsible for variation in malting traits. The first population, composed of 367 lines genotyped with 3,072 single-nucleotide polymorphism (SNP) markers, was a representative sample of the entire germplasm of the Montana State University barley breeding program, including feed, food, and malt lines. The second population, with 650 lines genotyped with 384 SNPs, consisted of 11 biparental families whose parents were cultivars and elite experimental lines developed strictly for malting purposes. Lines were phenotyped at the United States Department of Agriculture–Agricultural Research Service Cereal Crops Research Unit in Madison, WI. Mixed linear models were applied to the data using a Q+K approach in order to identify single marker–trait associations accounting for population structure and relatedness among lines. Fifty-four significant marker–trait associations were found. The results of this work give a comprehensive overview of the salient regions of the barley genome affecting malting traits that vary within a modern malting barley breeding program.}, number={1}, journal={JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS}, author={Pauli, Duke and Brown-Guedira, Gina and Blake, Thomas K.}, year={2015}, pages={29–40} }
 @article{islam_brown-guedira_van sanford_ohm_dong_mckendry_2016, title={Novel QTL associated with the Fusarium head blight resistance in Truman soft red winter wheat}, volume={207}, ISSN={["1573-5060"]}, DOI={10.1007/s10681-015-1550-9}, number={3}, journal={EUPHYTICA}, author={Islam, Md. Sariful and Brown-Guedira, Gina and Van Sanford, David and Ohm, Herb and Dong, Yanhong and McKendry, Anne L.}, year={2016}, month={Feb}, pages={571–592} }
 @article{yada_brown-guedira_alajo_ssemakula_mwanga_yeneho_2015, title={Simple sequence repeat marker analysis of genetic diversity among progeny of a biparental mapping population of sweetpotato}, volume={50}, number={8}, journal={HortScience}, author={Yada, B. and Brown-Guedira, G. and Alajo, A. and Ssemakula, G. N. and Mwanga, R. O. M. and Yeneho, G. C.}, year={2015}, pages={1143–1147} }
 @article{gurung_mamidi_bonman_xiong_brown-guedira_adhikari_2014, title={Genome-Wide Association Study Reveals Novel Quantitative Trait Loci Associated with Resistance to Multiple Leaf Spot Diseases of Spring Wheat}, volume={9}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0108179}, abstractNote={Accelerated wheat development and deployment of high-yielding, climate resilient, and disease resistant cultivars can contribute to enhanced food security and sustainable intensification. To facilitate gene discovery, we assembled an association mapping panel of 528 spring wheat landraces of diverse geographic origin for a genome-wide association study (GWAS). All accessions were genotyped using an Illumina Infinium 9K wheat single nucleotide polymorphism (SNP) chip and 4781 polymorphic SNPs were used for analysis. To identify loci underlying resistance to the major leaf spot diseases and to better understand the genomic patterns, we quantified population structure, allelic diversity, and linkage disequilibrium. Our results showed 32 loci were significantly associated with resistance to the major leaf spot diseases. Further analysis identified QTL effective against major leaf spot diseases of wheat which appeared to be novel and others that were previously identified by association analysis using Diversity Arrays Technology (DArT) and bi-parental mapping. In addition, several identified SNPs co-localized with genes that have been implicated in plant disease resistance. Future work could aim to select the putative novel loci and pyramid them in locally adapted wheat cultivars to develop broad-spectrum resistance to multiple leaf spot diseases of wheat via marker-assisted selection (MAS).}, number={9}, journal={PLOS ONE}, author={Gurung, Suraj and Mamidi, Sujan and Bonman, J. Michael and Xiong, Mai and Brown-Guedira, Gina and Adhikari, Tika B.}, year={2014}, month={Sep} }
 @article{petersen_lyerly_worthington_parks_cowger_marshall_brown-guedira_murphy_2015, title={Mapping of powdery mildew resistance gene Pm53 introgressed from Aegilops speltoides into soft red winter wheat}, volume={128}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-014-2430-8}, abstractNote={A powdery mildew resistance gene was introgressed from Aegilops speltoides into winter wheat and mapped to chromosome 5BL. Closely linked markers will permit marker-assisted selection for the resistance gene. Powdery mildew of wheat (Triticum aestivum L.) is a major fungal disease in many areas of the world, caused by Blumeria graminis f. sp. tritici (Bgt). Host plant resistance is the preferred form of disease prevention because it is both economical and environmentally sound. Identification of new resistance sources and closely linked markers enable breeders to utilize these new sources in marker-assisted selection as well as in gene pyramiding. Aegilops speltoides (2n = 2x = 14, genome SS), has been a valuable disease resistance donor. The powdery mildew resistant wheat germplasm line NC09BGTS16 (NC-S16) was developed by backcrossing an Ae. speltoides accession, TAU829, to the susceptible soft red winter wheat cultivar 'Saluda'. NC-S16 was crossed to the susceptible cultivar 'Coker 68-15' to develop F2:3 families for gene mapping. Greenhouse and field evaluations of these F2:3 families indicated that a single gene, designated Pm53, conferred resistance to powdery mildew. Bulked segregant analysis showed that multiple simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers specific to chromosome 5BL segregated with the resistance gene. The gene was flanked by markers Xgwm499, Xwmc759, IWA6024 (0.7 cM proximal) and IWA2454 (1.8 cM distal). Pm36, derived from a different wild wheat relative (T. turgidum var. dicoccoides), had previously been mapped to chromosome 5BL in a durum wheat line. Detached leaf tests revealed that NC-S16 and a genotype carrying Pm36 differed in their responses to each of three Bgt isolates. Pm53 therefore appears to be a new source of powdery mildew resistance.}, number={2}, journal={THEORETICAL AND APPLIED GENETICS}, author={Petersen, Stine and Lyerly, Jeanette H. and Worthington, Margaret L. and Parks, Wesley R. and Cowger, Christina and Marshall, David S. and Brown-Guedira, Gina and Murphy, J. Paul}, year={2015}, month={Feb}, pages={303–312} }
 @article{hao_parks_cowger_chen_wang_bland_murphy_guedira_brown-guedira_johnson_et al._2015, title={Molecular characterization of a new powdery mildew resistance gene Pm54 in soft red winter wheat}, volume={128}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-014-2445-1}, abstractNote={A new powdery mildew resistance gene Pm54 was identified on chromosome 6BL in soft red winter wheat. Powdery mildew is causing increasing damage to wheat production in the southeastern USA. To combat the disease, a continuing need exists to discover new genes for powdery mildew resistance and to incorporate those genes into breeding programs. Pioneer(®) variety 26R61 (shortened as 26R61) and AGS 2000 have been used as checks in the Uniform Southern Soft Red Winter Wheat Nursery for a decade, and both have provided good resistance across regions during that time. In the present study, a genetic analysis of mildew resistance was conducted on a RIL population developed from a cross of 26R61 and AGS 2000. Phenotypic evaluation was conducted in the field at Plains, GA, and Raleigh, NC, in 2012 and 2013, a total of four environments. Three quantitative trait loci (QTL) with major effect were consistently detected on wheat chromosomes 2BL, 4A and 6BL. The 2BL QTL contributed by 26R61 was different from Pm6, a widely used gene in the southeastern USA. The other two QTL were identified from AGS 2000. The 6BL QTL was subsequently characterized as a simple Mendelian factor when the population was inoculated with a single Blumeria graminis f. sp. tritici (Bgt) isolate in controlled environments. Since there is no known powdery mildew resistance gene (Pm) on this particular location of common wheat, the gene was designated Pm54. The closely linked marker Xbarc134 was highly polymorphic in a set of mildew differentials, indicating that the marker should be useful for pyramiding Pm54 with other Pm genes by marker-assisted selection.}, number={3}, journal={THEORETICAL AND APPLIED GENETICS}, author={Hao, Y. F. and Parks, R. and Cowger, C. and Chen, Z. B. and Wang, Y. Y. and Bland, D. and Murphy, J. P. and Guedira, M. and Brown-Guedira, Gina and Johnson, J. and et al.}, year={2015}, month={Mar}, pages={465–476} }
 @article{worthington_reberg-horton_brown-guedira_jordan_weisz_murphy_2015, title={Morphological Traits Associated with Weed-Suppressive Ability of Winter Wheat against Italian Ryegrass}, volume={55}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2014.02.0149}, abstractNote={ABSTRACTWeed‐suppressive wheat (Triticum aestivum L.) cultivars have been suggested as a complement to chemical and cultural methods of weed control. The objectives of this study were to assess the range of weed‐suppressive ability against Italian ryegrass [Lolium perenne L. ssp. multiflorum (Lam.) Husnot] existing in winter wheat lines adapted to North Carolina and to identify wheat morphological traits that could facilitate indirect selection for weed suppression in the southeastern United States. Fifty‐three commercially available cultivars and advanced experimental lines were overseeded with a uniform, high rate of Italian ryegrass, evaluated for various morphological traits throughout the growing season, and investigated for weed‐suppressive ability at a total of four field sites. Genotypic differences in Italian ryegrass seed head density (P ≤ 0.05) were detected among the wheat lines. Reduced Italian ryegrass seed head density was correlated (P ≤ 0.05) with high vigor during tillering and heading (Zadoks growth stage [GS] 25, 29, 55), erect growth habit (GS 29), low normalized difference vegetation index (NDVI) (GS 29), high leaf area index (LAI) at stem extension (GS 31), early heading date, and tall height throughout the growing season (GS 29, 31, 55, 70 to 80) in three of four sites. Multiple regression models show that 71% of variation in weed‐suppressive ability was accounted for by final height (GS 70 to 80) and either height or plant vigor at late tillering (GS 29). Thus, breeders could improve weed‐suppressive ability using weighted index selection for genotypes that are tall or vigorous during tillering with tall final height.}, number={1}, journal={CROP SCIENCE}, publisher={Crop Science Society of America}, author={Worthington, Margaret and Reberg-Horton, S. Chris and Brown-Guedira, Gina and Jordan, David and Weisz, Randy and Murphy, J. Paul}, year={2015}, pages={50–56} }
 @article{clark_costa_griffey_brown-guedira_dong_souza_murphy_van sanford_2014, title={Registration of Scab-Resistant KY06C-11-3-10 Soft Red Winter Wheat Germplasm}, volume={8}, ISSN={["1940-3496"]}, DOI={10.3198/jpr2013.07.0039crg}, abstractNote={Copyright © Crop Science Society of America. All rights reserved. No part of this periodical may be reproduced or trans mitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher.}, number={2}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Clark, Anthony J. and Costa, Jose M. and Griffey, Carl A. and Brown-Guedira, Gina L. and Dong, Yanhong and Souza, Edward J. and Murphy, J. Paul and Van Sanford, David A.}, year={2014}, month={May}, pages={211–216} }
 @article{worthington_reberg-horton_brown-guedira_jordan_weisz_murphy_2015, title={Relative Contributions of Allelopathy and Competitive Traits to the Weed Suppressive Ability of Winter Wheat Lines Against Italian Ryegrass}, volume={55}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2014.02.0150}, abstractNote={ABSTRACTAllelopathy and competitive ability have been identified as independent factors contributing to the weed suppressive ability of crop cultivars; however, it is not clear whether these factors have equal influence on weed suppression outcomes of winter wheat (Triticum aestivum L.) lines in the field. Fifty‐eight winter wheat lines adapted to the southeastern United States were screened for allelopathic activity against Italian ryegrass (Lolium perenne L. ssp. multiflorum [Lam.] Husnot) in an agar‐based seedling bioassay. Eight strongly and weakly allelopathic lines were identified and evaluated for weed suppressive ability and grain yield tolerance in a replicated field experiment conducted in North Carolina. Significant genotypic differences in weed suppressive ability were found in three of four study environments, while genotypic differences in yield tolerance were identified in all environments. Although the allelopathic activity of genotypes varied in the seedling bioassay, no correlations between allelopathy and weed suppressive ability or grain yield tolerance were observed. Weed suppressive ability was correlated with competitive traits, including vigor and erect growth habit during tillering (Zadoks GS 29), high leaf area index (LAI) at stem extension (GS 31), plant height at tillering and stem extension (GS 29, 31), grain yield in weedy conditions, and grain yield tolerance. Therefore, breeders in the southeastern United States should focus their efforts on improving competitive traits within adapted germplasm rather than selecting for cultivars with high allelopathic activity to achieve maximum gains in weed suppressive ability against Italian ryegrass.}, number={1}, journal={CROP SCIENCE}, publisher={Crop Science Society of America}, author={Worthington, Margaret and Reberg-Horton, S. Chris and Brown-Guedira, Gina and Jordan, David and Weisz, Randy and Murphy, J. Paul}, year={2015}, pages={57–64} }
 @article{bertucci_brown-guedira_murphy_cowger_2014, title={Genes Conferring Sensitivity to Stagonospora nodorum Necrotrophic Effectors in Stagonospora Nodorum Blotch-Susceptible US Wheat Cultivars}, volume={98}, ISSN={["1943-7692"]}, DOI={10.1094/pdis-08-13-0820-re}, abstractNote={ Stagonospora nodorum is a necrotrophic fungal pathogen that causes Stagonospora nodorum blotch (SNB), a yield- and quality-reducing disease of wheat. S. nodorum produces a set of necrotrophic effectors (NEs) that interact with the products of host sensitivity genes to cause cell death and increased susceptibility to disease. The focus of this study was determination of NE sensitivity among 25 winter wheat cultivars, many of them from the southeastern United States, that are susceptible to SNB, as well as the moderately resistant ‘NC-Neuse’. Thirty-three isolates of S. nodorum previously collected from seven southeastern U.S. states were cultured for NE production, and the culture filtrates were used in an infiltration bioassay. Control strains of Pichia pastoris that expressed SnToxA, SnTox1, or SnTox3 were also used. All SNB-susceptible cultivars were sensitive to at least one NE, while NC-Neuse was insensitive to all NEs tested. Among the sensitive lines, 32% contained sensitivity gene Tsn1 and 64% contained sensitivity gene Snn3. None were sensitive to SnTox1. Additionally, 10 molecular markers for sensitivity genes Tsn1, Snn1, Snn2, and Snn3 were evaluated for diagnostic potential. Only the marker Xfcp623 for Tsn1 was diagnostic, and it was in perfect agreement with the results of the infiltration bioassays. The results illuminate which NE sensitivity genes may be of concern in breeding for resistance to SNB in the southeastern United States. }, number={6}, journal={PLANT DISEASE}, author={Bertucci, Matthew and Brown-Guedira, Gina and Murphy, J. Paul and Cowger, Christina}, year={2014}, month={Jun}, pages={746–753} }
 @article{oliver_tinker_lazo_chao_jellen_carson_rines_obert_lutz_shackelford_et al._2013, title={SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species}, volume={8}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0058068}, abstractNote={A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.}, number={3}, journal={PLOS ONE}, author={Oliver, Rebekah E. and Tinker, Nicholas A. and Lazo, Gerard R. and Chao, Shiaoman and Jellen, Eric N. and Carson, Martin L. and Rines, Howard W. and Obert, Donald E. and Lutz, Joseph D. and Shackelford, Irene and et al.}, year={2013}, month={Mar} }
 @article{hao_wang_chen_bland_li_brown-guedira_johnson_2012, title={A conserved locus conditioning Soil-borne wheat mosaic virus resistance on the long arm of chromosome 5D in common wheat}, volume={30}, ISSN={["1572-9788"]}, DOI={10.1007/s11032-012-9731-x}, number={3}, journal={MOLECULAR BREEDING}, author={Hao, Yuanfeng and Wang, Yingying and Chen, Zhenbang and Bland, Dan and Li, Sishen and Brown-Guedira, Gina and Johnson, Jerry}, year={2012}, month={Oct}, pages={1453–1464} }
 @article{neelam_brown-guedira_huang_2013, title={Development and validation of a breeder-friendly KASPar marker for wheat leaf rust resistance locus Lr21}, volume={31}, ISSN={["1572-9788"]}, DOI={10.1007/s11032-012-9773-0}, number={1}, journal={MOLECULAR BREEDING}, author={Neelam, Kumari and Brown-Guedira, Gina and Huang, Li}, year={2013}, month={Jan}, pages={233–237} }
 @article{maxwell_lyerly_srnic_murphy_cowger_parks_marshall_brown-guedira_miranda_2012, title={MlNCD1: A Novel Aegilops tauschii-Derived Powdery Mildew Resistance Gene Identified in Common Wheat}, volume={52}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2011.11.0582}, abstractNote={ABSTRACTPowdery mildew is a major fungal disease in wheat, especially in cool maritime climates. A novel Aegilops tauschii Coss.‐derived wheat powdery mildew resistance gene present in the germplasm line NC96BGTD1 was genetically characterized as a monogenic trait in field trials using F2– and F4–derived lines from a NC96BGTD1 × ‘Saluda’ cross. Simple sequence repeat (SSR) markers were used to map and tag the resistance gene present in NC96BGTD1. Two dominant SSR markers flanking the resistance gene were identified. Xgwm635 mapped 5.5 and 8.3 cM distal to the resistance gene in the F2 and F4 generations, respectively. Xgpw328 mapped 16.2 cM proximal to the resistance gene in the F2 and 13.6 cM proximal to the resistance gene in the F4 generation. These SSR markers were previously mapped to the short arm of chromosome 7D and their positions were confirmed using Chinese Spring aneuploid and deletion stocks. Significant segregation distortion was observed in the F4 generation with markers distal to the resistance gene showing a preference for the A. tauschii alleles while markers proximal to the resistance gene showed less significant preference for Saluda alleles. Only the adult plant resistance gene Pm38 has been mapped to the short arm of chromosome 7D but to a more proximal position than the gene in NC96BGTD1. The resistance gene described herein should be temporarily designated MlNCD1.}, number={3}, journal={CROP SCIENCE}, author={Maxwell, J. J. and Lyerly, J. H. and Srnic, G. and Murphy, J. P. and Cowger, C. and Parks, R. and Marshall, D. and Brown-Guedira, G. and Miranda, L.}, year={2012}, pages={1162–1170} }
 @article{lewis_siler_ellis_souza_ng_dong_brown-guedira_jiang_ward_2012, title={Registration of 'MSU E5024' Wheat}, volume={6}, ISSN={["1936-5209"]}, DOI={10.3198/jpr2011.11.0598crc}, abstractNote={‘MSU E5024’ (Reg. No. CV‐1077, PI 664078) soft white winter wheat (Triticum aestivum L.) was developed by Michigan State University (MSU) AgBioResearch and released in 2011 via exclusive licensing agreements through MSU Technologies. In addition to researchers at MSU, USDA‐ARS researchers at the Soft Wheat Quality Laboratory (Wooster, OH) conducted quality evaluations during the development of MSU E5024. Deoxynivalenol testing was performed at the University of Minnesota, and molecular marker analyses were performed at the USDA‐ARS Regional Small Grains Genotyping Laboratory (Raleigh, NC). The objective of the cross was to create a high‐yielding soft white winter wheat cultivar adapted to Michigan and the surrounding region with good agronomic performance, acceptable quality, and good disease resistance. Soft white winter wheat is used in many wheat‐related industries and is a large portion of the wheat market in Michigan. MSU E5024 (experimental number E5024) is an F7–derived line developed using pedigree breeding. MSU E5024 exhibits a stable and high level of performance, including good yield, high test weight, resistance to powdery mildew [caused by Blumeria graminis (DC.) E.O. Speer], and improved resistance to Fusarium head blight (caused by Fusarium graminearum Schwabe) and preharvest sprouting. MSU E5024 is short, white chaffed, and awned. MSU E5024 is well adapted to Michigan and to Ontario, Canada).}, number={3}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Lewis, Janet M. and Siler, Lee and Ellis, Donna and Souza, Edward and Ng, Perry K. W. and Dong, Yanhong and Brown-Guedira, Gina and Jiang, Guo-Liang and Ward, Richard W.}, year={2012}, month={Sep}, pages={333–341} }
 @article{lewis_siler_ellis_souza_ng_dong_brown-guedira_marshall_kolmer_jiang_et al._2012, title={Registration of 'Red Ruby' Wheat}, volume={6}, ISSN={["1936-5209"]}, DOI={10.3198/jpr2011.09.0509crc}, abstractNote={‘Red Ruby’ (Reg. No. CV‐1072, PI 662035) soft red winter wheat (Triticum aestivum L.) was developed by the Michigan Agricultural Experiment Station and released in 2007 via an exclusive licensing agreement through Michigan State University Technologies. Red Ruby was selected from the cross Pioneer ‘2552’/Pioneer ‘2737W’ made in 1995. The original objective of the cross was the development of high‐yielding soft white winter wheats with good end‐use quality. Although soft white wheat is a very valuable commodity in Michigan, currently more soft red wheat is produced, and therefore there is also a high demand for improved soft red wheats. Red Ruby is a high‐yielding, F4–derived line with the original experimental number E1007R. A bulk breeding method was used to develop the cultivar, with bulk selections in early generations, followed by a headrow selection in the F5 and bulking again in later generations. In addition to standard yield‐test criteria, milling and baking performances also were considered for selection. Red Ruby was released because of its high yield, high test weight, and red grain color. Red Ruby is well adapted to Michigan.}, number={3}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Lewis, Janet M. and Siler, Lee and Ellis, Donna and Souza, Edward and Ng, Perry K. W. and Dong, Yanhong and Brown-Guedira, Gina and Marshall, David and Kolmer, Jim and Jiang, Guo-Liang and et al.}, year={2012}, month={Sep}, pages={324–332} }
 @article{horevaj_brown-guedira_milus_2012, title={Resistance in winter wheat lines to deoxynivalenol applied into florets at flowering stage and tolerance to phytotoxic effects on yield}, volume={61}, ISSN={["1365-3059"]}, DOI={10.1111/j.1365-3059.2011.02568.x}, abstractNote={In Europe and North America, deoxynivalenol (DON) is the most prevalent mycotoxin associated with wheat head blight caused by Fusarium graminearum and Fusarium culmorum. Because DON is toxic to plants and enhances the ability of the pathogen to spread within a spike, wheat lines with resistance to DON should be more resistant to head blight. Resistance to DON has been associated with resistance gene Fhb1 that confers resistance to spread within a spike. The objectives of this study were to determine if wheat lines resistant to head blight were also resistant to DON, if genes other than Fhb1 confer resistance to DON, and to identify lines able to fill grain in the presence of DON. Susceptible controls and diverse North American and European winter wheat lines with resistance to head blight were screened for molecular markers linked to known head blight resistance genes, and evaluated in a greenhouse for resistance to DON and relative yield after application of DON to spikes at flowering. Fhb1 appeared to have the unique ability to confer resistance to DON, as measured by the number of DON‐bleached primary florets. However, this resistance did not protect plants from the phytotoxic effects of DON on kernel formation as measured by the relative yield of treated spikes. Furthermore, measuring the relative yield loss following DON application may be useful for identifying lines with tolerance to head blight.}, number={5}, journal={PLANT PATHOLOGY}, author={Horevaj, P. and Brown-Guedira, G. and Milus, E. A.}, year={2012}, month={Oct}, pages={925–933} }
 @article{sthapit_gbur_brown-guedira_marshall_milus_2012, title={Characterization of Resistance to Stripe Rust in Contemporary Cultivars and Lines of Winter Wheat from the Eastern United States}, volume={96}, ISSN={["0191-2917"]}, DOI={10.1094/pdis-07-11-0612}, abstractNote={ Stripe rust, caused by Puccinia striiformis f. sp. tritici, has been an important disease of winter wheat (Triticum aestivum) in the eastern United States since 2000, when a new strain of the pathogen emerged. The new strain overcame the widely used resistance gene, Yr9, and was more aggressive and better adapted to warmer temperatures than the old strain. Host resistance is the most effective approach to manage stripe rust. Winter wheat lines with resistance to the new strain in the field are common, but the genes conferring this resistance are mostly unknown. The objectives of this research were to characterize the all-stage resistance and adult-plant resistance (APR) to stripe rust in a representative group of contemporary winter wheat cultivars and breeding lines and to identify the resistance genes when possible. Of the 50 lines evaluated for all-stage resistance at the seedling stage, nearly all were susceptible to the new strain. Based on a linked molecular marker, seven lines had resistance gene Yr17 that confers resistance to both old and new strains; however, this resistance was difficult to identify in the seedling stage. Of the 19 lines evaluated for APR, all expressed APR compared with a very susceptible check. Nine had race-specific APR to the new strain and nine had APR to both old and new strains. The remaining line, 26R61, had all-stage resistance to the old strain (conferred by resistance gene Yr9) and a high level of APR to the new strain. APR was expressed as low infection type, low percent leaf area diseased, and long latent period at heading stage under both low and high temperature regimes and could be identified as early as jointing stage. Based on tests for linked molecular markers, the most widely used slow-rusting APR genes, Yr18 and Yr29, were not present in any of the lines. The results of this research indicate that effective all-stage resistance was conferred only by Yr17 and that APR was common and likely conferred by unknown race-specific genes rather than genes conferring slow rusting that are more likely to be durable. }, number={5}, journal={PLANT DISEASE}, author={Sthapit, Jinita and Gbur, Edward E. and Brown-Guedira, Gina and Marshall, David S. and Milus, Eugene A.}, year={2012}, month={May}, pages={737–745} }
 @article{hao_chen_wang_bland_buck_brown-guedira_johnson_2011, title={Characterization of a major QTL for adult plant resistance to stripe rust in US soft red winter wheat}, volume={123}, ISSN={["0040-5752"]}, DOI={10.1007/s00122-011-1675-8}, abstractNote={Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of soft red winter wheat in the eastern region of the USA. Pioneer 26R61 has provided effective resistance to stripe rust for 10 years. To elucidate the genetic basis of the resistance, a mapping population of 178 recombinant inbred lines (RILs) was developed using single-seed descent from a cross between Pioneer 26R61 and the susceptible cultivar AGS 2000. A genetic map with 895 markers covering all 21 chromosomes was used for QTL analysis. One major QTL was detected, explaining up to 56.0% of the mean phenotypic variation, flanked by markers Xbarc124 and Xgwm359, and assigned to the distal 22% of the short arm of wheat chromosome 2A. Evidence showed that it was different from Yr17 derived from Ae. ventricosa, the only formally named Yr gene in 2AS, and the QTL was temporarily designated as YrR61. In addition, a minor QTL, QYr.uga-6AS, probably conditioned high-temperature adult plant resistance. The QTL explained 6-7% of the trait variation. Preliminary test of the flanking markers for YrR61, in two cultivars and two promising breeding lines with Pioneer 26R61 in their pedigree, indicated that YrR61 was present in these cultivars and lines, and these markers could therefore be used in marker-assisted selection.}, number={8}, journal={THEORETICAL AND APPLIED GENETICS}, author={Hao, Yuanfeng and Chen, Zhenbang and Wang, Yingying and Bland, Dan and Buck, James and Brown-Guedira, Gina and Johnson, Jerry}, year={2011}, month={Dec}, pages={1401–1411} }
 @article{kuraparthy_sood_guedira_gill_2011, title={Development of a PCR assay and marker-assisted transfer of leaf rust resistance gene Lr58 into adapted winter wheats}, volume={180}, ISSN={["1573-5060"]}, DOI={10.1007/s10681-011-0383-4}, abstractNote={Leaf rust resistance gene Lr58 derived from Aegilops triuncialis L. was transferred to the hard red winter wheat (HRWW) cultivars Jagger and Overley by standard backcrossing and marker-assisted selection (MAS). A co-dominant PCR-based sequence tagged site (STS) marker was developed based on the sequence information of the RFLP marker (XksuH16) diagnostically detecting the alien segment in T2BS·2BL-2tL(0.95). STS marker Xncw-Lr58-1 was used to select backcross F1 plants with rust resistance. The co-dominant marker polymorphism detected by primer pair NCW-Lr58-1 efficiently identified the homozygous BC3F2 plants with rust resistance gene Lr58. The STS marker Xncw-Lr58-1 showed consistent diagnostic polymorphism between the resistant source and the wheat cultivars selected by the US Wheat Coordinated Agricultural Project. The utility and compatibility of the STS marker in MAS programs involving robust genotyping platforms was demonstrated in both agarose-based and capillary-based platforms. Screening backcross derivatives carrying Lr58 with various rust races at seedling stage suggested the transferred rust resistance in adapted winter wheats is stable in both cultivar backgrounds. Lr58 in adapted winter wheat backgrounds could be used in combination with other resistance genes in wheat rust resistance breeding.}, number={2}, journal={EUPHYTICA}, author={Kuraparthy, Vasu and Sood, Shilpa and Guedira, Gina-Brown and Gill, Bikram S.}, year={2011}, month={Jul}, pages={227–234} }
 @article{maloney_lyerly_wooten_anderson_livingston_brown-guedira_marshall_murphy_2011, title={Marker Development and Quantitative Trait Loci in a Fall-Sown Oat Recombinant Inbred Population}, volume={51}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2010.04.0224}, abstractNote={ABSTRACTMarker‐assisted selection for improved winter survival in oat (Avena sativa L.) is difficult because the number of simple sequence repeat (SSR) markers available in this species is limited. The objectives of this research were to increase the number of SSR markers on the ‘Fulghum’ × ‘Norline’ recombinant inbred population genetic map and to scan for quantitative trait loci (QTL) associated with winter field survival, crown freezing tolerance, vernalization response, and heading date. New SSR markers were developed from ‘Kanota’ and ‘Ogle’ genomic DNA libraries enriched for eight microsatellite motifs. New primers were evaluated for amplification, reproducibility, and polymorphism in 11 oat lines. Simple sequence repeat markers showing high‐quality polymorphism between Fulghum and Norline were subsequently examined in 128 recombinant inbred lines. Sixty‐five new SSR, four single nucleotide polymorphism (SNP), and one cleaved amplified polymorphic sequence (CAPS) markers were added to the Fulghum × Norline linkage map. This brought the total number of markers mapped on the population to 101. Phenotypic data for winter hardiness component traits in the population were obtained in previous field and controlled chamber experiments. All previously mapped markers and new SSR markers were evaluated and QTL identified. Marker loci on linkage group FN1_3_38 accounted for multiple QTL associated with winter hardiness component traits. The addition of new SSR markers to the Fulghum × Norline map in regions with winter hardiness component trait QTL will enhance marker assisted selection for these important traits.}, number={2}, journal={CROP SCIENCE}, author={Maloney, P. V. and Lyerly, J. H. and Wooten, D. R. and Anderson, J. M. and Livingston, D. P., III and Brown-Guedira, G. and Marshall, D. and Murphy, J. P.}, year={2011}, month={Mar}, pages={490–502} }
 @article{li_chen_wu_zhang_chu_see_brown-guedira_zemetra_souza_2011, title={Quantitative Trait Loci Analysis for the Effect of Rht-B1 Dwarfing Gene on Coleoptile Length and Seedling Root Length and Number of Bread Wheat}, volume={51}, ISSN={["0011-183X"]}, DOI={10.2135/cropsci2011.03.0116}, abstractNote={ABSTRACTIt has been documented that the dwarfing genes, Rht‐B1b and Rht‐D1b, can reduce wheat (Triticum aestivum L.) coleoptile length (CL), but their effects on number of roots (RN) and root length (RL) have not been determined. Our objectives were to identify quantitative trait loci (QTL) controlling CL, RN, and RL and to determine if any of the QTL correspond to wheat dwarfing genes. A population consisting of 159 recombinant inbred lines (RILs) was derived from the cross of Rio Blanco (Rht‐B1b, Rht‐D1a), a semidwarf cultivar with short CL, and IDO444 (Rht‐B1a, Rht‐D1a), a tall germplasm with long CL. The CL, RN, longest root length (LRL), and total root length (TRL) were evaluated at two temperature regimes (18 and 22°C). A major QTL mapped to the Rht‐B1 locus on chromosome 4B explained 64% of the phenotypic variation for CL, 9% for LRL, 26% for TRL, and 14% for plant height. The CL of the semidwarf RILs was significantly less than that of the tall lines while the reverse results were observed for LRL and TRL. Our results indicated that the Rht‐B1 gene had the pleiotropic effect of decreasing CL while increasing LRL and TRL. None of the six QTL for RN were mapped to the regions containing the Rht‐B1 locus although semidwarf RILs had more roots than the tall lines. This study suggested that selection of the Rht‐B1b allele tended to increase root biomass, perhaps ameliorating its negative effect of reduced CL.}, number={6}, journal={CROP SCIENCE}, author={Li, P. and Chen, J. and Wu, P. and Zhang, J. and Chu, C. and See, D. and Brown-Guedira, G. and Zemetra, R. and Souza, E.}, year={2011}, month={Nov}, pages={2561–2568} }
 @article{mago_brown-guedira_dreisigacker_breen_jin_singh_appels_lagudah_ellis_spielmeyer_et al._2011, title={An accurate DNA marker assay for stem rust resistance gene Sr2 in wheat}, volume={122}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-010-1482-7}, abstractNote={The stem rust resistance gene Sr2 has provided broad-spectrum protection against stem rust (Puccinia graminis Pers. f. sp. tritici) since its wide spread deployment in wheat from the 1940s. Because Sr2 confers partial resistance which is difficult to select under field conditions, a DNA marker is desirable that accurately predicts Sr2 in diverse wheat germplasm. Using DNA sequence derived from the vicinity of the Sr2 locus, we developed a cleaved amplified polymorphic sequence (CAPS) marker that is associated with the presence or absence of the gene in 115 of 122 (95%) diverse wheat lines. The marker genotype predicted the absence of the gene in 100% of lines which were considered to lack Sr2. Discrepancies were observed in lines that were predicted to carry Sr2 but failed to show the CAPS marker. Given the high level of accuracy observed, the marker provides breeders with a selection tool for one of the most important disease resistance genes of wheat.}, number={4}, journal={THEORETICAL AND APPLIED GENETICS}, author={Mago, R. and Brown-Guedira, Gina and Dreisigacker, S. and Breen, J. and Jin, Y. and Singh, R. and Appels, R. and Lagudah, E. S. and Ellis, J. and Spielmeyer, W. and et al.}, year={2011}, month={Mar}, pages={735–744} }
 @article{olson_brown-guedira_marshall_stack_bowden_jin_rouse_pumphrey_2010, title={Development of Wheat Lines Having a Small Introgressed Segment Carrying Stem Rust Resistance Gene Sr22}, volume={50}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2009.11.0652}, abstractNote={ABSTRACTThe wheat stem rust resistance gene Sr22 confers resistance to Puccinia graminis f. sp. tritici Pers. race TTKSK (also known as Ug99) that developed in Africa and is an immediate threat to world wheat production. The resistance gene is present on a chromosomal translocation derived from Triticum boeoticum Boiss., which has a genome that is partially homologous to the A genome of T. aestivum L. Sr22 has been deployed in a limited number of cultivars due to poor agronomic performance of lines carrying the resistance gene. Linkage analysis of simple sequence repeat (SSR) markers on chromosome 7A was performed to identify loci closely linked to Sr22. The most tightly linked proximal and distal SSR marker loci were Xcfa2123 and Xwmc633, respectively. A two‐step process was then used to develop resistant lines having smaller chromosome segments derived from the diploid donor. First, individuals in which a single recombination event had occurred between wheat and the Sr22 introgression were identified in the mapping populations. In spite of reduced recombination between T. boeoticum and T. aestivum chromosomes, sufficient recombination events were found among 398 F3:4 lines derived from recombinant F2 progeny to recover multiple resistant individuals with smaller alien introgressions. Resistant lines were identified having less than 6% of the chromosome arm derived from T. boeoticum. These lines may provide a more agronomically desirable source of Sr22 that can be readily deployed in cultivars resistant to Ug99.}, number={5}, journal={CROP SCIENCE}, author={Olson, Eric L. and Brown-Guedira, Gina and Marshall, David and Stack, Ellen and Bowden, Robert L. and Jin, Yue and Rouse, Matthew and Pumphrey, Michael O.}, year={2010}, pages={1823–1830} }
 @article{guedira_brown-guedira_van sanford_sneller_souza_marshall_2010, title={Distribution of Rht Genes in Modern and Historic Winter Wheat Cultivars from the Eastern and Central USA}, volume={50}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2009.10.0626}, abstractNote={ABSTRACTOver 70% of wheat (Triticum aestivum L.) cultivars grown worldwide have a semidwarf phenotype controlled by the major genes Rht‐B1, Rht‐D1, and Rht8c The objective of this study was to determine their frequency in a set of historic and modern soft and hard winter wheat cultivars grown in the central and eastern USA. Three hundred sixty‐two cultivars that were developed from 1808 to 2008 were evaluated with molecular markers for Rht‐B1, Rht‐D1, and Rht8c All cultivars released before 1964 (41 soft winter wheat and 6 hard winter wheat) had wild‐type (tall) alleles at all three loci. After introduction of the dwarfing genes, the percentage of tested lines carrying either Rht‐B1b or Rht‐D1b increased rapidly to greater than 90% of modern varieties. Among soft winter wheat cultivars, the Rht‐D1b dwarfing gene was the most frequent being present in 45% of all lines tested and Rht‐B1b was present in 28%, while in the hard winter wheat cultivars the Rht‐B1b allele is the most prevalent in 77% of lines. Only 8% of the hard cultivars tested had the Rht‐D1b allele. The presence of the 192‐base pair (bp) allele of the microsatellite marker Xgwm261 indicated that Rht8c was less frequently used as a source of dwarfing in U.S. winter wheat germplasm, being present in 8 and 3% of the soft winter wheat and the hard winter wheats, respectively. A number of modern cultivars were identified that did not carry any of the dwarfing genes assayed and may possess alternative reduced height genes.}, number={5}, journal={CROP SCIENCE}, author={Guedira, M. and Brown-Guedira, G. and Van Sanford, D. and Sneller, C. and Souza, E. and Marshall, D.}, year={2010}, pages={1811–1822} }
 @article{olson_brown-guedira_marshall_jin_mergoum_lowe_dubcovsky_2010, title={Genotyping of US Wheat Germplasm for Presence of Stem Rust Resistance Genes Sr24, Sr36 and Sr1RS(Amigo)}, volume={50}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2009.04.0218}, abstractNote={The stem rust resistance genes Sr24, Sr26, Sr36, and Sr1RSAmigo confer resistance to race TTKSK (= Ug99) of Puccinia graminis f. sp. tritici Pers. (Pgt). A collection of 776 cultivars and breeding lines of wheat (Triticum aestivum L.) from all growing regions of the United States were screened with simple sequence repeat and sequence tagged site markers linked to Sr24, Sr26, Sr36, and Sr1RSAmigo to determine frequencies of these genes in U.S. wheat germplasm. Marker efficacy in predicting the presence of these genes was evaluated via comparison with assayed seedling infection type. Among the lines evaluated, the most predominant gene is Sr24, present in hard winter, hard spring, and soft winter wheat lines. Resistance in soft winter wheat is primarily due to Sr36 The 1RS·1AL rye translocation carrying Sr1RSAmigo is present at equal frequencies in hard winter and soft winter wheat. Utilization of marker‐assisted selection for stem rust resistance genes can hasten the development of wheat cultivars resistant to TTKSK and its variants and allow for the development of resistance gene pyramids for more durable stem rust resistance.}, number={2}, journal={CROP SCIENCE}, author={Olson, Eric L. and Brown-Guedira, Gina and Marshall, David S. and Jin, Yue and Mergoum, Mohamed and Lowe, Lago and Dubcovsky, Jorge}, year={2010}, pages={668–675} }
 @article{lewis_siler_souza_ng_dong_brown-guedira_jiang_ward_2010, title={Registration of 'Red Amber' Wheat}, volume={4}, ISSN={["1936-5209"]}, DOI={10.3198/jpr2009.10.0587crc}, abstractNote={‘Red Amber’ (Reg. No. CV‐1046, PI 658657) soft red winter wheat (Triticum aestivum L.) was developed by the Michigan Agricultural Experiment Station and released March 2008 via an exclusive licensing agreement through Michigan State University (MSU) Technologies. Red Amber was selected from the cross Pioneer variety ‘2555’/‘Lowell’ made in 1995. The cultivar is an F10 derived line, and the original experimental number with MSU is D8006R. In addition to standard yield test criteria, milling and baking performances also were considered for selection. Red Amber was released because of its good grain yield, high flour yield, and resistance to powdery mildew [caused by Blumeria graminis (DC.) Speer]. Red Amber is well adapted to Michigan. The name was given because it is a red wheat released from a breeding program that was previously dedicated to white wheat breeding, and amber is valued for its color quality.}, number={3}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Lewis, Janet M. and Siler, Lee and Souza, Edward and Ng, Perry K. W. and Dong, Yanhong and Brown-Guedira, Gina and Jiang, Guo-Liang and Ward, Richard W.}, year={2010}, month={Sep}, pages={215–223} }
 @article{costa_bockelman_brown-guedira_cambron_chen_cooper_cowger_dong_grybauskas_jin_et al._2010, title={Registration of the Soft Red Winter Wheat Germplasm MD01W233-06-1 Resistant to Fusarium Head Blight}, volume={4}, ISSN={["1936-5209"]}, DOI={10.3198/jpr2010.01.0034crg}, abstractNote={Fusarium head blight (FHB) [caused by Fusarium graminearum Schwabe; telomorph Gibberella zeae (Schwein.) Petch] is a major disease of winter wheat (Triticum aestivum L.) in the US mid‐Atlantic region. The objective of this research was to derive soft red winter wheat (SRWW) germplasm with enhanced FHB resistance for this region. MD01W233–06–1 (Reg. No. GP‐857, PI No. 658682) is a soft red winter wheat (SRWW) (Triticum aestivum L.) germplasm line developed at the University of Maryland and released by the Maryland Agricultural Experiment Station in 2009. MD01W233–06–1 was selected from the cross ‘McCormick’/‘Choptank’ made in 2001. McCormick and Choptank are SRWW cultivars adapted to the US mid‐Atlantic region. MD01W233–06–1 was selected as an F3:5 line selection in Queenstown, MD in June 2006. MD01W233–06–1 has type II resistance to FHB that is different from that of ‘Sumai 3’. Additionally, it has resistance to the Ug99 race of stem rust. These characteristics make this line a valuable contribution for breeding for enhanced FHB resistance in the US mid‐Atlantic.}, number={3}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Costa, Jose M. and Bockelman, Harold E. and Brown-Guedira, Gina and Cambron, Sue E. and Chen, Xianming and Cooper, Aaron and Cowger, Christina and Dong, Yanghong and Grybauskas, Arvydas and Jin, Yue and et al.}, year={2010}, month={Sep}, pages={255–260} }
 @article{lagudah_krattinger_herrera-foessel_singh_huerta-espino_spielmeyer_brown-guedira_selter_keller_2009, title={Gene-specific markers for the wheat gene Lr34/Yr18/Pm38 which confers resistance to multiple fungal pathogens}, volume={119}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-009-1097-z}, abstractNote={The locus Lr34/Yr18/Pm38 confers partial and durable resistance against the devastating fungal pathogens leaf rust, stripe rust, and powdery mildew. In previous studies, this broad-spectrum resistance was shown to be controlled by a single gene which encodes a putative ATP-binding cassette transporter. Alleles of resistant and susceptible cultivars differed by only three sequence polymorphisms and the same resistance haplotype was found in the three independent breeding lineages of Lr34/Yr18/Pm38. Hence, we used these conserved sequence polymorphisms as templates to develop diagnostic molecular markers that will assist selection for durable multi-pathogen resistance in breeding programs. Five allele-specific markers (cssfr1-cssfr5) were developed based on a 3 bp deletion in exon 11 of the Lr34-gene, and one marker (cssfr6) was derived from a single nucleotide polymorphism in exon 12. Validation of reference genotypes, well characterized for the presence or absence of the Lr34/Yr18/Pm38 resistance locus, demonstrated perfect diagnostic values for the newly developed markers. By testing the new markers on a larger set of wheat cultivars, a third Lr34 haplotype, not described so far, was discovered in some European winter wheat and spelt material. Some cultivars with uncertain Lr34 status were re-assessed using the newly derived markers. Unambiguous identification of the Lr34 gene aided by the new markers has revealed that some wheat cultivars incorrectly postulated as having Lr34 may possess as yet uncharacterised loci for adult plant leaf and stripe rust resistance.}, number={5}, journal={THEORETICAL AND APPLIED GENETICS}, author={Lagudah, Evans S. and Krattinger, Simon G. and Herrera-Foessel, Sybil and Singh, Ravi P. and Huerta-Espino, Julio and Spielmeyer, Wolfgang and Brown-Guedira, Gina and Selter, Liselotte L. and Keller, Beat}, year={2009}, month={Sep}, pages={889–898} }
 @article{hall_brown-guedira_klatt_fritz_2009, title={Genetic analysis of resistance to soil-borne wheat mosaic virus derived from Aegilops tauschii}, volume={169}, ISSN={["0014-2336"]}, DOI={10.1007/s10681-009-9910-y}, number={2}, journal={EUPHYTICA}, author={Hall, M. D. and Brown-Guedira, G. and Klatt, A. and Fritz, A. K.}, year={2009}, month={Sep}, pages={169–176} }
 @article{maxwell_lyerly_cowger_marshall_brown-guedira_murphy_2009, title={MlAG12: a Triticum timopheevii-derived powdery mildew resistance gene in common wheat on chromosome 7AL}, volume={119}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-009-1150-y}, abstractNote={Wheat powdery mildew is an economically important disease in cool and humid environments. Powdery mildew causes yield losses as high as 48% through a reduction in tiller survival, kernels per head, and kernel size. Race-specific host resistance is the most consistent, environmentally friendly and, economical method of control. The wheat (Triticum aestivum L.) germplasm line NC06BGTAG12 possesses genetic resistance to powdery mildew introgressed from the AAGG tetraploid genome Triticum timopheevii subsp. armeniacum. Phenotypic evaluation of F(3) families derived from the cross NC06BGTAG12/'Jagger' and phenotypic evaluation of an F(2) population from the cross NC06BGTAG12/'Saluda' indicated that resistance to the 'Yuma' isolate of powdery mildew was controlled by a single dominant gene in NC06BGTAG12. Bulk segregant analysis (BSA) revealed simple sequence repeat (SSR) markers specific for chromosome 7AL segregating with the resistance gene. The SSR markers Xwmc273 and Xwmc346 mapped 8.3 cM distal and 6.6 cM proximal, respectively, in NC06BGTAG12/Jagger. The multiallelic Pm1 locus maps to this region of chromosome 7AL. No susceptible phenotypes were observed in an evaluation of 967 F(2) individuals in the cross NC06BGTAG12/'Axminster' (Pm1a) which indicated that the NC06BGTAG12 resistance gene was allelic or in close linkage with the Pm1 locus. A detached leaf test with ten differential powdery mildew isolates indicated the resistance in NC06BGTAG12 was different from all designated alleles at the Pm1 locus. Further linkage and allelism tests with five other temporarily designated genes in this very complex region will be required before giving a permanent designation to this gene. At this time the gene is given the temporary gene designation MlAG12.}, number={8}, journal={THEORETICAL AND APPLIED GENETICS}, author={Maxwell, Judd J. and Lyerly, Jeanette H. and Cowger, Christina and Marshall, David and Brown-Guedira, Gina and Murphy, J. Paul}, year={2009}, month={Nov}, pages={1489–1495} }
 @article{cowger_patton-ozkurt_brown-guedira_perugini_2009, title={Post-Anthesis Moisture Increased Fusarium Head Blight and Deoxynivalenol Levels in North Carolina Winter Wheat}, volume={99}, ISSN={["0031-949X"]}, DOI={10.1094/PHYTO-99-4-0320}, abstractNote={ Current models for forecasting Fusarium head blight (FHB) and deoxynivalenol (DON) levels in wheat are based on weather near anthesis, and breeding for resistance to FHB pathogens often relies on irrigation before and shortly after anthesis to encourage disease development. The effects of post-anthesis environmental conditions on FHB are poorly understood. We performed a field experiment at Kinston, NC, to explore the effects of increasing duration of post-anthesis moisture on disease incidence, disease severity, Fusarium-damaged kernels (FDK), percent infected kernels, and DON. The experiment had a split-plot design, and one trial was conducted in each of two successive years. Main plots consisted of post-anthesis mist durations of 0, 10, 20, or 30 days. Subplots were of eight cultivars in the first year and seven in the second year, two being susceptible to FHB and the remainder each with varying degrees of apparent type I and type II resistance. Plots were inoculated by spraying Fusarium graminearum macroconidia at mid-anthesis. Averaging across years and cultivars, 10 or 20 days of post-anthesis mist had the same effect (P ≥ 0.198) and were associated with an approximately fourfold increase in mean disease incidence and eightfold increase in disease severity compared with 0 days of mist (P ≤ 0.0002). In both years, mean FDK percentages at 0 and 10 days post-anthesis mist were the same and significantly lower than FDK percentages under 20 or 30 days of post-anthesis mist. Mist duration had a significant effect on percent kernels infected with Fusarium spp. as detected by a selective medium assay of 2007 samples. Averaging across all cultivars, in both years, DON levels increased significantly for 10 days compared with 0 days of mist, and increased again with 20 days of mist (P ≤ 0.04). This is the first investigation to show that extended post-flowering moisture can have a significant enhancing effect on FHB, FDK, DON, and percent infected kernels of wheat. For all disease and toxin assays, cultivar rankings were significantly noncorrelated among mist durations in at least 1 year, suggesting that FHB screening programs might rank genotypes differently under extended post-anthesis moisture than without it. Our findings also imply that accurate forecasts of DON in small grains must take account of post-anthesis weather conditions. }, number={4}, journal={PHYTOPATHOLOGY}, author={Cowger, Christina and Patton-Ozkurt, Jennifer and Brown-Guedira, Gina and Perugini, Leandro}, year={2009}, month={Apr}, pages={320–327} }
 @article{brown-guedira_griffey_kolb_mckendry_murphy_van sanford_2008, title={Breeding Fhb-resistant soft winter wheat: Progress and prospects}, volume={36}, ISSN={["1788-9170"]}, DOI={10.1556/crc.36.2008.suppl.b.5}, abstractNote={Soft winter wheat ( Triticum aestivum L.) breeding programs in the US have used two general approaches to developing FHB-resistant cultivars: 1) incorporation of Fhb 1 plus other minor QTL from Asian wheat cultivars and their derivatives and 2) reliance on resistance native to the soft winter wheat gene pool. Although each approach has shown some success, it is believed that the two must be integrated to develop the highest levels of resistance. The most favorable scenario for integration is the incorporation of Fhb 1 into adapted material with good native resistance, high yield and test weight, and superior milling and baking quality.}, journal={CEREAL RESEARCH COMMUNICATIONS}, author={Brown-Guedira, Gina and Griffey, Carl and Kolb, Fred and Mckendry, Anne and Murphy, J. Paul and Van Sanford, David}, year={2008}, pages={31–35} }
 @article{brown-guedira_2008, title={Wheat woes}, volume={22}, number={9}, journal={Scientist}, author={Brown-Guedira, G.}, year={2008}, pages={60–60} }
 @article{perugini_murphy_marshall_brown-guedira_2008, title={Pm37, a new broadly effective powdery mildew resistance gene from Triticum timopheevii}, volume={116}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-007-0679-x}, abstractNote={Powdery mildew is an important foliar disease in wheat, especially in areas with a cool or maritime climate. A dominant powdery mildew resistance gene transferred to the hexaploid germplasm line NC99BGTAG11 from T. timopheevii subsp. armeniacum was mapped distally on the long arm of chromosome 7A. Differential reactions were observed between the resistance gene in NC99BGTAG11 and the alleles of the Pm1 locus that is also located on chromosome arm 7AL. Observed segregation in F2:3 lines from the cross NC99BGTAG11xAxminster (Pm1a) demonstrate that germplasm line NC99BGTAG11 carries a novel powdery mildew resistance gene, which is now designated as Pm37. This new gene is highly effective against all powdery mildew isolates tested so far. Analyses of the population with molecular markers indicate that Pm37 is located 16 cM proximal to the Pm1 complex. Simple sequence repeat (SSR) markers Xgwm332 and Xwmc790 were located 0.5 cM proximal and distal, respectively, to Pm37. In order to identify new markers in the region, wheat expressed sequence tags (ESTs) located in the distal 10% of 7AL that were orthologous to sequences from chromosome 6 of rice were targeted. The two new EST-derived STS markers were located distal to Pm37 and one marker was closely linked to the Pm1a region. These new markers can be used in marker-assisted selection schemes to develop wheat cultivars with pyramids of powdery mildew resistance genes, including combinations of Pm37 in coupling linkage with alleles of the Pm1 locus.}, number={3}, journal={THEORETICAL AND APPLIED GENETICS}, author={Perugini, L. D. and Murphy, J. P. and Marshall, D. and Brown-Guedira, G.}, year={2008}, month={Feb}, pages={417–425} }
 @article{narasimhamoorthy_gill_fritz_nelson_brown-guedira_2006, title={Advanced backcross QTL analysis of a hard winter wheat x synthetic wheat population}, volume={112}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-005-0159-0}, abstractNote={Advanced backcross quantitative trait locus (AB-QTL) analysis was used to identify QTLs for yield and yield components in a backcross population developed from a cross between hard red winter wheat (Triticum aestivum L.) variety Karl 92 and the synthetic wheat line TA 4152-4. Phenotypic data were collected for agronomic traits including heading date, plant height, kernels per spike, kernel weight, tiller number, biomass, harvest index, test weight, grain yield, protein content, and kernel hardness on 190 BC2F(2:4) lines grown in three replications in two Kansas environments. Severity of wheat soil-borne mosaic virus (WSBMV) reaction was evaluated at one location. The population was genotyped using 151 microsatellite markers. Of the ten putative QTLs identified, seven were located on homologous group 2 and group 3 chromosomes. The favorable allele was contributed by cultivated parent Karl 92 at seven QTLs including a major one for WSBMV resistance, and by the synthetic parent at three QTLs: for grain hardness, kernels per spike, and tiller number.}, number={5}, journal={THEORETICAL AND APPLIED GENETICS}, author={Narasimhamoorthy, B and Gill, BS and Fritz, AK and Nelson, JC and Brown-Guedira, GL}, year={2006}, month={Mar}, pages={787–796} }
 @article{brooks_see_brown-guedira_2006, title={SNP-based improvement of a microsatellite marker associated with Karnal bunt resistance in wheat}, volume={46}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2005.05-0065}, abstractNote={Marker‐assisted selection (MAS) has become the technology of choice for introgressing important traits with indistinct phenotypes into agronomically elite cultivars. Karnal bunt (KB, causal agent Tilletia indica Mitra) is an economically important fungal pathogen of wheat (Triticum aestivum L.) which has caused economic losses in the USA since it was first reported in 1996. To protect U.S. wheat from this emerging disease and the losses incurred from export quarantines, genetic sources of resistance are needed by breeders to improve U.S. germplasm. Resistance to KB is difficult to score phenotypically, making MAS an ideal choice for deploying this trait into U.S. wheat. Here we describe the conversion of a codominant microsatellite marker, Xgwm538, associated with a quantitative trait locus (QTL) for KB resistance into a single nucleotide polymorphism (SNP) based marker. The SNP marker was developed to improve gel‐based resolution and amplification consistency. The gwm538 primers amplify three fragments in the KB resistant line HD29: 137‐, 147‐, and a 152‐bp fragment that maps to the long arm of chromosome 4B and is linked to the KB QTL. By cloning and sequencing all three fragments, we were able to exploit a SNP and design a new primer to selectively amplify the 152‐bp fragment of interest (gwm538snp). Amplification consistency is improved with gwm538snp since the amplification of competing nontarget fragments is eliminated, and ambiguity is reduced since heterozygous plants are easily identified among backcross progeny.}, number={4}, journal={CROP SCIENCE}, author={Brooks, Steven A. and See, Deven R. and Brown-Guedira, Gina}, year={2006}, pages={1467–1470} }
 @article{gill_friebe_raupp_wilson_cox_sears_brown-guedira_fritz_2006, title={Wheat Genetics Resource Center: The first 25 years}, volume={89}, ISBN={["0-12-000807-6"]}, ISSN={["2213-6789"]}, DOI={10.1016/S0065-2113(05)89002-9}, abstractNote={The Wheat Genetics Resource Center, a pioneering center without walls, has served the wheat genetics community for 25 years. The Wheat Genetics Resource Center (WGRC) assembled a working collection of over 11,000 wild wheat relatives and cytogenetic stocks for conservation and use in wheat genome analysis and crop improvement. Over 30,000 samples from the WGRC collection of wheat wild relatives, cytogenetic stocks, and improved germplasm have been distributed to scientists in 45 countries and 39 states in the United States. The WGRC and collaborators have developed standard karyotypes of 26 species of the Triticum/Aegilops complex, rye, and some perennial genera of the Triticeae. They have developed over 800 cytogenetic stocks including addition, substitution, and deletion lines. The anchor karyotypes, technical innovations, and associated cytogenetic stocks are a part of the basic tool kit of every wheat geneticist. They have cytogenetically characterized over six‐dozen wheat–alien introgression lines. The WGRC has released 47 improved germplasm lines incorporating over 50 novel genes against pathogens and pests; some genes have been deployed in agriculture. The WGRC hosted over three‐dozen scientists especially from developing countries for advanced training. The WGRC was engaged in international agriculture through several collaborating projects. Particularly noteworthy was the collaborative project with Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT) on the production of synthetic wheats. It is estimated that "by the year 2003–2004, 26% of all new advanced lines made available through CIMMYT screening nurseries to cooperators for either irrigated or semi‐arid conditions were synthetic derivatives." The WGRC is applying genomics tools to further expedite the use of exotic germplasm in wheat crop improvement.}, journal={ADVANCES IN AGRONOMY, VOL 89}, publisher={2006}, author={Gill, Bikram S. and Friebe, Bernd and Raupp, W. John and Wilson, Duane L. and Cox, T. Stan and Sears, Rollin G. and Brown-Guedira, Gina L. and Fritz, Allan K.}, year={2006}, pages={73–136} }