@article{adhikari_olukolu_paudel_pandey_halterman_louws_2024, title={Genotyping-by-Sequencing Reveals Population Differentiation and Linkage Disequilibrium in <i>Alternaria linariae</i> from Tomato}, volume={2}, ISSN={["1943-7684"]}, DOI={10.1094/PHYTO-07-23-0229-R}, abstractNote={ Alternaria linariae is an economically important foliar pathogen that causes early blight disease in tomatoes. Understanding genetic diversity, population genetic structure, and evolutionary potential is crucial to contemplating effective disease management strategies. We leveraged genotyping-by-sequencing (GBS) technology to compare genome-wide variation in 124 isolates of Alternaria spp. ( A. alternata, A. linariae, and A. solani) for comparative genome analysis and to test the hypotheses of genetic differentiation and linkage disequilibrium (LD) in A. linariae collected from tomatoes in western North Carolina. We performed a pangenome-aware variant calling and filtering with GBSapp and identified 53,238 variants conserved across the reference genomes of three Alternaria spp. The highest marker density was observed on chromosome 1 (7 Mb). Both discriminant analysis of principal components and Bayesian model-based STRUCTURE analysis of A. linariae isolates revealed three subpopulations with minimal admixture. The genetic differentiation coefficients (FST) within A. linariae subpopulations were similar and high (0.86), indicating that alleles in the subpopulations are fixed and the genetic structure is likely due to restricted recombination. Analysis of molecular variance indicated higher variation among populations (89%) than within the population (11%). We found long-range LD between pairs of loci in A. linariae, supporting the hypothesis of low recombination expected for a fungal pathogen with limited sexual reproduction. Our findings provide evidence of a high level of population genetic differentiation in A. linariae, which reinforces the importance of developing tomato varieties with broad-spectrum resistance to various isolates of A. linariae. }, journal={PHYTOPATHOLOGY}, author={Adhikari, Tika B. and Olukolu, Bode A. and Paudel, Rajan and Pandey, Anju and Halterman, Dennis and Louws, Frank J.}, year={2024}, month={Feb} }
 @article{cham_adams_wadl_ojeda-zacarias_rutter_jackson_shoemaker_yencho_olukolu_2024, title={Metagenome-enabled models improve genomic predictive ability and identification of herbivory-limiting genes in sweetpotato}, volume={11}, ISSN={["2052-7276"]}, DOI={10.1093/hr/uhae135}, abstractNote={Abstract Plant–insect interactions are often influenced by host- or insect-associated metagenomic community members. The relative abundance of insects and the microbes that modulate their interactions were obtained from sweetpotato (Ipomoea batatas) leaf-associated metagenomes using quantitative reduced representation sequencing and strain/species-level profiling with the Qmatey software. Positive correlations were found between whitefly (Bemisia tabaci) and its endosymbionts (Candidatus Hamiltonella defensa, Candidatus Portiera aleyrodidarum, and Rickettsia spp.) and negative correlations with nitrogen-fixing bacteria that implicate nitric oxide in sweetpotato–whitefly interaction. Genome-wide associations using 252 975 dosage-based markers, and metagenomes as a covariate to reduce false positive rates, implicated ethylene and cell wall modification in sweetpotato–whitefly interaction. The predictive abilities (PA) for whitefly and Ocypus olens abundance were high in both populations (68%–69% and 33.3%–35.8%, respectively) and 69.9% for Frankliniella occidentalis. The metagBLUP (gBLUP) prediction model, which fits the background metagenome-based Cao dissimilarity matrix instead of the marker-based relationship matrix (G-matrix), revealed moderate PA (35.3%–49.1%) except for O. olens (3%–10.1%). A significant gain in PA after modeling the metagenome as a covariate (gGBLUP, ≤11%) confirms quantification accuracy and that the metagenome modulates phenotypic expression and might account for the missing heritability problem. Significant gains in PA were also revealed after fitting allele dosage (≤17.4%) and dominance effects (≤4.6%). Pseudo-diploidized genotype data underperformed for dominance models. Including segregation-distorted loci (SDL) increased PA by 6%–17.1%, suggesting that traits associated with fitness cost might benefit from the inclusion of SDL. Our findings confirm the holobiont theory of host–metagenome co-evolution and underscore its potential for breeding within the context of G × G × E interactions.}, number={7}, journal={HORTICULTURE RESEARCH}, author={Cham, Alhagie K. and Adams, Alison K. and Wadl, Phillip A. and Ojeda-Zacarias, Ma del Carmen and Rutter, William B. and Jackson, D. Michael and Shoemaker, D. Dewayne and Yencho, G. Craig and Olukolu, Bode A.}, year={2024}, month={Jul} }
 @article{amankwaah_williamson_reynolds_ibrahem_pecota_zhang_olukolu_truong_carey_felde_et al._2023, title={Development of NIRS calibration curves for sugars in baked sweetpotato}, volume={7}, ISSN={["1097-0010"]}, DOI={10.1002/jsfa.12800}, abstractNote={Abstract}, journal={JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE}, author={Amankwaah, Victor A. and Williamson, Sharon and Reynolds, Rong and Ibrahem, Ragy and Pecota, Kenneth V. and Zhang, Xiaofei and Olukolu, Bode A. and Truong, Van-Den and Carey, Edward and Felde, Thomas Zum and et al.}, year={2023}, month={Jul} }
 @article{slonecki_rutter_olukolu_yencho_jackson_wadl_2023, title={Genetic diversity, population structure, and selection of breeder germplasm subsets from the USDA sweetpotato (Ipomoea batatas) collection}, volume={13}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2022.1022555}, abstractNote={Sweetpotato (Ipomoea batatas) is the sixth most important food crop and plays a critical role in maintaining food security worldwide. Support for sweetpotato improvement research in breeding and genetics programs, and maintenance of sweetpotato germplasm collections is essential for preserving food security for future generations. Germplasm collections seek to preserve phenotypic and genotypic diversity through accession characterization. However, due to its genetic complexity, high heterogeneity, polyploid genome, phenotypic plasticity, and high flower production variability, sweetpotato genetic characterization is challenging. Here, we characterize the genetic diversity and population structure of 604 accessions from the sweetpotato germplasm collection maintained by the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Plant Genetic Resources Conservation Unit (PGRCU) in Griffin, Georgia, United States. Using the genotyping-by-sequencing platform (GBSpoly) and bioinformatic pipelines (ngsComposer and GBSapp), a total of 102,870 polymorphic SNPs with hexaploid dosage calls were identified from the 604 accessions. Discriminant analysis of principal components (DAPC) and Bayesian clustering identified six unique genetic groupings across seven broad geographic regions. Genetic diversity analyses using the hexaploid data set revealed ample genetic diversity among the analyzed collection in concordance with previous analyses. Following population structure and diversity analyses, breeder germplasm subsets of 24, 48, 96, and 384 accessions were established using K-means clustering with manual selection to maintain phenotypic and genotypic diversity. The genetic characterization of the PGRCU sweetpotato germplasm collection and breeder germplasm subsets developed in this study provide the foundation for future association studies and serve as precursors toward phenotyping studies aimed at linking genotype with phenotype.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Slonecki, Tyler J. and Rutter, William B. and Olukolu, Bode A. and Yencho, G. Craig and Jackson, D. Michael and Wadl, Phillip A.}, year={2023}, month={Feb} }
 @article{amankwaah_williamson_olukolu_truong_carey_ssali_yencho_2023, title={Interrelations of & alpha;- and & beta;-amylase activity with starch, sugars, and culinary and nutritional quality attributes in sweetpotato storage roots}, volume={7}, ISSN={["1097-0010"]}, url={https://doi.org/10.1002/jsfa.12832}, DOI={10.1002/jsfa.12832}, abstractNote={Abstract}, journal={JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE}, author={Amankwaah, Victor A. A. and Williamson, Sharon and Olukolu, Bode A. A. and Truong, Van-Den and Carey, Edward and Ssali, Reuben and Yencho, George Craig}, year={2023}, month={Jul} }
 @article{adams_kristy_gorman_balint-kurti_yencho_olukolu_2023, title={Qmatey: an automated pipeline for fast exact matching-based alignment and strain-level taxonomic binning and profiling of metagenomes}, volume={24}, ISSN={["1477-4054"]}, url={https://doi.org/10.1093/bib/bbad351}, DOI={10.1093/bib/bbad351}, abstractNote={Abstract}, number={6}, journal={BRIEFINGS IN BIOINFORMATICS}, author={Adams, Alison K. and Kristy, Brandon D. and Gorman, Myranda and Balint-Kurti, Peter and Yencho, G. Craig and Olukolu, Bode A.}, year={2023}, month={Sep} }
 @article{brůna_aryal_dudchenko_sargent_mead_buti_cavallini_hytönen_andrés_pham_et al._2022, title={A chromosome-length genome assembly and annotation of blackberry (<i>Rubus argutus</i>, cv. “Hillquist”)}, volume={11}, ISSN={2160-1836}, url={http://dx.doi.org/10.1093/g3journal/jkac289}, DOI={10.1093/g3journal/jkac289}, abstractNote={Abstract}, number={ue 2}, journal={G3 Genes|Genomes|Genetics}, publisher={Oxford University Press (OUP)}, author={Brůna, Tomáš and Aryal, Rishi and Dudchenko, Olga and Sargent, Daniel James and Mead, Daniel and Buti, Matteo and Cavallini, Andrea and Hytönen, Timo and Andrés, Javier and Pham, Melanie and et al.}, editor={Pyhäjärvi, TEditor}, year={2022}, month={Nov} }
 @article{mugisa_karungi_musana_odama_alajo_chelangat_anyanga_oloka_gonçalves dos santos_talwana_et al._2022, title={Combining ability and heritability analysis of sweetpotato weevil resistance, root yield, and dry matter content in sweetpotato}, volume={13}, ISSN={1664-462X}, url={http://dx.doi.org/10.3389/fpls.2022.956936}, DOI={10.3389/fpls.2022.956936}, abstractNote={Efficient breeding and selection of superior genotypes requires a comprehensive understanding of the genetics of traits. This study was aimed at establishing the general combining ability (GCA), specific combining ability (SCA), and heritability of sweetpotato weevil (Cylasspp.) resistance, storage root yield, and dry matter content in a sweetpotato multi-parental breeding population. A population of 1,896 F1clones obtained from an 8 × 8 North Carolina II design cross was evaluated with its parents in the field at two sweetpotato weevil hotspots in Uganda, using an augmented row-column design. Clone roots were further evaluated in three rounds of a no-choice feeding laboratory bioassay. Significant GCA effects for parents and SCA effects for families were observed for most traits and all variance components were highly significant (p ≤ 0.001). Narrow-sense heritability estimates for weevil severity, storage root yield, and dry matter content were 0.35, 0.36, and 0.45, respectively. Parental genotypes with superior GCA for weevil resistance included “Mugande,” NASPOT 5, “Dimbuka-bukulula,” and “Wagabolige.” On the other hand, families that displayed the highest levels of resistance to weevils included “Wagabolige” × NASPOT 10 O, NASPOT 5 × “Dimbuka-bukulula,” “Mugande” × “Dimbuka-bukulula,” and NASPOT 11 × NASPOT 7. The moderate levels of narrow-sense heritability observed for the traits, coupled with the significant GCA and SCA effects, suggest that there is potential for their improvement through conventional breedingviahybridization and progeny selection and advancement. Although selection for weevil resistance may, to some extent, be challenging for breeders, efforts could be boosted through applying genomics-assisted breeding. Superior parents and families identified through this study could be deployed in further research involving the genetic improvement of these traits.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Mugisa, Immaculate and Karungi, Jeninah and Musana, Paul and Odama, Roy and Alajo, Agnes and Chelangat, Doreen M. and Anyanga, Milton O. and Oloka, Bonny M. and Gonçalves dos Santos, Iara and Talwana, Herbert and et al.}, year={2022}, month={Sep} }
 @article{chen_samayoa_yang_olukolu_york_sanchez-gonzalez_xue_glaubitz_bradbury_romay_et al._2021, title={A conserved genetic architecture among populations of the maize progenitor, teosinte, was radically altered by domestication}, volume={118}, ISSN={["1091-6490"]}, DOI={10.1073/pnas.2112970118j1of10}, number={43}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Chen, Qiuyue and Samayoa, Luis Fernando and Yang, Chin Jian and Olukolu, Bode A. and York, Alessandra M. and Sanchez-Gonzalez, Jose de Jesus and Xue, Wei and Glaubitz, Jeffrey C. and Bradbury, Peter J. and Romay, Maria Cinta and et al.}, year={2021}, month={Oct} }
 @article{oloka_da silva pereira_amankwaah_mollinari_pecota_yada_olukolu_zeng_yencho_2021, title={Discovery of a major QTL for root-knot nematode (Meloidogyne incognita) resistance in cultivated sweetpotato (Ipomoea batatas)}, volume={134}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/s00122-021-03797-z}, DOI={10.1007/s00122-021-03797-z}, abstractNote={Abstract}, number={7}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Oloka, Bonny Michael and da Silva Pereira, Guilherme and Amankwaah, Victor A. and Mollinari, Marcelo and Pecota, Kenneth V. and Yada, Benard and Olukolu, Bode A. and Zeng, Zhao-Bang and Yencho, G. Craig}, year={2021}, month={Apr}, pages={1945–1955} }
 @article{samayoa_olukolu_yang_chen_stetter_york_sanchez-gonzalez_glaubitz_bradbury_romay_et al._2021, title={Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte}, volume={17}, ISSN={["1553-7404"]}, url={https://doi.org/10.1371/journal.pgen.1009797}, DOI={10.1371/journal.pgen.1009797}, abstractNote={Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to large-effect mutations versus variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load in the maize population that we predicted from sequence data. Parental breeding values were highly consistent between outcross and selfed offspring, indicating that additive effects determine most of the genetic value even in the presence of strong inbreeding depression. We developed a novel linkage scan to identify quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, small-effect partially recessive effects in linkage disequilibrium underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against some large effect variants, but polygenic load is harder to purge and overall segregating mutational burden increased in maize compared to teosinte.}, number={12}, journal={PLOS GENETICS}, publisher={Public Library of Science (PLoS)}, author={Samayoa, Luis Fernando and Olukolu, Bode A. and Yang, Chin Jian and Chen, Qiuyue and Stetter, Markus G. and York, Alessandra M. and Sanchez-Gonzalez, Jose de Jesus and Glaubitz, Jeffrey C. and Bradbury, Peter J. and Romay, Maria Cinta and et al.}, editor={Walsh, BruceEditor}, year={2021}, month={Dec} }
 @article{kuster_yencho_olukolu_2021, title={ngsComposer: an automated pipeline for empirically based NGS data quality filtering}, volume={22}, ISSN={["1477-4054"]}, DOI={10.1093/bib/bbab092}, abstractNote={Abstract}, number={5}, journal={BRIEFINGS IN BIOINFORMATICS}, author={Kuster, Ryan D. and Yencho, G. Craig and Olukolu, Bode A.}, year={2021}, month={Sep} }
 @article{zhou_olukolu_gemenet_wu_gruneberg_cao_fei_zeng_george_khan_et al._2020, title={Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations}, volume={52}, ISSN={1061-4036 1546-1718}, url={http://dx.doi.org/10.1038/s41588-020-00717-7}, DOI={10.1038/s41588-020-00717-7}, abstractNote={Despite advances in sequencing technologies, assembly of complex plant genomes remains elusive due to polyploidy and high repeat content. Here we report PolyGembler for grouping and ordering contigs into pseudomolecules by genetic linkage analysis. Our approach also provides an accurate method with which to detect and fix assembly errors. Using simulated data, we demonstrate that our approach is of high accuracy and outperforms three existing state-of-the-art genetic mapping tools. Particularly, our approach is more robust to the presence of missing genotype data and genotyping errors. We used our method to construct pseudomolecules for allotetraploid lawn grass utilizing PacBio long reads in combination with restriction site-associated DNA sequencing, and for diploid Ipomoea trifida and autotetraploid potato utilizing contigs assembled from Illumina reads in combination with genotype data generated by single-nucleotide polymorphism arrays and genotyping by sequencing, respectively. We resolved 13 assembly errors for a published I. trifida genome assembly and anchored eight unplaced scaffolds in the published potato genome.}, number={11}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={Zhou, Chenxi and Olukolu, Bode and Gemenet, Dorcus C. and Wu, Shan and Gruneberg, Wolfgang and Cao, Minh Duc and Fei, Zhangjun and Zeng, Zhao-Bang and George, Andrew W. and Khan, Awais and et al.}, year={2020}, month={Oct}, pages={1256–1264} }
 @article{chen_samayoa_yang_bradbury_olukolu_neumeyer_romay_sun_lorant_buckler_et al._2020, title={The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication}, volume={16}, ISSN={["1553-7404"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85085904066&partnerID=MN8TOARS}, DOI={10.1371/journal.pgen.1008791}, abstractNote={The genetics of domestication has been extensively studied ever since the rediscovery of Mendel’s law of inheritance and much has been learned about the genetic control of trait differences between crops and their ancestors. Here, we ask how domestication has altered genetic architecture by comparing the genetic architecture of 18 domestication traits in maize and its ancestor teosinte using matched populations. We observed a strongly reduced number of QTL for domestication traits in maize relative to teosinte, which is consistent with the previously reported depletion of additive variance by selection during domestication. We also observed more dominance in maize than teosinte, likely a consequence of selective removal of additive variants. We observed that large effect QTL have low minor allele frequency (MAF) in both maize and teosinte. Regions of the genome that are strongly differentiated between teosinte and maize (high FST) explain less quantitative variation in maize than teosinte, suggesting that, in these regions, allelic variants were brought to (or near) fixation during domestication. We also observed that genomic regions of high recombination explain a disproportionately large proportion of heritable variance both before and after domestication. Finally, we observed that about 75% of the additive variance in both teosinte and maize is “missing” in the sense that it cannot be ascribed to detectable QTL and only 25% of variance maps to specific QTL. This latter result suggests that morphological evolution during domestication is largely attributable to very large numbers of QTL of very small effect.}, number={5}, journal={PLOS GENETICS}, publisher={Public Library of Science (PLoS)}, author={Chen, Qiuyue and Samayoa, Luis Fernando and Yang, Chin Jian and Bradbury, Peter J. and Olukolu, Bode A. and Neumeyer, Michael A. and Romay, Maria Cinta and Sun, Qi and Lorant, Anne and Buckler, Edward S. and et al.}, editor={Mauricio, RodneyEditor}, year={2020}, month={May} }
 @article{wadl_olukolu_branham_jarret_yencho_jackson_2018, title={Genetic Diversity and Population Structure of the USDA Sweetpotato (Ipomoea batatas) Germplasm Collections Using GBSpoly}, volume={9}, ISSN={1664-462X}, url={http://dx.doi.org/10.3389/fpls.2018.01166}, DOI={10.3389/fpls.2018.01166}, abstractNote={Sweetpotato (Ipomoea batatas) plays a critical role in food security and is the most important root crop worldwide following potatoes and cassava. In the United States (US), it is valued at over $700 million USD. There are two sweetpotato germplasm collections (Plant Genetic Resources Conservation Unit and US Vegetable Laboratory) maintained by the USDA, ARS for sweetpotato crop improvement. To date, no genome-wide assessment of genetic diversity within these collections has been reported in the published literature. In our study, population structure and genetic diversity of 417 USDA sweetpotato accessions originating from 8 broad geographical regions (Africa, Australia, Caribbean, Central America, Far East, North America, Pacific Islands, and South America) were determined using single nucleotide polymorphisms (SNPs) identified with a genotyping-by-sequencing (GBS) protocol, GBSpoly, optimized for highly heterozygous and polyploid species. Population structure using Bayesian clustering analyses (STRUCTURE) with 32,784 segregating SNPs grouped the accessions into four genetic groups and indicated a high degree of mixed ancestry. A neighbor-joining cladogram and principal components analysis based on a pairwise genetic distance matrix of the accessions supported the population structure analysis. Pairwise FST values between broad geographical regions based on the origin of accessions ranged from 0.017 (Far East – Pacific Islands) to 0.110 (Australia – South America) and supported the clustering of accessions based on genetic distance. The markers developed for use with this collection of accessions provide an important genomic resource for the sweetpotato community, and contribute to our understanding of the genetic diversity present within the US sweetpotato collection and the species.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Wadl, Phillip A. and Olukolu, Bode A. and Branham, Sandra E. and Jarret, Robert L. and Yencho, G. Craig and Jackson, D. Michael}, year={2018}, month={Aug} }
 @article{wu_lau_cao_hamilton_sun_zhou_eserman_gemenet_olukolu_wang_et al._2018, title={Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement}, volume={9}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-018-06983-8}, DOI={10.1038/s41467-018-06983-8}, abstractNote={Abstract}, number={1}, journal={Nature Communications}, publisher={Springer Nature}, author={Wu, Shan and Lau, Kin H. and Cao, Qinghe and Hamilton, John P. and Sun, Honghe and Zhou, Chenxi and Eserman, Lauren and Gemenet, Dorcus C. and Olukolu, Bode A. and Wang, Haiyan and et al.}, year={2018}, month={Nov} }
 @article{xiaodong_olukolu_yang_balint-kurti_2018, title={Identification of a locus in maize controlling response to a host-selective toxin derived from Cochliobolus heterostrophus, causal agent of southern leaf blight}, volume={131}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/s00122-018-3175-6}, DOI={10.1007/s00122-018-3175-6}, abstractNote={A host-selective, proteinaceous maize toxin was identified from the culture filtrate of the maize pathogen Cochliobolus heterostrophus. A dominant gene for toxin susceptibility was identified on maize chromosome 4. A toxic activity was identified from the culture filtrate (CF) of the fungus Cochliobolus heterostrophus, causal agent of the maize disease southern leaf blight (SLB) with differential toxicity on maize lines. Two independent mapping populations; a 113-line recombinant inbred line population and a 258-line association population, were used to map loci associated with sensitivity to the CF at the seedling stage. A major QTL on chromosome 4 was identified at the same locus using both populations. Mapping in the association population defined a 400 kb region that contained the sensitivity locus. By comparing CF-sensitivity of the parents of the RIL population with that of the F 1  progeny, we determined that the sensitivity allele was dominant. No relationship was observed between CF-sensitivity in seedlings and SLB susceptibility in mature plants; however, a significant correlation (- 0.58) was observed between SLB susceptibility and CF-sensitivity in seedlings. The activity of the CF was light-dependent and was sensitive to pronase, indicating that the toxin was proteinaceous.}, number={12}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Xiaodong, Xie and Olukolu, Bode and Yang, Qin and Balint-Kurti, Peter}, year={2018}, month={Sep}, pages={2601–2612} }
 @article{olukolu_tracy_wisser_de vries_balint-kurti_2016, title={A Genome-Wide Association Study for Partial Resistance to Maize Common Rust}, volume={106}, ISSN={["1943-7684"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84975087459&partnerID=MN8TOARS}, DOI={10.1094/phyto-11-15-0305-r}, abstractNote={Quantitative resistance to maize common rust (causal agent Puccinia sorghi) was assessed in an association mapping population of 274 diverse inbred lines. Resistance to common rust was found to be moderately correlated with resistance to three other diseases and with the severity of the hypersensitive defense response previously assessed in the same population. Using a mixed linear model accounting for the confounding effects of population structure and flowering time, genome-wide association tests were performed based at 246,497 single-nucleotide polymorphism loci. Three loci associated with maize common rust resistance were identified. Candidate genes at each locus had predicted roles, mainly in cell wall modification. Other candidate genes included a resistance gene and a gene with a predicted role in regulating accumulation of reactive oxygen species.}, number={7}, journal={PHYTOPATHOLOGY}, author={Olukolu, Bode A. and Tracy, William F. and Wisser, Randall and De Vries, Brian and Balint-Kurti, Peter J.}, year={2016}, month={Jul}, pages={745–751} }
 @article{olukolu_bian_de vries_tracy_wisser_holland_balint-kurti_2016, title={The Genetics of Leaf Flecking in Maize and Its Relationship to Plant Defense and Disease Resistance}, volume={172}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.15.01870}, DOI={10.1104/pp.15.01870}, abstractNote={Leaf flecking in maize may be related to disease resistance and to a diverse set of metabolic pathways. Physiological leaf spotting, or flecking, is a mild-lesion phenotype observed on the leaves of several commonly used maize (Zea mays) inbred lines and has been anecdotally linked to enhanced broad-spectrum disease resistance. Flecking was assessed in the maize nested association mapping (NAM) population, comprising 4,998 recombinant inbred lines from 25 biparental families, and in an association population, comprising 279 diverse maize inbreds. Joint family linkage analysis was conducted with 7,386 markers in the NAM population. Genome-wide association tests were performed with 26.5 million single-nucleotide polymorphisms (SNPs) in the NAM population and with 246,497 SNPs in the association population, resulting in the identification of 18 and three loci associated with variation in flecking, respectively. Many of the candidate genes colocalizing with associated SNPs are similar to genes that function in plant defense response via cell wall modification, salicylic acid- and jasmonic acid-dependent pathways, redox homeostasis, stress response, and vesicle trafficking/remodeling. Significant positive correlations were found between increased flecking, stronger defense response, increased disease resistance, and increased pest resistance. A nonlinear relationship with total kernel weight also was observed whereby lines with relatively high levels of flecking had, on average, lower total kernel weight. We present evidence suggesting that mild flecking could be used as a selection criterion for breeding programs trying to incorporate broad-spectrum disease resistance.}, number={3}, journal={Plant Physiology}, publisher={Oxford University Press (OUP)}, author={Olukolu, Bode A. and Bian, Yang and De Vries, Brian and Tracy, William F. and Wisser, Randall J. and Holland, James B. and Balint-Kurti, Peter J.}, year={2016}, month={Sep}, pages={1787–1803} }
 @article{samayoa_malvar_olukolu_holland_butron_2015, title={Genome-wide association study reveals a set of genes associated with resistance to the Mediterranean corn borer (Sesamia nonagrioides L.) in a maize diversity panel}, volume={15}, ISSN={["1471-2229"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84924054437&partnerID=MN8TOARS}, DOI={10.1186/s12870-014-0403-3}, abstractNote={Corn borers are the primary maize pest; their feeding on the pith results in stem damage and yield losses. In this study, we performed a genome-wide association study (GWAS) to identify SNPs associated with resistance to Mediterranean corn borer in a maize diversity panel using a set of more than 240,000 SNPs.Twenty five SNPs were significantly associated with three resistance traits: 10 were significantly associated with tunnel length, 4 with stem damage, and 11 with kernel resistance. Allelic variation at each significant SNP was associated with from 6 to 9% of the phenotypic variance. A set of genes containing or physically close to these SNPs are proposed as candidate genes for borer resistance, supported by their involvement in plant defense-related mechanisms in previously published evidence. The linkage disequilibrium decayed (r(2) < 0.10) rapidly within short distance, suggesting high resolution of GWAS associations.Most of the candidate genes found in this study are part of signaling pathways, others act as regulator of expression under biotic stress condition, and a few genes are encoding enzymes with antibiotic effect against insects such as the cystatin1 gene and the defensin proteins. These findings contribute to the understanding the complex relationship between plant-insect interactions.}, number={1}, journal={BMC PLANT BIOLOGY}, author={Samayoa, Luis Fernando and Malvar, Rosa Ana and Olukolu, Bode A. and Holland, James B. and Butron, Ana}, year={2015}, month={Feb} }
 @article{wang_he_strauch_olukolu_nielsen_li_balint-kurti_2015, title={Maize homologs of hydroxycinnamoyltransferase, a key enzyme in lignin biosynthesis, bind the nucleotide binding leucine-rich repeat Rp1 proteins to modulate the defense response}, volume={169}, number={3}, journal={Plant Physiology}, author={Wang, G. F. and He, Y. J. and Strauch, R. and Olukolu, B. A. and Nielsen, D. and Li, X. and Balint-Kurti, P. J.}, year={2015}, pages={2230–2243} }
 @article{staton_zhebentyayeva_olukolu_fang_nelson_carlson_abbott_2015, title={Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes}, volume={16}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-015-1942-1}, abstractNote={Chinese chestnut (Castanea mollissima) has emerged as a model species for the Fagaceae family with extensive genomic resources including a physical map, a dense genetic map and quantitative trait loci (QTLs) for chestnut blight resistance. These resources enable comparative genomics analyses relative to model plants. We assessed the degree of conservation between the chestnut genome and other well annotated and assembled plant genomic sequences, focusing on the QTL regions of most interest to the chestnut breeding community.The integrated physical and genetic map of Chinese chestnut has been improved to now include 858 shared sequence-based markers. The utility of the integrated map has also been improved through the addition of 42,970 BAC (bacterial artificial chromosome) end sequences spanning over 26 million bases of the estimated 800 Mb chestnut genome. Synteny between chestnut and ten model plant species was conducted on a macro-syntenic scale using sequences from both individual probes and BAC end sequences across the chestnut physical map. Blocks of synteny with chestnut were found in all ten reference species, with the percent of the chestnut physical map that could be aligned ranging from 10 to 39 %. The integrated genetic and physical map was utilized to identify BACs that spanned the three previously identified QTL regions conferring blight resistance. The clones were pooled and sequenced, yielding 396 sequence scaffolds covering 13.9 Mbp. Comparative genomic analysis on a microsytenic scale, using the QTL-associated genomic sequence, identified synteny from chestnut to other plant genomes ranging from 5.4 to 12.9 % of the genome sequences aligning.On both the macro- and micro-synteny levels, the peach, grape and poplar genomes were found to be the most structurally conserved with chestnut. Interestingly, these results did not strictly follow the expectation that decreased phylogenetic distance would correspond to increased levels of genome preservation, but rather suggest the additional influence of life-history traits on preservation of synteny. The regions of synteny that were detected provide an important tool for defining and cataloging genes in the QTL regions for advancing chestnut blight resistance research.}, journal={BMC GENOMICS}, author={Staton, Margaret and Zhebentyayeva, Tetyana and Olukolu, Bode and Fang, Guang Chen and Nelson, Dana and Carlson, John E. and Abbott, Albert G.}, year={2015}, month={Oct} }
 @article{vontimitta_olukolu_penning_johal_balint-kurti_2015, title={The genetic basis of flecking and its relationship to disease resistance in the IBM maize mapping population}, volume={128}, ISSN={["1432-2242"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84938651542&partnerID=MN8TOARS}, DOI={10.1007/s00122-015-2588-8}, abstractNote={In this paper, we determine the genetic architecture controlling leaf flecking in maize and investigate its relationship to disease resistance and the defense response. Flecking is defined as a mild, often environmentally dependent lesion phenotype observed on the leaves of several commonly used maize inbred lines. Anecdotal evidence suggests a link between flecking and enhanced broad-spectrum disease resistance. Neither the genetic basis underlying flecking nor its possible relationship to disease resistance has been systematically evaluated. The commonly used maize inbred Mo17 has a mild flecking phenotype. The IBM-advanced intercross mapping population, derived from a cross between Mo17 and another commonly used inbred B73, has been used for mapping a number of traits in maize including several related to disease resistance. In this study, flecking was assessed in the IBM population over 6 environments. Several quantitative trait loci for flecking were identified, with the strongest one located on chromosome 6. Low but moderately significant correlations were observed between stronger flecking and higher disease resistance with respect to two diseases, southern leaf blight and northern leaf blight and between stronger flecking and a stronger defense response.}, number={11}, journal={THEORETICAL AND APPLIED GENETICS}, author={Vontimitta, Vijay and Olukolu, Bode A. and Penning, Bryan W. and Johal, Gurmukh and Balint-Kurti, P. J.}, year={2015}, month={Nov}, pages={2331–2339} }
 @article{olukolu_negeri_dhawan_venkata_sharma_garg_gachomo_marla_chu_hasan_et al._2013, title={A Connected Set of Genes Associated with Programmed Cell Death Implicated in Controlling the Hypersensitive Response in Maize}, volume={193}, ISSN={["0016-6731"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84876366651&partnerID=MN8TOARS}, DOI={10.1534/genetics.112.147595}, abstractNote={Abstract}, number={2}, journal={GENETICS}, author={Olukolu, Bode A. and Negeri, Adisu and Dhawan, Rahul and Venkata, Bala P. and Sharma, Pankaj and Garg, Anshu and Gachomo, Emma and Marla, Sandeep and Chu, Kevin and Hasan, Anna and et al.}, year={2013}, month={Feb}, pages={609-+} }
 @article{fang_blackmon_staton_nelson_kubisiak_olukolu_henry_zhebentyayeva_saski_cheng_et al._2013, title={A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map}, volume={9}, ISSN={["1614-2950"]}, DOI={10.1007/s11295-012-0576-6}, abstractNote={Three Chinese chestnut bacterial artificial chromosome (BAC) libraries were developed and used for physical map construction. Specifically, high information content fingerprinting was used to assemble 126,445 BAC clones into 1,377 contigs and 12,919 singletons. Integration of the dense Chinese chestnut genetic map with the physical map was achieved via high-throughput hybridization using overgo probes derived from sequence-based genetic markers. A total of 1,026 probes were anchored to the physical map including 831 probes corresponding to 878 expressed sequence tag-based markers. Within the physical map, three BAC contigs were anchored to the three major fungal blight-resistant quantitative trait loci on chestnut linkage groups B, F, and G. A subset of probes corresponding to orthologous genes in poplar showed only a limited amount of conserved gene order between the poplar and chestnut genomes. The integrated genetic and physical map of Chinese chestnut is available at www.fagaceae.org/physical_maps .}, number={2}, journal={TREE GENETICS & GENOMES}, author={Fang, Guang-Chen and Blackmon, Barbara P. and Staton, Margaret E. and Nelson, C. Dana and Kubisiak, Thomas L. and Olukolu, Bode A. and Henry, David and Zhebentyayeva, Tatyana and Saski, Christopher A. and Cheng, Chun-Huai and et al.}, year={2013}, month={Apr}, pages={525–537} }
 @article{kubisiak_nelson_staton_zhebentyayeva_smith_olukolu_fang_hebard_anagnostakis_wheeler_et al._2012, title={A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica)}, volume={9}, ISSN={1614-2942 1614-2950}, url={http://dx.doi.org/10.1007/S11295-012-0579-3}, DOI={10.1007/S11295-012-0579-3}, abstractNote={The Chinese chestnut (Castanea mollissima) carries resistance to Cryphonectria parasitica, the fungal pathogen inciting chestnut blight. The pathogen, introduced from Asia, devastated the American chestnut (Castanea dentata) throughout its native range early in the twentieth century. A highly informative genetic map of Chinese chestnut was constructed to extend genomic studies in the Fagaceae and to aid the introgression of Chinese chestnut blight resistance genes into American chestnut. Two mapping populations were established with three Chinese chestnut parents, ‘Mahogany’, ‘Nanking’, and ‘Vanuxem’, totaling 337 progeny. The transcriptome-based genetic map was created with 329 simple sequence repeat and 1,064 single nucleotide polymorphism markers all derived from expressed sequence tag sequences. Genetic maps for each parent were developed and combined to establish 12 consensus linkage groups spanning 742 cM, providing the the most comprehensive genetic map for a Fagaceae species to date. Over 75 % of the mapped markers from the Chinese chestnut consensus genetic map were placed on the physical map using overgo hybridization, providing a fully integrated genetic and physical map resource for Castanea spp. About half (57 %) of the Chinese chestnut genetic map could be assigned to regions of segmental homology with 58 % of the peach (Prunus persica) genome assembly. A three quantitative trait loci (QTL) model for blight resistance was verified using the new genetic markers and an existing interspecies (C. mollissima × C. dentata) F2 mapping population. Two of the blight resistance QTLs in chestnut shared synteny with two QTLs for powdery mildew resistance in peach, indicating the potential conservation of disease resistance genes at these loci.}, number={2}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Kubisiak, T. L. and Nelson, C. D. and Staton, M. E. and Zhebentyayeva, T. and Smith, C. and Olukolu, B. A. and Fang, G.-C. and Hebard, F. V. and Anagnostakis, S. and Wheeler, N. and et al.}, year={2012}, month={Nov}, pages={557–571} }
 @article{olukolu_mayes_stadler_quat ng_fawole_dominique_azam-ali_abbott_kole_2011, title={Genetic diversity in Bambara groundnut (Vigna subterranea (L.) Verdc.) as revealed by phenotypic descriptors and DArT marker analysis}, volume={59}, ISSN={0925-9864 1573-5109}, url={http://dx.doi.org/10.1007/S10722-011-9686-5}, DOI={10.1007/S10722-011-9686-5}, number={3}, journal={Genetic Resources and Crop Evolution}, publisher={Springer Science and Business Media LLC}, author={Olukolu, Bode A. and Mayes, Sean and Stadler, Florian and Quat Ng, N. and Fawole, Iyiwole and Dominique, Dumet and Azam-Ali, Sayed N. and Abbott, Albert G. and Kole, Chittaranjan}, year={2011}, month={Mar}, pages={347–358} }
 @article{liang_zhebentyayeva_olukolu_wilde_reighard_abbott_2010, title={Comparison of gene order in the chromosome region containing a TERMINAL FLOWER 1 homolog in apricot and peach reveals microsynteny across angiosperms}, volume={179}, ISSN={0168-9452}, url={http://dx.doi.org/10.1016/j.plantsci.2010.06.018}, DOI={10.1016/j.plantsci.2010.06.018}, abstractNote={The TERMINAL FLOWER 1 (TFL1) plays crucial roles in regulating the vegetative to reproductive phase transition and maintaining the inflorescence meristem. We characterized one apricot (Pa_GBa141J23) and one peach (Pp_NBa103A15) BAC clone harboring a TFL1 gene. Sequence analysis revealed that the apricot and peach TFL1 (PaTFL1 and PpTFL1) genes display a similar exon–intron organization to homologs from other eudicot species and the defined amino acid domains are preserved. Phylogenetic analysis grouped PaTFL1 and PpTFL1 with the Arabidopsis ortholog. Numerous cis-elements present in the upstream regulatory region of the Arabidopsis TFl1 were identified in the PaTFL1 and PpTFL1 promoter regions. Two TFL1 alleles involving SSR polymorphism exist in the ‘Nemared’ peach cultivar. All nine genes annotated in the apricot Pa_GBa141J23 BAC have the same gene order in the peach genome. Syntenic regions are present in angiosperm species around the TFL1 locus, with the size of syntenic region decreasing from eudicots to monocots.}, number={4}, journal={Plant Science}, publisher={Elsevier BV}, author={Liang, Haiying and Zhebentyayeva, Tetyana and Olukolu, Bode and Wilde, Dayton and Reighard, Gregory L. and Abbott, Albert}, year={2010}, month={Oct}, pages={390–398} }