Maize Genetics | Publications

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2024

Publication Title	PDF
Morales N, Anche MT, Kaczmar NS, Lepak N, Ni P, Romay MC, Santanonio N, Buckler ES, Gore MA, Mueller LA, Robbins KR (2024). Spatio-temporal modeling of high-throughput multispectral aerial images improves agronomic trait genomic prediction in hybrid maize. Genetics iyae037. https://doi.org/10.1093/genetics/iyae037
Wrightsman T, Ferebee TH, Romay MC, AuBuchon-Elder T, Phillips AR, Syring M, Kellogg ES, Buckler ES (2024). Current genomic deep learning architectures generalize across grass species but not alleles. bioRxiv https://doi.org/10.1101/2024.04.11.589024
Long EM, Stitzer M, Monier B, Schulz AJ, Romay MC, Robbins KR, Buckler ES (2024). Muller’s Ratchet in Action: The Erosion of Sexual Reproduction Genes in Domesticated Cassava (Manihot esculenta). bioRxiv https://doi.org/10.1101/2024.02.14.580345
Hsu SK, Emmett BD, Haffke AJ, Costa-Neto G, Schulz AJ, Lepak N, La T, AuBuchon-Elder TM, O’Hale C, Raglin SS, Ojeda-Rivera JO, Kent AD, Kellog EA, Romay MC, Buckler ES (2024). Contrasting Rhizonsphere Nitrogen Dynamics in Andropogoneae Grasses: Implications for Sustainable Agriculture. bioRxiv https://doi.org/10.1101/2024.06.03.597142
Li T, Xu H, Teng S, Suo M, Bahitwa R, Xu M, Qian Y, Ramstein GP, Song B, Buckler ES, Wang H (2024). Modeling 0.6 million genes for the rational design of functionalcis- regulatory variants and de novo design of cis-regulatorysequences. PNAS 121(26):2319811121 https://www.pnas.org/doi/10.1073/pnas.2319811121

2023

Publication Title	PDF
Wu Y, Li D, Hu H, Li H, Ramstein GP, Zhou S, Zhang X, Bao Z, Zhang Y, Song B, Zhou Y, Zhou Y, Gagnon E, Särkinen T, Knapp S, Zhang C, Städler T, Buckler ES, Huang S (2023). Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell 186(11):2313. https://doi.org/10.1016/j.cell.2023.04.008
Song B, Buckler ES, Stitzer MC (2023). New whole-genome alignment tools are needed for tapping into plant diversity Trends in Plant Science(in press) https://doi.org/10.1016/j.tplants.2023.08.013
Ribeiro CAG, Tinoco SMS, de Souza VF, Negri BF, Gault CM, Pastina MM, Magalhaes JV, Guimarães LJM, de Barros EG, Buckler ES, Guimaraes CT (2023). Genome-Wide Association Study for Root Morphology and Phosphorus Acquisition Efficiency in Diverse Maize Panels. International Journal of Molecular Sciences 24(7):6233. https://doi.org/10.3390/ijms24076233
Phillips AR, Seetharam AS, Albert PS, AuBuchon-Elder T, Birchler JA, Buckler ES, Gillespie LJ, Hufford MB, Llaca V, Romay MC, Soreng RJ, Kellogg ES, Ross-Ibarra J (2023). A happy accident: a novel turfgrass reference genome. G3: Genes, Genomes, Genetics13(6):jkad073. https://doi.org/10.1093/g3journal/jkad073
Pardo J, Wai CM, Harman M, Nguyen A, Kremling KA, Romay MC, Lepak N, Bauerle TL, Buckler ES, Thompson AM, VanBuren R (2023). Cross-species predictive modeling reveals conserved drought responses between maize and sorghum. Proceedings of the National Academy of Sciences 120(10):e2216894120. https://doi.org/10.1073/pnas.2216894120
Lima DC, Washburn JD, Varela JI, Chen Q, Gage JL, Romay MC, Holland J, Ertl D, . . . Bohn M, Buckler ES, Edwards J, Flint-Garcia S, Gore MA, Hirsch CN, Knoll JE, McKay J, Minyo R, Murray SC, Ortez OA, Schnable JC, Sekhon RS, Singh MP, Sparks EE, Thompson A, Tuinstra M, Wallace J, Weldekidan T, Xu W, de Leon N (2023). Genomes to Fields 2022 Maize genotype by Environment Prediction Competition. BMC Research Notes 16(1):148. https://doi.org/10.1186/s13104-023-06421-z
Lima DC, Aviles AC, Alpers RT, Perkins A, Schoemaker DL, Costa M, Kaeppler S, Ertl D, Romay MC, Gage JL, Holland J, Beissinger T, Bohn M, Buckler ES, Edwards J, Flint-Garcia S, Gore MA, Hirsch CN, Knoll JE, McKay J, Minyo R, Murray SC, Schnable J, . . . Wallace J, Washburn J, Weldekidan T, Xu W, de Leon N (2023). 2020-2021 Field Seasons of Maize G x E Project within Maize Genomes to Fields Initiative. Research Square (preprint). https://doi.org/10.21203/rs.3.rs-2908766/v1
Lima DC, Aviles AC, Alpers RT, McFarland BA, Kaeppler S, Ertl D, Romay MC, Gage JL, Holland J, Beissinger T, Bohn M, Buckler ES, Edwards J, Flint-Garcia S, Hirsch CN, Hood E, Hooker DC, Knoll JE, Kolkman JM, Liu S, McKay J, . . . , Singh MP, Thomison P, Thompson A, Tuinstra M, Wallace J, Washburn JD, Weldekidan T, Wisser RJ, Xu W, de Leon N (2023). 2018–2019 field seasons of the Maize Genomes to Fields (G2F) G x E project. BMC Genomic Data 24(1):29. https://doi.org/10.1186/s12863-023-01129-2
Khaipho-Burch M, Cooper M, Crossa J, de Leon N, Holland J, Lewis R, McCouch S, Murray SC, Rabbi I, Ronald P, Ross-Ibarra J, Weigel D, Buckler ES (2023). Scale up trials to validate modified crops’ benefits. Nature 621:470. https://doi.org/10.1038/d41586-023-02895-w
Khaipho-Burch M, Ferebee T, Giri A, Ramstein G, Monier B, Yi E, Romay MC, Buckler ES (2023). Elucidating the patterns of pleiotropy and its biological relevance in maize. PLoS Genetics 19(3):e1010664. https://doi.org/10.1371/journal.pgen.1010664.
Gorjifard S, Jores T, Tonnies J, Mueth NA, Bubb KL, Wrightsman T, Buckler ES, Fields S, Cuperus JT, Queitsch C (2023). Features that Govern Terminator Strength in Plants. bioRxiv https://doi.org/10.1101/2023.06.16.545379
Ferebee TH, Buckler ES (2023). Exploring the utility of regulatory network-based machine learning for gene expression prediction in maize. bioRxiv https://doi.org/10.1101/2023.05.11.540406

2022

Publication Title	PDF
Long EM, Romay MC, Ramstein G, Buckler ES, Robbins KR (2022). Utilizing evolutionary conservation to detect deleterious mutations and improve genomic prediction in cassava. Frontiers in Plant Science 13:1041925. https://doi.org/10.3389/fpls.2022.1041925
Morales N, Anche MT, Kaczmar NS, Lepak N, Ni P, Romay MC, Santanonio N, Buckler ES, Gore MA, Mueller LA, Robbins KR (2022).Spatio-temporal modeling of high-throughput multi-spectral aerial images improves agronomic trait genomic prediction in hybrid maize. bioRxiv https://doi.org/10.1101/2022.10.18.512728
Wilcox MC, Burgueño JA, Jeffers D, Rodriguez-Chanona E, Guadarrama-Espinoza A, Kehel Z, Chepetla D, Shrestha R, Swarts KL, Buckler ES, Hearne S, Chen C (2022). Mining alleles for tar spot complex resistance from CIMMYT's maize Germplasm Bank. Frontiers in Sustainable Food Systems 6:937200 doi:10.3389/fsufs.2022.937200
Wrightsman T, Marand AP, Crisp PA, Springer NM, Buckler ES (2022). Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks.The Plant Genome 15(3) https://doi.org/10.1002/tpg2.20249
Zhang X, Zhu Y, Kremling KAG, Romay MC, Bukowski R, Sun Q, Gao S, ES, Lu F (2022). Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact. Theoretical Applied Genetics 135:273–290 https://doi.org/10.1007/s00122-021-03965-1
Long EM, Bradbury PJ, Romay MC, Buckler ES, Robbins KR (2022). Genome-wide imputation using the practical haplotype graph in the heterozygous crop cassava. G3 Genes\|Genomes\|Genetics 12(1):jkab383 https://doi.org/10.1093/g3journal/jkab383
Bradbury PJ, Casstevens T, Jensen SE, Johnson LC, Miller ZR, Monier B, Romay MC, Song B, Buckler ES (2022). The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. Bioinformatics https://doi.org/10.1093/bioinformatics/btac410
Oren E, Dafna A,Tzuri G, Halperin I, Isaacson T, Elkabetz M, Meir A,Saar U, Ohali S, La T, Romay C, Tadmor Y, Schaffer AA, Buckler ES, Cohen R, Burger J, Gur A (2022). Pan-genome and multi-parental framework for high-resolution trait dissection in melon (Cucumis melo). The Plant Genome https://doi.org/10.1111/tpj.16021
Ramstein GP, Buckler ES (2022). Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize. Genome Biology 23(18) https://doi.org/10.1186/s13059-022-02747-2
Monier B, Casstevens T, Bradbury PJ, Buckler ES (2022). rTASSEL: An R interface to TASSEL for analyzing genomic diversity. Journal of Open Source Software, 7(76):4530 https://doi.org/10.21105/joss.04530
Khaipho-Burch M, Ferebee T, Giri A, Ramstein G, Monier B, Yi E, Romay MC, Buckler ES (2022). Elucidating the patterns of pleiotropy and its biological relevance in maize. bioRxiv https://doi.org/10.1101/2022.07.20.500810
Barnes AC, Rodríguez-Zapata F, Juárez-Núñez KA, Gates DJ, Janzen GM, Kur A, Wang L, Jensen SE, Estévez-Palmas JM, Crow, Kavi HS, Pil HD, Stokes RL, Knizner KT, Aguilar-Rangel MR, . . . , Buckler ES, Ross-Ibarra J, Hufford MB, Sawers RJH, Rellán-Álvarez R (2022). An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time. PNAS 119 (27) e2100036119 hhttps://www.pnas.org/doi/10.1073/pnas.2100036119
Barrett CB, Benton T, Fanzo J, Herrero M, Nelson RJ, Bageant E, Buckler ES, Cooper K, Culotta I, Fan S, Gandhi R, James S . . . Miller A, Misra K, Mude A, Shen J, Sibanda LM, Song C, Steiner R, Thornton P, Wood S (2022). Socio-Technical Innovation Bundles for Agri-Food Systems Transformation, Springer Nature, https://library.oapen.org/handle/20.500.12657/54421
Wu Y, Johnson L, Song B, Romay C, Stitzer M, Siepel A, Buckler ES, Scheben A (2022). A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants. The Plant Genome e20204 https://doi.org/10.1002/tpg2.20204
Phillips AR, Seetharam AS, AuBuchon-Elder T, Buckler ES, Gillespie LJ, Hufford M, Llaca V, Romay C, Soreng RJ, Kellogg E, Ross-Ibarra J (2022). A happy accident: a novel turfgrass reference genome. bioRxiv https://doi.org/10.1101/2022.03.08.483531
Gage JL, Mali S, McLoughlin F, Khaipho-Burch M, Monier B, Bailey-Serres J, Vierstra RD, Buckler ES (2022). Variation in upstream open reading frames contributes to allelic diversity in maize protein abundance. PNAS 119(14):e2112516119 https://doi.org/10.1073/pnas.2112516119
Jordan KW, Bradbury PJ, Miller ZR, Nyine M, He F, Fraser M, Anderson J, Mason E, Katz A, Pearce S, Carter AJ, Prather S, Pumphrey M, Chen J, Cook J . . . Akhunova A, Bai G, Bowden R, Fiedler J, Faris J, Dubcovsky J, Guttieri M, Brown-Guedira G, Buckler ES, Jannink JL, Akhunov ED (2022). Development of the Wheat Practical Haplotype Graph Database as a resource for genotyping data storage and genotype imputation. G3 Genes\|Genomes\|Genetics 12(2): jkab390 https://doi.org/10.1093/g3journal/jkab390
Oren E, Tzuri G, Dafna A, Rees ER, Song B, Freilich S, Elkind Y, Isaacson T, Schaffer AA, Tadmor Y, Burger J, Buckler ES, Gur A (2022). QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon Recombinant Inbred Lines population supported by de novo assembly of their parental genomes. Horticulture Research uhab081 https://doi.org/10.1093/hr/uhab081
Song B, Marco-Sola S, Moreto M, Johnson L, Buckler ES, Stitzer MC (2022). AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication. PNAS 119(1):e2113075119 https://www.pnas.org/content/119/1/e2113075119

2021

Publication Title	PDF
Samayoa LF, Olukolu BA, Yang CJ, Chen Q, Stetter MG, York AM, Sanchez-Gonzalez JJ, Glaubitz JC, Bradbury PJ, Romay MC, Sun Q, Yang J, Ross-Ibarra J, Buckler ES, Doebley JF, Holland JB (2021). Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte. PLoS Genetics 17(12):e1009797 https://doi.org/10.1371/journal.pgen.1009797
Baseggio M, Murray M, Wu D, Ziegler G, Kaczmar N, Chamness J, Hamilton JP, Buell CR,Vatamaniuk OK, Buckler ES, Smith ME, Baxter I, Tracy WF, Gore MA (2021). Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels G3 Genes\|Genomes\|Genetics 11(8):jkab186 https://doi.org/10.1093/g3journal/jkab186
Ferguson JN, Fernandes SB, Monier B, Miller ND, Allan D, Dmitrieva A, Schmuker P, Lozano R, Valluru R, Buckler ES, Gore MA, Brown PJ, Spalding EP, Leakey ADB (2021). Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions. Plant Physiology 187(3):1481–1500 https://doi.org/10.1093/plphys/kiab346
Wrightsman T, Marand AP, Crisp PA, Springer NM, Buckler ES (2021). Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks. bioRxiv https://doi.org/10.1101/2021.11.11.468292
Dafna A, Halperin I, Oren E, Isaacson T, Tzuri G, Meir A, Schaffer AA, Burger J, Tadmor Y, Buckler ES, Gur A (2021). Underground heterosis for melons yield. Journal of Experimental Botany 72(18):6205-6218 https://doi.org/10.1093/jxb/erab219
Long EM, Bradbury PJ, Romay MC, Buckler ES, Robbins KR (2021). Genome-wide imputation using the practical haplotype graph in the heterozygous crop cassava. G3 Genes\|Genomes\|Genetics jkab383 https://doi.org/10.1093/g3journal/jkab383
Chen Q, Samayoa LF, Yang CJ, Olukolu BA, York AM, Sanchez-Gonzalez JJ, Xue W, Glaubitz JC, Bradbury PJ, Romay MC, Sun Q, Buckler ES, Holland JB, Doebley JF (2021). A conserved genetic architecture among populations of the maize progenitor, teosinte, was radically altered by domestication. PNAS 118(43):e2112970118 https://doi.org/10.1073/pnas.2112970118
Zhang X, Zhu Y, Kremling KAG, Romay MC, Bukowski R, Sun Q, Gao S, ES, Lu F (2021). Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact. Theoretical Applied Genetics https://doi.org/10.1007/s00122-021-03965-1
Ramstein G, Buckler ES (2021). Prediction of evolutionary constraint by genomic annotations improves prioritization of causal variants in maize. bioRxiv https://doi.org/10.1101/2021.09.03.458856
Giri A, Khaipho-Burch M, Buckler ES, Ramstein GP (2021). Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize. PLOS Genetics 17(10):e1009568 https://doi.org/10.1371/journal.pgen.1009568
Lozano R, Booth GT, Omar BY, Li B, Buckler ES, Lis JT, Pino del Carpio D, Jannink J (2021). RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants. G3 Genes\|Genomes\|Genetics jkab273 https://doi.org/10.1093/g3journal/jkab273
Bradbury PJ, Casstevens T, Jensen SE, Johnson LC, Miller ZR, Monier B, Romay MC, Song B, Buckler ES (2021). The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. bioRxiv https://doi.org/10.1101/2021.08.27.457652
Washburn JD, Cimen E, Ramstein G, Reeves T, O’Briant P, McLean G, Cooper M, Hammer G, Buckler ES (2021). Predicting phenotypes from genetic, environment, management, and historical data using CNNs. Theoretical and Applied Genetics https://doi.org/10.1007/s00122-021-03943-7
Jensen SE, Johnson LC, Casstevens T, Buckler ES (2021). Predicting protein domain temperature adaptation across the prokaryote-eukaryote divide. bioRxiv https://doi.org/10.1101/2021.07.13.452245
Jensen SE, Buckler ES (2021). Pfam domain adaptation profiles reflect plant species’ evolutionary history. bioRxiv https://doi.org/10.1101/2021.07.13.452250
Wu X, Feng H, Wu D, Yan S, Zhang P, Wang W, Zhang J, Ye J, Dai G, Fan Y, Li W, Song B, Geng Z, Yang W, Chen G, Qin F, Terzaghi W, Stitzer M, Li L, Xiong L, Yan J, Buckler E, Yang W, Dai M (2021). Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance. Genome Biology 22(1):1-26 https://doi.org/10.1186/s13059-021-02377-0
Wang L, Huang Y, Liu Z, He J, Jiang X, He F, Lu Z, Yang S, Chen P, Yu H, Zeng B, Ke L, Xie Z, Larkin RM, Jiang D, Ming R, Buckler ES, Deng X, Xu Q (2021). Somatic variations led to the selection of acidic and acidless orange cultivars. Nature Plants https://doi.org/10.1038/s41477-021-00941-x
Pignon CP, Fernandes SB, Valluru R, Bandillo N, Lozano R, Buckler ES, Gore MA, Long SP, Brown PJ, Leakey ADB (2021). Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes. Plant Physiology kiab395 https://doi.org/10.1093/plphys/kiab395
Diepenbrock CH, Ilut DC, Magallanes-Lundback M, Kandianis CB, Lipka AE, Bradbury PJ, Holland JB, Hamilton JP, Wooldridge E, Vaillancourt B, Góngora-Castillo E, Wallace JG, Cepela J, Mateos-Hernandez M, Owens BF, Tiede T, Buckler ES, Rocheford T, Buell CR, Gore MA, DellaPenna D (2021). Eleven biosynthetic genes explain the majority of natural variation for carotenoid levels in maize grain. The Plant Cell 33(4): 882–900 https://doi.org/10.1093/plcell/koab032
Wu Y, Johnson L, Song B, Romay C, Stitzer M, Siepel A, Buckler ES, Scheben A (2021). A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants. bioRxiv https://doi.org/10.1101/2021.06.01.446647
Song B, Buckler ES, Wang H, Wu Y, Rees E, Kellogg EA, Gates DJ, Khaipho-Burch M, Bradbury PJ, Ross-Ibarra J, Hufford MB, and Romay MC (2021). Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize. Genome Research https://doi.org/10.1101/gr.266528.120
Jores T, Tonnies J, Wrightsman T, Buckler ES, Cuperus JT, Fields S, Queitsch C (2021). Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters. Nature Plants 7:842–855 https://doi.org/10.1038/s41477-021-00932-y
Washburn JD, Cimen E, Ramstein G, Reeves T, O’Briant P, McLean G, Cooper M, Hammer G, Buckler ES (2021). Predicting phenotypes from genetic, environment, management, and historical data using CNNs. bioRxiv https://doi.org/10.1101/2021.05.27.446033
Swarts KL, Bauer E, Glaubitz JC, Ho T, Johnson L, Li Y, Yu L, Miller Z, Romay MC, Schoen CC, Wang T, Zhang Z, Buckler ES, Bradbury PJ (2021). Joint analysis of days to flowering reveals independent temperate adaptations in maize. Heredity 126:929–941 https://doi.org/10.1038/s41437-021-00422-z
Blanc J, Kremling KAG, Buckler ES, Josephs EB (2021). Local adaptation contributes to gene expression divergence in maize. G3 11(2):jkab004 https://doi.org/10.1093/g3journal/jkab004

2021

2020

Publication Title	PDF
Ding Y, Weckwerth PR, Poretsky E, Murphy KM, Sims J, Saldivar E, Christensen SA, Char SN, Yang B, Tong A, Shen Z, Kremling KA, Buckler ES, Kono T, Nelson DR, Bohlmann J, Bakker MG, Vaughan MM, Khalil AS, Betsiashvili M, Dressano K, Köllner TG, Briggs SP, Zerbe P, Schmelz EA, Huffaker A (2020). Genetic elucidation of interconnected antibiotic pathways mediating maize innate immunity. Nature Plants https://doi.org/10.1038/s41477-020-00787-9
Chen S, Su M, Kremling KA, Lepak NK, Romay MC, Sun Q, Bradbury PJ, Buckler ES, Ku H (2020). Identification of miRNA-eQTLs in maize mature leaf by GWAS. BMC Genomics 21(689) https://doi.org/10.1186/s12864-020-07073-0
Tu X, Mejía-Guerra MK, Valdes Franco JA, Tzeng D, Chu P, Shen W, Wei Y, Dai X, Li P, Buckler ES, Zhong S (2020). Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors. Nature Communications 11(5089) https://doi.org/10.1038/s41467-020-18832-8.
Valdes Franco JA, Gage JL, Johnson LC, Bradbury P, Miller ZR, Buckler ES, Romay MC (2020). A maize practical haplotype graph leverages diverse NAM assemblies. bioRxiv https://doi.org/10.1101/2020.08.31.268425.
Blanc J, Kremling KAG, Buckler ES, Josephs EB (2020). Local adaptation contributes to gene expression divergence in maize. bioRxiv https://doi.org/10.1101/2020.08.01.231217
Song B, Wang H, Wu Y, Rees E, Gates DJ, Burch M, Bradbury PJ, Ross-Ibarra J, Kellogg EA, Hufford MB, Romay MC, Buckler ES (2020). Constrained non-coding sequence provides insights into regulatory elements and loss of gene expression in maize. bioRxiv https://doi.org/10.1101/2020.07.11.19257
Monier B, Casstevens TM, Buckler ES (2020). rTASSEL: an R interface to TASSEL for association mapping of complex traits. bioRxiv https://doi.org/10.1101/2020.07.21.209114
Cimen E, Jensen SE, Buckler ES (2020). Building a tRNA thermometer to estimate microbial adaptation to temperature. Nucleic Acids Research 48(21):12004–12015 https://doi.org/10.1093/nar/gkaa1030
Chen Q, Samayoa LF, Yang CJ, Bradbury PJ, Olukolu BA, Neumeyer MA, Romay MC, Sun Q, Lorant A, Buckler ES, Ross-Ibarra J, Holland JB, Doebley JF (2020). The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication. PLOS Genetics 16(5): e1008791. https://doi.org/10.1371/journal.pgen.1008791
Iragaba P, Kawuki PS, Bauchet G, Ramu P, Tufan HA, Earle ED, Gore MA, Wolfe M (2020). Genomic characterization of Ugandan smallholder farmer‐preferred cassava varieties. Crop Science 2020:1-12 https://doi.org/10.1002/csc2.20152
Gage JL, Monier B, Giri A, Buckler ES (2020). Ten years of the maize Nested Association Mapping population: impact, limitations, and future directions. The Plant Cell May 2020 tpc.00951.2019 https://doi.org/10.1105/tpc.19.00951
Baseggio M, Murray M, Magallanes‐Lundback M, Kaczmar N, Chamness J, Buckler ES, Smith ME, DellaPenna D, Tracy WF, Gore MA (2020). Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn. The Plant Genome 2020;e20008. https://doi.org/10.1002/tpg2.20008
Falcon CM, Kaeppler SM, Spalding EP, Miller ND, Haase N, AlKhalifah N, Bohn M, Buckler ES, Campbell DA, Ciampitti I, Coffey L, Edwards J, Ertl D, Flint‐Garcia S, Gore MA, Graham C, ... , de Leon N. (2020). Relative utility of agronomic, phenological, and morphological traits for assessing genotype‐by‐environment interaction in maize inbreds. Crop Science 60(1):62-81 https://doi.org/10.1002/csc2.20035
dos Santos JPR, Fernandes SB, Lozano R, Buckler ES, Garcia AAF, Gore MA (2020). Novel bayesian networks for genomic prediction of developmental traits in biomass sorghum. G3: Genes, Genomes, Genetics 10(2): 769-781 https://doi.org/10.1534/g3.119.400759
Jensen S, Charles JR, Muleta K, Bradbury P, Casstevens T, Deshpande SP, Gore MA, Gupta R, Ilut DC, Johnson L, Lozano R, Miller Z, Ramu P, Rathore A, Romay MC, Upadhyaya HD, Varshney R, Morris GP, Pressoir G, Buckler ES, Ramstein G (2020). A sorghum Practical Haplotype Graph facilitates genome-wide imputation and cost-effective genomic prediction. Plant Genome. 2020;e20009. https://doi.org/10.1002/tpg2.20009
McFarland BA, AlKhalifah N, Bohn M, Bubert J, Buckler ES, Ciampitti I, Edwards J, Ertl D, Falcon CM, Flint-Garcia S, Gage J, Gore MA, Graham C, Hirsch D, Holland JB, Hod E, ... , De Leon N (2020). Maize Genomes to Fields (G2F): 2014 –2017 field seasons: genotype, phenotype, climatic, soil and inbred ear image datasets. BMC Res Notes 13(71) https://doi.org/10.1186/s13104-020-4922-8
Ramstein GP, Larsson SJ, Cook JP, Edwards JW, Ersoz ES, Flint-Garcia S, Gardner CA, Holland JB, Lorenz AJ, McMullen MD, Millard MJ, Rocheford TR, Tuinstra MR, Bradbury PJ, Buckler ES, Romay MC (2020). Dominance effects and functional enrichments improve prediction of agronomic traits in hybrid maize. Genetics 215(1):215-230 https://doi.org/10.1534/genetics.120.303025
Tu X, Mejia-Guerra MK, Valdes Franco JA, Tzeng D, Chu P, Dai X, Li P, Buckler ES, Zhong S (2020). Decoding the regulatory architecture of the maize leaf. bioRxiv https://doi.org/10.1101/2020.01.07.898056
Wang H, Cimen E, Singh N, Buckler ES. (2020). Deep learning for plant genomics and crop improvement. Current Opinion in Plant Biology 54:34-41 https://doi.org/10.1016/j.pbi.2019.12.010

2019

Publication Title	PDF
Baseggio M, Murray M, Magallanes-Lundback M, Kaczmar N, Chamness J, Buckler ES, Smith ME, DellaPenna D, Tracy WF Gore MA (2019). Genome-wide association and genomic prediction models of tocochromanols in fresh sweet corn kernels. The Plant Genome 11:180038. doi: 10.3835/plantgenome2018.06.0038
Ricci WA, Lu Z, Ji L, Marand. AP, Ethridge CL, Murphy NG, Noshay JM, Galli M, Mejía-Guerra MK, Colomé-Tatché M, Johannes F, Rowley MJ, Corces VG, Zhai J, Scanlon MJ, Buckler ES, Gallavotti A, Springer NM, Schmitz RJ, Zhang X (2019). Widespread long-range cis-regulatory elements in the maize genome. Nature Plants 5:1237–1249. https://doi.org/10.1038/s41477-019-0547-0.
Kremling KAG, Diepenbrock CH, Gore MA, Buckler ES, Bandillo NB (2019). Transcriptome-wide association supplements genome-wide association in Zea mays. G3: Genes, Genomes, Genetics 9 (9): 3023-3033 https://doi.org/10.1534/g3.119.400549
Gage JL, Richards E, Lepak N, Kaczmar N, Soman C, Chowdhary G, Gore MA, Buckler ES (2019). In-field whole plant maize architecture characterized by Latent Space Phenotyping. The Plant Phenome Journal 2(1):1-11 https://doi.org/10.2135/tppj2019.07.0011
Gates DJ, Runcie D, Janzen GM, Navarro AR, Willcox M, Sonder K, Snodgrass SJ, Rodríguez-Zapata F, Sawers RJH, Rellán-Álvarez R, Buckler ES, Hearne S, Hufford MB, Ross-Ibarra J (2019). Single-gene resolution of locally adaptive genetic variation in Mexican maize. bioRxiv https://doi.org/10.1101/706739
Ding Y, Murphy KM, Poretsky E, Mafu S, Yang B, Char SN, Christensen SA, Saldivar E, Wu M, Wang Q, Ji L, Schmitz RJ, Kremling KA, Buckler ES, Shen Z, Briggs SP, Bohlmann J, Sher A, Castro-Falcon G, Hughes CC, Huffaker A, Zerbe P, Schmelz EA (2019). Multiple genes recruited from hormone pathways partition maize diterpenoid defences. Nature Plants 5:1043-1056. https://doi.org/10.1038/s41477-019-0509-6
Lozano R, Gazave E, dos Santos JPR, Stetter M, Valluru R, Bandillo N, Fernandes SB, Brown PJ, Shakoor N, Mockler TC, Ross-Ibarra J, Buckler ES, Gore MA (2019). Comparative evolutionary analysis and prediction of deleterious mutation patterns between sorghum and maize. bioRxiv https://doi.org/10.1101/777623
Valluru R, Gazave EE, Fernandes SB, Ferguson JN, Lozano R, Hirannaiah P, Zuo T, Brown PJ, Leakey ADB, Gore MA, Buckler ES, Bandillo N. (2019). Deleterious mutation burden and its association with complex traits in sorghum (sorghum bicolor). Genetics doi.org/10.1534/genetics.118.301742.
Mejia-Guerra MK, Buckler ES (2019). k-mer grammar uncovers maize regulatory architecture. BMC Plant Biology 19:103. https://doi.org/10.1186/s12870-019-1693-2
Zhou S, Zhang YK, Kremling KA, Ding Y, Bennett JS, Bae JS, Kim DK, Kolomiets MV, Schmelz EA, Schroeder FC, Buckler ES, Jander G (2019). Ethylene signaling regulates natural variation in the abundance of antifungal acetylated diferuloylsucroses and Fusarium graminearum resistance in maize seedling roots. New Phytologist 221 doi: 10.1111/nph.15520.
Zhou S, Kremling K, Bandillo N, Richter A, Zhang YK, Ahern KR, Artyukhin AB, Hui JX, Younkin GC, Schroeder FC, Buckler ES, Jander G (2019) Metabolome-scale genome-wide association studies reveal chemical diversity and genetic control of maize specialized metabolites. The Plant Cell doi.org/10.1105/tpc.18.00772
Washburn JD, Mejia-Guerra MK, Ramstein G, Kremling KA, Valluru R, Buckler ES, Wang H. (2019) Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence. PNAS doi.org/10.1073/pnas.1814551116.
Oren O, Tzuri G, Vexler L, Dafna A, Meir A, Saar U, Faigenboim A, Kenigswald M, Portnoy V, Schaffer AA, Levi A, Buckler ES, Katzir N, Burger J, Tadmor Y, Gur A. (2019) Multi-allelic APRR2 gene is associated with fruit pigment accumulation in melon and watermelon. Journal of Experimental Botany 70(15):3781–3794 https://doi.org/10.1093/jxb/erz182
Yang CJ, Samayoa LF, Bradbury PJ, Olukolu BA, Xue W, York AM, Tuholski MR, Wang W, Daskalska LL, Neumeyer MA, Sanchez-Gonzalez JDJ, Romay MC, Glaubitz JC, Sun Q, Buckler ES, Holland JB, Doebley JF. (2019) The genetic architecture of teosinte catalyzed and constrained maize domestication. PNAS doi.org/10.1073/pnas.1820997116.

2018

Publication Title	PDF
Valluru R, Gazave EE, Fernandes SB, Ferguson JN, Lozano R, Hirannaiah P, Zou T, Brown PJ, Leakey ADB, Gore MA, Buckler ES, Bandillo N (2018). Leveraging mutational burden for complex trait prediction in sorghum. bioRxiv doi.org/10.1101/357418
Gault C, Kremling KA, Buckler ES (2018). Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy. Plant Genome 11(3) doi: 10.3835/plantgenome2018.02.0012
Li B, Kremling KA, Wu P, Bukowski R, Romay C, Xie E, Buckler ES, Chen M. (2018). Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation. Genome Research 28 (10), 1555-1565.
Wallace JG, Rodgers-Melnick E, Buckler ES. (2018) On the road to breeding 4.0: unraveling the good, the bad, and the boring of crop quantitative genomics. Annual Review of Genetics 52:421-444.
Ramstein, GP, Jensen, SE. & Buckler, ES. (2018). Breaking the curse of dimensionality to identify causal variants in Breeding 4. Theoretical and Applied Genetics https://doi.org/10.1007/s00122-018-3267-3
Walters WA, Jin ZJ, Youngblut N, Wallace JG, Sutter J, Zhang W, Gonzalez-Pena A, Peiffer J, Koren O, Shi Q, Knight R, Glavina del Rion T, Tringe SG, Buckler ES, Dangl JL, Let RE. (2018). Large-scale replicated field study of maize rhizosphere identifies heritable microbes. PNAS doi.org/10.1073/pnas.1800918115.
Springer NM, Anderson SN, Andorf CM, Ahern KR, Bai F, Barad O, Barbazuk WB, Bass HW, Baruch K, Ben-Zvi G, Buckler ES, et al. (2018). The maize W22 genome provides a foundation for functional genomics and transposon biology. Nature Genetics doi.org/10.1038/s41588-018-0158-0.
Kremling KA, Chen SY, Su MH, Lepak NK, Romay MC, Swarts KL, Lu F, Lorant A, Bradbury PJ, Buckler ES. (2018). Dysregulation of expression correlates with rare-allele burden and fitness loss in maize. Nature 555:520.
Sun S, Zhou Y, Chen J, Shi J, Zhao H, Zhao H, Song W, Zhang M, Cui Y, Dong X, Liu H, Ma X, Jiao Y, Wang B, Wei X, Stein JC, Glaubitz JC, Lu F, Yu G, Liang C, Fengler K, Li B, Rafalski A, Schnable PS, Ware DH, Buckler ES, Lai J. (2018). Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nature Genetics https://doi.org/10.1038/s41588-018-0182-0.
AlKhalifah N, Campbell DA, Falcon CM, Gardiner JM, Miller ND, Romay MC, Walls R,Walton R,Yeh C, Bohn M, Bubert J, Buckler ES. (2018). Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets. BMC Research Notes 11:452 https://doi.org/10.1186/s13104-018-3508-1
Jones MW, Penning BW, Jamann TM, Glaubitz JC, Romay MC, Buckler ES, Redinbaugh MG. (2018). Diverse chromosomal locations of quantitative trait loci for tolerance to maize chlorotic mottle virus in five maize populations. Phytopathology doi.org/10.1094/PHYTO-09-17-0321-R.
Zhou S, Zhang YK, Kremling KA, Ding Y, Bennett JS, Bae JS, Kim DK, Kolomiets MV, Schmelz EA, Schroeder FC, Buckler ES, Jander G. (2018). Ethylene signaling regulates natural variation in the abundance of antifungal acetylated diferuloylsucroses and Fusarium graminearum resistance in maize seedling roots. New Phytologist https://doi.org/10.1111/nph.15520
Zhou S, Kremling K, Bandillo N, Richter A, Zhang Y, Ahern K, Artyukhin A, Hui J, Schroeder F, Buckler ES, Jander G. (2018). Metabolome-scale genome-wide association studies reveal chemical diversity and genetic control of maize specialized metabolites. The Plant Cell 31(5):937-955 https://doi.org/10.1105/tpc.18.00772
Wallace JG, Kremling KA., Kovar LL, Buckler ES. (2018). Quantitative genetic analysis of the maize leaf microbiome. Phytobiomes Journal doi.org/10.1094/PBIOMES-02-18-0008-R
Li Y, Chen L, Li C, Bradbury PJ, Shi Y, Song Y, Zhang D, Zhang Z, Buckler ES, Li Y, Wang T. (2018). Increased experimental conditions and marker densities identified more genetic loci associated with southern and northern leaf blight resistance in maize. Scientific Reports 8:6848
Wang J, Zhou Z, Zhang Z, Li H, Liu D, Zhang Q, Bradbury PJ, Buckler ES, Zhang Z. (2018). Expanding the BLUP alphabet for genomic prediction adaptable to the genetic architectures of complex traits. Heredity doi.org/10.1038/s41437-018-0075-0.

2017

Publication Title	PDF
Romero-Navarro JA, Willcox M, Burgueño J, Romay MC, Swarts KL, Trachsel S, Preciado E, Terron A, Delgado HV, Vidal V, Ortega A, Ortiz-Monasterio I, Vincente FS, Atlin G, Wenzl P, Hearne S, Buckler ES (2017). A study of allelic diversity underlying flowering-time adaptation in maize landraces. Nature Genetics 49:476.
Punna R, Esuma W, Kawuki R, Rabbi IY, Egesi C, Bredeson JV, Bart RS, Verma J, Buckler ES, Lu F (2017). Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation. Nature Genetics 49:959.
Swarts KL, Gutaker RM, Benz B, Blake M, Bukowski R, Holland JB, Kruse-Peeples M, Lepak N, Prim L, Romay MC, Ross-Ibarra J, Sanchez-Gonzalez JJ, Schmidt C, Schuenemann VJ, Krause J, Matson RG, Weigel D, Buckler ES, Burbano HA (2017). Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science 357(6350):512.
Strable J, Wallace J, Briggs S, Unger-Wallace E, Bradbury PJ, Buckler ES, Vollbrecht (2017). Maize YABBY genes drooping leaf1 and drooping leaf2 affect agronomic traits by regulating leaf architecture. The Plant Cell 29(7):1622-1641. https://doi.org/10.1105/tpc.16.00477.
Zhang X, Pérez-Rodriguez P, Burgueño J, Olsen M, Buckler ES, Atlin G, Prasanna BM, Vargas M, San Vincente F, Crossa J (2017). Rapid Cycling Genomic Selection in a Multiparental Tropical Maize Population. G3: Genes, Genomes Genetics 7(7):2315.
Migicovsky Z, Sawler J, Gardner KM, Aradhya MK, Prins BH, Schwaninger HR, Bustamante CD, Buckler ES, Zhong GY, Brown PJ, Myles S (2017). Patterns of genomic and phenomic diversity in wine and table grapes. Horticulture Research 4:17035.
Varshney RK, Shi C, Thudi M, Mariac C, Wallace J, Qi P, Zhang H, Zhao Y, Wang X, Rathore A, Srivastava RK, Chitikineni A, Fan G, Bajaj P, Punnuri S, Gupta SK, Wang H, Jiang Y, Couderc M, Katta MAVSK, Paudel DR, Mungra KD, Chen W, Harris-Shultz KR, Garg V, Desai N, ..., Xu X (2017). Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nature Biotechnology 35(10):969.
Yang J, Mezmouk S, Baumgarten A, Buckler ES, Guill KE, McMullen MD, Mumm RH, Ross-Ibarra J (2017). Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize. PLOS Genetics doi: doi.org/10.1371/journal.pgen.1007019.
Zhang D, Easterling K A, Pitra NJ, Coles MC, Buckler ES, Bass HW, Matthews PD (2017). Non-Mendelian single-nucleotide polymorphism inheritance and atypical meiotic configurations are prevalent in hop. The Plant Genome 10(3):doi:10.3835/plantgenome2017.04.0032.
He Y, Wang M, Dukowic-Schulze S, Zhou A, Tiang CL, Shilo S, Sidhu GK, Eichten S, Bradbury PJ, Springer NM, Buckler ES, Levy AA, Sun Q, Pillardy J, Kianian PMA, KianianSF, Chen C, Pawlowski WP (2017). Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize. PNAS 114(46):12231.
Diepenbrock CH, Kandianis CB, Lipka AE, Magallanes-Lundback M, Vaillancourt B, Góngora-Castillo E, Wallace JG, Cepela J, Mesberg A, Bradbury PJ, Ilut DC, Mateos-Hernandez M, Hamilton J, Owens BF, Tiede T, Buckler ES, Rocheford T, Buell CR, Gore MA, DellaPenna D (2017). Novel loci underlie natural variation in vitamin E levels in maize grain. The Plant Cell 29(1):2374.
Bukowski R, Guo X, Lu Y, Zou C, He B, Rong Z, Wang B, Xu D, Yang B, Xie C, Fan L, Gao S, Xu X, Zhang G, Li Y, Jiao Y, Doebley JF, Ross-Ibarra J, Lorant A, Buffalo V, Romay MC, Buckler ES, Ware D, Lai J, Sun Q, Xu Y (2017). Construction of the third-generation Zea mays haplotype map. GigaScience 7(4):gix134.
Gage JL, Jarquin D, Romay MC, Lorenz A, Buckler ES, Kaeppler S, Alkhalifah N, Bohn M, Campbell DA, Edwards J, Ertl D, Flint-Garcia S, Gardiner J, Good B, Hirsch CN, Holland J, Hooker DC, Knoll J, Kolkman J, Kruger G, Lauter N, Lawrence-Dill CJ, Lee E, Lynch J, Murray SC, Nelson R, Petzoldt J, Rocheford T, Schnable J, Schnable PS, Scully B, ... , de Leon N (2017). The effect of artificial selection on phenotypic plasticity in maize. Nature Communications 8(1):1348.
Larsson SJ, Peiffer JA, Edwards JW, Ersoz ES, Flint-Garcia S, Holland JB, McMullen MD, Tuinstra MR, Romay MC, Buckler ES (2017). Genetic analysis of lodging in diverse maize hybrid. bioRxiv doi.org/10.1101/185769.

2016

Publication Title	PDF
Liu X, Huang M, Fan B, Buckler ES, Zhang Z. (2016) Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies. PLoS Genetics 12(2): e1005767.
Punnuri SM, Wallace JG, Knoll JE, Hyma KE, Mitchell SE, Buckler ES, Varshney RK, Singh BP. (2016) Development of a high density linkage map and tagging leaf spot resistance in pearl millet using GBS markers. The Plant Genome 9(2):1-13. https://doi.org/10.3835/plantgenome2015.10.0106.
Wu X, Li Y, Shi Y, Song Y, Zhang D, Li C, Buckler ES, Li Y, Zhang Z, Wang T. (2016) Joint-linkage mapping and GWAS reveal extensive genetic loci that regulate male inflorescence size in maize. Plant Biotechnology Journal 14(7):1551-1562. https://doi.org/10.1111/pbi.12519.
Tang Y, Liu X, Wang J, Li M, Wang Q, Tian F, Su Z, Pan Y, Liu D, Lipka AE, Buckler ES, Zhang Z. (2016) GAPIT Version 2: Enhanced Integrated Tool for Genomic Association and Prediction. The Plant Genome 9(2):1-9. https://doi.org/10.3835/plantgenome2015.11.0120.
Li Y, Li C, Bradbury PJ, Liu X, Lu F, Romay MC, Glaubitz JC, Wu X, Peng B, Shi Y, Song Y, Zhang D, Li1 Y, Zhang Z, Buckler ES, Wang T (2016) Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population. The Plant Journal 86:391-402. https://doi.org/10.1111/tpj.13174.
Li C, Li Y, Shi Y, Song Y, Zhang D, Buckler ES, Zhang Z, Wang T (2016). Analysis of recombination QTLs, segregation distortion, and epistasis for fitness in maize multiple populations using ultra-high-density markers. Theoretical and Applied Genetics 123(9):1775.
Wallace JG, Zhans X, Beyene Y, Semagn K, Olsen M, Prasanna BM, Buckler ES (2016). Genome-wide Association for Plant Height and Flowering Time across 15 Tropical Maize Populations under Managed Drought Stress and Well-Watered Conditions in Sub-Saharan Africa. Crop Science 56(5):2365.
Rodgers-Melnick E, Vera DL, Bass HW, Buckler ES (2016). Open Chromatin Reveals the Functional Maize Genome. PNAS 113(22):E3177.
Bergelson J, Buckler ES, Ecker JR, Nordborg M, Weigel D (2016). A Proposal Regarding Best Practices for Validating the Identity of Genetic Stocks and the Effects of Genetic Variants. The Plant Cell 28(3):606-609. https://doi.org/10.1105/tpc.15.00502
Handrick V, Robert CA, Ahern KR, Zhou S, Machado RA, Maag D, Glauser G, Fernandez-Penny FE, Chandran JN, Rodgers-Melnik E, Schneider B, Buckler ES, Boland W, Gershenzon J, Jander G, Erb M, Köllner TG (2016). Biosynthesis of 8-O-Methylated Benzoxazinoid Defense Compounds in Maize. The Plant Cell 28(7):1682.
Toubiana D, Xue W, Zhang N, Kremling K, Gur A, Pilosof S, Gibon Y, Stitt M, Buckler ES, Fernie AR, Fait A (2016). Correlation-Based Network Analysis of Metabolite and Enzyme Profiles Reveals a Role of Citrate Biosynthesis in Modulating N and C Metabolism in Zea mays. Frontiers in Plant Science 7:1022. https://doi.org/10.3389/fpls.2016.01022
McCaw ME, Wallace JG, Albert PS, Buckler ES, Birchler JA (2016). Fast-Flowering Mini-Maize: Seed to Seed in 60 Days. Genetics 204(1):35-42. https://doi.org/10.1534/genetics.116.191726.
Zhang D, Pitra N, Coles M, Buckler ES, Matthews P (2016). Non-Mendelian inheritance of SNP markers reveals extensive chromosomal translocations in dioecious hops (Humulus lupulus L.). bioRxiv doi: http://dx.doi.org/10.1101/069849.
Esuma W, Herselman L, Labuschange MT, Ramu P, Lu F, Baguma Y, Buckler ES, Kawuki (2016). Genome-wide association mapping of provitamin A carotenoid content in cassava. Euphytica 212: 97–110. https://doi.org/10.1007/s10681-016-1772-5
Richter A, Schaff C, Zhang Z, Lipka AE, Tian F, Kollner TG, Schnee C, Preiss S, Irmisch S, Jander G, Boland W, Gershenzon J, Buckler ES, Degenhardt J (2016). Characterization of biosynthetic pathways for the production of the volatile homoterpenes DMNT and TMTT in Zea mays. The Plant Cell 28(10):2651.
Li C, Sun B, Li Y, Liu C, Wu X, Zhang D, Shi Y, Song Y, Buckler ES, Zhang Z, Wang T, Li Y (2016). Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations. BCM Genomics 17:894.
Hirsch C, Hirsch CD, Brohammer AB, Bowman MJ, Soifer I, Barad O, Shem-Tov D, Baruch K, Lu F, Hernandez AG, Fields CJ, Wright CL, Koehler K, Springer NM, Buckler ES, Buell CR, de Leon N, Kaeppler SM, Childs K, Mikel MM (2016). Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize. The Plant Cell doi: 10.1105/tpc.16.00353.
Buckler ES, Ilut DC, Wang X, Kretzschmar T, Gore MA, Mitchell SE (2016). rAmpSeq: Using repetitive sequences for robust genotyping. bioRxiv https://doi.org/10.1101/096628.

2015

Publication Title	PDF
Wallace JG, Upadhyaya HD, Vetriventhan M, Buckler ES, Hash TC, Ramu P. (2015) The genetic makeup of a global barnyard millet germplasm collection. The Plant Genome 8(1). https://doi.org/10.3835/plantgenome2014.10.0067
Takuno S, Ralph P, Swarts KL, Elshire RJ, Glaubitz JC, Buckler ES, Hufford MB, Ross-Ibarra J. (2015) Independent molecular basis of convergent highland adaptation in maize. Genetics 200(4):1297 https://doi.org/10.1534/genetics.115.178327
Ramstein GP, Lipka AE, Lu F, Costich DE, Cherney JH, Buckler ES, Casler MD. (2015) Genome-wide association study based on multiple imputation with low-depth sequencing data: application to biofuel traits in reed canarygrass. G3 5(5):891-909 doi:10.1534/g3.115.017533.
Rodgers-Melnick E, Bradbury PJ, Elshire RJ, Glaubitz JC, Acharya CB, Mitchell SE, Li C, Li Y, Buckler ES. (2015) Recombination in diverse maize is stable, predictable, and associated with genetic load. PNAS 112(12):3823. https://doi.org/10.1073/pnas.1413864112
Lu F, Romay MC, Glaubitz JC, Bradbury PJ, Elshire RJ, Wang T, Li Y, Li Y, Semagn K, Zhang X, Hernandez AG, Mikel MA, Soifer I, Barad O, Buckler ES. (2015) High-resolution genetic mapping of maize pan-genome sequence anchors. Nature Communications 6(6914) doi:10.1038/ncomms7914.
Li C, Li Y, Shi Y, Song Y, Zhang D, Buckler ES, Zhang Z, Wang T, Li Y. (2015) Genetic Control of the Leaf Angle and Leaf Orientation Value as Revealed by Ultra-High Density Maps in Three Connected Maize Populations. PLoS ONE 10(3): e0121624. doi: https://doi.org/10.1371/journal.pone.0121624
Zhang N, Gibon Y, Wallace JG, Lepak N, Li P, Dedow L, Chen C, So Y-S, Kremling K, Bradbury PJ, Brutnell T, Sitt M, Buckler ES. (2015) Genome-wide association of carbon and nitrogen metabolism in the maize Nested Association Mapping population. Plant Physiology 168:575-583.
Lasky JR, Upadhyaya HD, Ramu P, Deshpande S, Hash CT, Bonnette J, Juenger TE, Hyma K, Acharya C, Mitchell SE, Buckler ES, Brenton Z, Kresovich S, Moriss GP. (2015) Genome-environment associations in sorghum landraces predict adaptive traits. Science Advances 1(6):e1400218.
Upadhyaya HD, Vetriventhan M, Deshpande SP, Sivasubramani S, Wallace JG, Buckler ES, Hash CT, Ramu P. (2015) Population genetics and structure of a global foxtail millet germplasm collection. The Plant Genome 8(3):1-13. https://doi.org/10.3835/plantgenome2015.07.0054
Liu Z, Cook J, Melia-Hancock S, Guill K, Bottoms C, Garcia A, Ott O, Nelson R, Recker J, Balint-Kurti P, Larsson S, Lepak N, Buckler ES, Trimble L, Tracy W, McMullen MD, Flint-Garcia SA. (2015) Expanding maize genetic resources with predomestication alleles: Maize–teosinte introgression populations. The Plant Genome 9(1):1-11 https://doi.org/10.3835/plantgenome2015.07.0053.
Li C, Li Y, Bradbury PJ, Wu X, Shi Y, Song Y, Zhang D, Rogers-Melnick E, Buckler ES, Zhang Z, Li Y, Wang T. (2015) Construction of high-quality recombination maps with low-coverage genomic sequencing for joint linkage analysis in maize. BMC Biology 13:78.

2014

Publication Title	PDF
Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, Buckler ES. (2014) TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline. PLoS ONE 9(2):e90346 https://doi.org/10.1371/journal.pone.0090346
Peiffer JA, Romay MC, Gore MA, Flint-Garcia SA, Zhang Z, Millard MJ, Gardner CA, McMullen MD, Holland JB, Bradbury PJ, Buckler ES. (2014) The Genetic Architecture of Maize Height. G enetics 196(4):1337. https://doi.org/10.1534/genetics.113.159152
Hirsch CN, Flint-Garcia S, Beissinger TM, Eichten SR, Deshpande S, Barry K, McMullen MD, Holland JB, Buckler ES, Springer NM, Buell RC, de Leon N, Kaeppler SM. (2014) Insights into the effects of long-term artificial selection on seed size in maize. Genetics 198(1):409-421 https://doi.org/10.1534/genetics.114.167155.
Wang Q, Tian F, Pan Y, Buckler ES, Zhang Z. (2014) A SUPER Powerful Method for Genome Wide Association Study. PLoS ONE 9(9): e107684. https://doi.org/10.1371/journal.pone.0107684.
Owens BF, Lipka AE, Magallanes-Lundback M, Tiede T, Diepenbrock CH, Kandianis CB, Kim E, Cepela J, Mateos-Hernandez M, Buell CR, Buckler ES, DellaPenna D, Gore ME, Rocheford TR. (2014) A Foundation for Provitamin A Biofortification of Maize: Genome-Wide Association and Genomic Prediction Models of Carotenoid Levels. Genetics 198(4):1699-1716 https://doi.org/10.1534/genetics.114.169979.
Yan J, Lipka AE, Schmelz EA, Buckler ES, Jander G. (2014) Accumulation of 5-hydroxynorvaline in maize (Zea mays) leaves is induced by insect feeding and abiotic stress. Journal of Experimental Botany 66(2):593–602. https://doi.org/10.1093/jxb/eru385.
Zhang X, Perez-Rodriguez P, Semagn K, Beyene Y, Babu R, Lopez Cruz MA, San Vicente F, Olsen M, Buckler ES, Jannink J-L, Prasanna BM, Crossa J. (2014) Genomic Prediction in biparental tropical maize populations in water-stressed and well-watered environments using low-density and GBS SNPs. Heredity 114:291–299. https://doi.org/10.1038/hdy.2014.99
Li M, Liu X, Bradbury PJ, Yu J, Zhang Y-M, Todhunter RJ, Buckler ES. (2014) Enrichment of statistical power for genome-wide association studies. BMC Biology 12:73. https://doi.org/10.1186/s12915-014-0073-5
Lipka AE, Lu F, Cherney JH, Buckler ES, Casler MD, Costich DE. (2014) Accelerating the switchgrass (Panicum virgatum L.) breeding cycle using genomic selection approaches. PLoS ONE 9(11): e112227. https://doi.org/10.1371/journal.pone.0112227.
Zila CY, Ogut F, Romay MC, Gardner CA, Buckler ES, Holland JB. (2014) Genome-wide association study of Fusariumear rot disease in the U.S.A. maize inbred line collection. BMC Plant Biology 14:372. https://doi.org/10.1186/s12870-014-0372-6
Swarts K, Li H, Romero Navarro JA, An D, Hearne S, Acharya CB, Glaubitz JC, Mitchell SE, Elshire RJ, Buckler ES, Bradbury PJ. (2014) Novel methods to optimize genotypic imputation for low-coverage, next-generation sequence data in crop plants. The Plant Genome 7(3). https://doi.org/10.3835/plantgenome2014.05.0023.
Wallace JG, Bradbury PJ, Zhang N, Gibon Y, Stitt M, Buckler ES. (2014) Association mapping across numerous traits reveals patterns of functional variation in maize. PLoS Genetics 10(12):e1004845. https://doi.org/10.1371/journal.pgen.1004845

2013

Publication Title	PDF
Lu F, Lipka AE, Elshire RJ, Glaubitz JC, Cherney JH, Casler MD, Buckler ES, Costich DE. (2013) Switchgrass genomic diversity, ploidy and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genetics 9(1):e1003215. https://doi.org/10.1371/journal.pgen.1003215.
Larsson SJ, Lipka AE, Buckler ES. (2013) Lessons from Dwarf8 on strengths and weaknesses in structured association mapping. PLoS Genetics 9(2):e1003246. https://doi.org/10.1371/journal.pgen.1003246.
Wallace JG, Larsson SJ, Buckler ES. (2013) Entering the second century of maize quantitative genetics. Heredity 112:30–38. https://doi.org/10.1038/hdy.2013.6.
Maron L, Guimareas C, Matias K, Albert PS, Birchler JA, Bradbury PJ, Buckler ES, Coluccio AE, Danilova TV, Kudrna D, Magalhaes JV, Pineros M, Schatz MC, Wing R, Kochian LV. (2013) Aluminum tolerance is associated with higher MATE1 gene copy-number in maize. PNAS 110(13):5241-5246. https://doi.org/10.1073/pnas.1220766110.
Peiffer JA, Spor A, Koren O, Jin Z, Tringe SG, Dangl JL, Buckler ES, Ley RE. (2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions. PNAS 110(16):6548-6553. https://doi.org/10.1073/pnas.1302837110
Lipka AE, Gore MA, Magallanes-Lundback M, Mesberg A, Lin H, Tiede T, Chen C, Buell CR, Buckler ES, Rocheford T, DellaPenna D. (2013) Genome-wide association study and pathway level analysis of tocochromanol levels in maize grain. G3 3(8):1287-1299. https://doi.org/10.1534/g3.113.006148.
Peiffer JA, Flint-Garcia SA, De Leon N, McMullen MD, Kaeppler SM, Buckler ES. (2013) The genetic architecture of maize stalk strength. PLoS ONE 8(6):e67066. https://doi.org/10.1371/journal.pone.0067066
Romay MC, Millard M, Glaubitz JC, Peiffer JA, Swarts K, Casstevens T, Elshire RJ, Acharya CB, Mitchell SE, Flint-Garcia S, McMullen MD, Holland JB, Buckler ES, Gardner C. (2013) Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biology 14:R55. https://doi.org/10.1186/gb-2013-14-6-r55
McCouch S, Baute GJ, Bradeen J, Bramel P, Bretting PK, Buckler ES, Burke JM, Charest D, Cloutier S, Cole G, Dempewolf H, Dingkuhn M, Feuillet C, Gepts P, Grattapaglia D, Guarino L, Jackson S, Knapp S, Langridge P, Lawton-Rauh A, Lijua Q, Lusty C, Michael T, Myles S, Naito K, Nelson RL, Pontarollo R, Richards CM, Rieseberg L, Ross-Ibarra J, ... , Zamir D. (2013) Agriculture: Feeding the future. Nature 499:23-24. https://doi.org/10.1038/499023a
Morris GP, Rhodes DH, Brenton Z, Ramu P, Thayil VM, Desphande S, Hash CT, Acharya C, Mitchell SE, Buckler ES, Yu J, Kresovich S. (2013) Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits. G3 3(11):2085-2094. https://doi.org/10.1534/g3.113.008417.
Crossa J, Beyene Y, Kassa S, Perez P, Hickey JM, Chen C, de los Campos G, Burgueno J, Windhausen VS, Buckler ES, Jannink JL, Lopez Cruz MA, Babu R. (2013) Genomic prediction in maize breeding populations with genotyping-by-sequencing. G3 3(11):1903-1926. https://doi.org/10.1534/g3.113.008227.
Meihls LN, Handrick V, Glauser F, Barbier H, Kaur H, Haribal MM, Lipka AE, Gershenzon J, Buckler ES, Erb M, Kollner TG, Jander G. (2013) Natural variation in maize aphid resistance is associated with 2,4-Dihydroxy-7-Methoxy-1,4-Benzoxazin-3-One Glucoside Methyltransferase activity. The Plant Cell 25(6):2341-2355. https://doi.org/10.1105/tpc.113.112409
Miller AJ, Matasci N, Schwaninger H, Aradhya MK, Prins B, Zhong G-Y, Simon C, Buckler ES, Myles S. (2013) Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls. PLoS ONE 8(11): e78680. https://doi.org/10.1371/journal.pone.0078680.
Sawler J, Reisch B, Aradhya MK, Prins B, Zhong G-Y, Schwaninger H, Simon C, Buckler ES, Myles S. (2013) Genomics assisted ancestry deconvolution in grape. PLoS ONE 8(11): e80791. https://doi.org/10.1371/journal.pone.0080791.
Chitwood DH, Ranjan A, Martinez CC, Headland LR, Thiem T, Kumar R, Covington MF, Hatcher T, Naylor DT, Zimmerman S, Downs N, Raymundo N, Buckler ES, Maloof JN, Aradhya MK, Prins B, Li L, Myles S, Sinha N. (2013) A modern ampelography: a genetic basis for leaf shape and venation patterning in grape. Plant Physiology 164(1):259-272. https://doi.org/10.1104/pp.113.229708.
Chen C, Mitchell SE, Elshire RJ, Buckler ES, El-Kassaby YA. (2013) Mining conifers’ mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform. Tree Genetics & Genomes 9:1537-1544. https://doi.org/10.1007/s11295-013-0657-1

2012

Publication Title	PDF
Cook JP, McMullen MD, Holland JB, Tian F, Bradbury PJ, Ross-Ibarra J, Buckler ES, Flint-Garcia S. (2012) Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels. Plant Physiology 158(2):824-834. https://doi.org/10.1104/pp.111.185033.
Morrell PL, Buckler ES, Ross-Ibarra J. (2012) Crop genomics: advances and applications. Nature Review Genetics 13:85-96. https://doi.org/10.1038/nrg3097.
Hufford MB, Xun X, van Heerwaarden J, Pyhäjärvi T, Chia JM, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J, Morrell PL, Shannon LM, Song C, Springer NM, Swanson-Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross-Ibarra J. (2012) Comparative population genomics of maize domestication and improvement. Nature Genetics 44:808-811. https://doi.org/10.1038/ng.2309.
Chia JM, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, Elshire RJ, Gaut B, Geller L, Glaubitz JC, Gore M, Guill KE, Holland J, Hufford MB, Lai J, Li M, Liu X, Lu Y, McCombie R, Nelson R, Poland J, Prasanna BM, Pyhäjärvi T, Rong T, Sekhon RS, Sun Q, Tenaillon MI, Tian F, Wang J, Xu X, Zhang Z, Kaeppler SM, Ross-Ibarra J, McMullen MD, Buckler ES, Zhang G, Xu Y, Ware D. (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics 44:803-807. https://doi.org/10.1038/ng.2313.
Lipka AE, Tian F, Wang Q, Peiffer J, Li M, Bradbury PJ, Gore MA, Buckler ES, Zhang Z. (2012) GAPIT: Genome Association and Prediction Integrated Tool. Bioinformatics 28(18):2397-2399. https://doi.org/10.1093/bioinformatics/bts444.
Hung H-Y, Shannon LM, Tian F, Bradbury PJ, Chen C, Flint Garcia S, McMullen MD, Ware D, Buckler ES, Doebley JF, Holland JB. (2012) ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize. PNAS 109(28):11068-11069. https://doi.org/10.1101/gr.140277.112.
Li X, Zhu C, Yeh C-T, Wu W, Takacs EM, Petsch KA, Tian F, Bai G, Buckler ES, Muehlbauer GJ, Timmermans MCP, Scanlon MJ, Schnable PS, Yu J. (2012) Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Research 22:2436-2444. http://www.genome.org/cgi/doi/10.1101/gr.140277.112.
Ersoz ES, Wright MH, Pangilinan JL, Sheehan MJ, Buckler ES, Tobias C, Casler MD, Costich DE. (2012) SNP discovery with EST and NextGen sequencing in switchgrass (Panicum virgatum L.). PLoS One 7(9): e44112. https://doi.org/10.1371/journal.pone.0044112
Chen C, DeClerck G, Tian F, Spooner W, McCouch S, Buckler ES. (2012) PICARA, an analytical pipeline providing probabilistic inference about a priori candidate genes underlying genome-wide association QTL in plants. PLoS One 7(11):e46596. https://doi.org/10.1371/journal.pone.0046596.
Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE, Harriman J, Glaubitz JC, Buckler ES, Kresovich S. (2012) Population genomic and genome-wide association studies of agroclamatic traits in sorghum. PNAS 110(2):453-458. https://doi.org/10.1073/pnas.1215985110.
Varshney RK, Ribaut JM, Buckler ES, Tuberosa R, Rafalski JA, Langridge P. (2012) Can genomics boost productivity of orphan crops? Nature 30: 1172-1176. https://doi.org/10.1038/nbt.2440.
Chandler K, Lipka AE, Owens BF, Li H, Buckler ES, Rocheford T, Gore MA. (2012) Genetic Analysis of Visually Scored Orange Kernel Color in Maize. Crop Science 53(1):189-200. https://doi.org/10.2135/cropsci2012.02.0129.

2011

Publication Title	PDF
Tian F, Bradbury PJ, Brown PJ, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler EB. (2011) Genome-wide association study of maize identifies genes affecting leaf architecture. Nature Genetics 43:159-162. https://doi.org/10.1038/ng.746.
Kump KL, Bradbury PJ, Buckler ES, Belcher AR, Oropeza-Rosas M, Wisser RJ, Zwonitzer JC, Kresovich S, McMullen MD, Ware D, Balint-Kurti PJ, Holland JB. (2011) Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nature Genetics 43:163–168. https://doi.org/10.1038/ng.747.
Myles S, Boyko AR, Owens CL, Brown PJ, Grassi F, Aradhya MK, Prins B, Reynolds A, Chia JM, Ware D, Bustamante CD, Buckler ES. (2011) Genetic structure and domestication history of the grape. PNAS 108:3530-3535. https://doi.org/10.1073/pnas.1009363108.
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6(5): e19379. https://doi.org/10.1371/journal.pone.0019379.
Poland JA, Bradbury PJ, Buckler ES, Nelson RJ. (2011) Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. PNAS 108:6893-6898. https://doi.org/10.1073/pnas.1010894108.
Li H, Bradbury P, Ersoz E, Buckler ES, Wang J. (2011) Joint QTL Linkage Mapping for Multiple-Cross Mating Design Sharing One Common Parent. PLoS ONE 6(3): e17573. https://doi.org/10.1371/journal.pone.0017573.
Hamblin M, Buckler ES, Jannink JL. (2011) Population genetics of genomics-based crop improvement methods. Trends in Genetics 27(3):98-106. c
Brown P, Upadyayula N, Mahone GS, Tian F, Bradbury PJ, Myles S, Holland JB, Flint-Garcia S, McMullen MD, Buckler ES, Rocheford TR. (2011) Distinct Genetic Architectures for Male and Female Inflorescence Traits of Maize. PLoS Genetics 7(11):e1002383. https://doi.org/10.1371/journal.pgen.1002383.
Hung H-Y, Browne CJ, Guill KE, Coles N, Eller M, Garcia A, Lepak N, Melia-Hancock S, Oropeza-Rosas M, Salvo S, Upadyayula N, Buckler ES, Flint-Garcia S, McMullen MD, Rocheford TR, Holland JB. (2011) The relationship between parental genetic or phenotypic divergence and progeny variation in the maize Nested Association Mapping population. Heredity 108:490-499. https://doi.org/10.1038/hdy.2011.103.
Ganal MW, Durstewitz G, Polley A, Berard A, Buckler ES, Charcosset A, Clarke JD, Graner E-M, Hansen M, Joets J, Le Paslier MC, McMullen MD, Montalent P, Rose M, Schon CC, Sun Q, Walter H, Martin OC, Falque M. (2011) A large maize (Zea Mays L.) SNP genotyping array: Development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS ONE 6(12): e28334. https://doi.org/10.1104/pp.111.185033.

2010

Publication Title	PDF	PDF
Zhang N, Gur A, Gibon Y, Sulpice R, Flint-Garcia S, McMullen MD, Stitt M, Buckler ES. (2010) Genetic analysis of central carbon metabolism unveils an amino acid substitution that alters maize NAD-dependent isocitrate dehydrogenase activity. PLoS ONE 5(4):e9991. https://doi.org/10.1371/journal.pone.0009991.
Krill AM, Kirst M, Kochian LV, Buckler ES, Hoekenga OA. (2010) Association and linkage analysis of aluminum tolerance genes in maize. PLoS ONE 5(4):e9958. https://doi.org/10.1371/journal.pone.0009958.
Myles S, Chia J-M, Hurwitz B, Simon C, Zhong GY, Buckler ES, Ware D. (2010) Rapid genomic characterization of the genus vitis. PLoS ONE 5(1):e8219. https://doi.org/10.1371/journal.pone.0008219.
Zhang Z, Ersoz E, Lai C-Q, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu J, Arnett DK, Ordovas JM, Buckler ES. (2010) Mixed linear model approach adapted for genome-wide association studies. Nature Genetics 42:355-360. https://doi.org/10.1038/ng.546.
Yan J, Bermudez Kandianis C, Harjes CE, Bai L, Kim E, Yang X, Skinner DJ, Fu Z, Mitchell SE, Li Q, Salas Fernandez MG, Zaharieva M, Babu R, Fu Y, Palacios N, Li J, DellaPenna D, Brutnell T, Buckler ES, Warburton ML, Rocheford T. (2010) Rare genetic variation at Zea mays crtRB1 increases β-carotene in maize grain. Nature Genetics 42:322–327. https://doi.org/10.1038/ng.551.
Glover JD, Reganold JP, Bell LW, Borevitz J, Brummer EC, Buckler ES, Cox CM, Cox TS, Crews TE, Culman SW, DeHaan LR, Eriksson D, Gill BS, Holland J, Hu F, Hulke BS, Ibrahim AMH, Jackson W, Jones SS, Murray SC, Paterson AH, Ploschuk E, Sacks EJ, Snapp S, Tao D, Van Tassel DL, Wade JL, Wyse DL, Xu Y. (2010) Increased food and ecosystem security via perennial grains. Science 328:1638-1639. https://doi.org/10.1126/science.1188761.
Huang X, Sang T, Zhao Q, Wei X, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang Q, Li J, Han B. (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics 42:961-967. https://doi.org/10.1038/ng.695.
Youens-Clark K, Buckler ES, Casstevens T, Chen C, DeClerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D. (2010) Gramene database in 2010: updates and extensions. Nucleic Acids Research 39: D1085–D1094. https://doi.org/10.1093/nar/gkq1148.
Costich DE, Friebe B, Sheehan MJ, Casler MD, Buckler ES. (2010) Genome-size variation in switchgrass (panicum virgatum): flow cytometry and cytology reveal rampant aneuploidy. The Plant Genome 3:130–141. https://doi.org/10.3835/plantgenome2010.04.0010.
Zhang N, Gibon Y, Gur A, Chen C, Lepak N, Höhne M, Zhang Z, Kroon D, Tschoep H, Stitt M, Buckler ES. (2010) Fine quantitative trait loci mapping of carbon and nitrogen metabolism enzyme activities and seedling biomass in the intermated maize IBM mapping population. Plant Physiology 154:1753-1765. https://doi.org/10.1104/pp.110.165787.
Glover JD, Reganold JP, Bell LW, Borevitz J, Brummer EC, Buckler ES, Cox CM, Cox TS, Crews TE, Culman SW, DeHaan LR, Eriksson D, Gill BS, Holland J, Hu F, Hulke BS, Ibrahim AMH, Jackson W, Jones SS, Murray SC, Paterson AH, Ploschuk E, Sacks EJ, Snapp S, Tao D, Van Tassel DL, Wade JL, Wyse DL, Xu Y. (2010) Perennial Questions of Hydrology and Climate—Response. Science 330:33-34. https://doi.org/10.1126/science.330.6000.33-b.
Setter T, Yan J, Warburton M, Ribaut JM, Xu Y, Sawkins M, Buckler ES, Zhang Z, Gore M. (2010) Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought. Journal of Experimental Botany 62(2):701-716. https://doi.org/10.1093/jxb/erq308.

2009

Publication Title	PDF	PDF
Tian F, Stevens NM, and Buckler ES. (2009) Tracking footprints of maize domestication and evidence for a massive selective sweep on chromosome 10. PNAS. 106:9979-9986. https://doi.org/10.1073/pnas.0901122106.
Bernardo AN, Bradbury PJ, Ma H, Hu S, Bowdens RL, Buckler ES, Bai G. (2009) Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays. Biomed Central Genomics 10:251. https://doi.org/10.1186/1471-2164-10-251.
Pressoir G, Brown PJ, Zhu W, Upadyayula N, Rocheford T, Buckler ES, Kresovich S. (2009) Natural variation in maize architecture is mediated by allelic differences at the PINOID co-ortholog barren inflorescence2. The Plant Journal 58:4,618-628. https://doi.org/10.1111/j.1365-313X.2009.03802.x.
Gore MA, Wright MH, Ersoz ES, Bouffard P, Szekeres ES, Jarvie TP, Hurwitz BL, Narechania A, Harkins TT, Grills GS, Ware DH, Buckler ES. (2009) Large-scale discovery of gene-enriched SNPs. The Plant Genome 2:121-133. https://doi.org/10.3835/plantgenome2009.01.0002.
Yu J, Zhang Z, Zhu C, Tabanao DA, Pressoir G, Tuinstra MR, Kresovich S, Todhunter RJ, Buckler ES. (2009) Simulation appraisal of the adequacy of number of background markers for relationship estimation in association mapping. The Plant Genome 2:63-77. https://doi.org/10.3835/plantgenome2008.09.0009.
Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, Costich DE, Buckler ES. (2009) Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21:2194-2202. https://doi.org/10.1105/tpc.109.068437.
Zhang Z, Buckler ES, Casstevens TM, Bradbury PJ. (2009) Software engineering the mixed model for genome-wide association studies on large samples. Briefings in Bioinformatics 10(6):664-675. https://doi.org/10.1093/bib/bbp050.
Flint-Garcia SA, Buckler ES, Tiffin P, Ersoz E, Springer NM. (2009) Heterosis is prevalent for multiple traits in diverse maize germplasm. PLoS ONE 4(10):e7433. https://doi.org/10.1371/journal.pone.0007433.
Yan J, Shah T, Warburton ML, Buckler ES, McMullen MD, Crouch J. (2009) Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers. PLoS ONE 4(12):e8451. https://doi.org/10.1371/journal.pone.0008451.
McMullen MD, Kresovich S, Villeda HS, Bradbury PJ, Li H, Sun Q, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C, Brown P, Browne C, Eller M, Guill K, Harjes C, Kroon D, Lepak N, Mitchell SE, Peterson B, Pressoir G, Romero S, Oropeza Rosas M, Salvo S, Yates H, Hanson M, Jones E, Smith S, Glaubitz JC, Goodman M, Ware D, Holland JB, Buckler ES. (2009) Genetic properties of the maize nested association mapping population. Science 325:737-740. https://doi.org/10.1126/science.1174320.
Buckler ES, Holland JB, Bradbury PJ, Acharya C, Brown P, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, Goodman MM, Harjes C, Guill K, Kroon DE, Larsson S, Lepak NK, Li H, Mitchell SE, Pressoir G, Peiffer JA, Oropeza Rosas M, Rocheford TR, Romay MC, Romero S, Salvo S, Villeda HS, da Silva HS, Sun Q, Tian F, Upadyayula N, Ware D, Yates H, Yu J, Zhang Z, Kresovich S, McMullen MD. (2009) The genetic architecture of maize flowering time. Science 325:714-718.https://doi.org/10.1126/science.1174276.
Gore MA, Chia J-M, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES. (2009) A first-generation haplotype map of maize. Science 326: 1115-1117. https://doi.org/10.1126/science.1177837.

2008 - 2007

Publication Title	PDF
Ersoz ES, Yu J, Buckler ES (2007) Applications of Linkage Disequilibrium and Association Mapping in Crop Plants. Varshney RK, Tuberosa R (eds) Genomics-Assisted Crop Improvement. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-6295-7_5.
Zhang Z, Todhunter RJ, Buckler ES, Van Vleck LD. (2007) Use of marker based relationships with multiple-trait derivative-free restricted maximum likelihood. Journal of Animal Science 85:881-885. https://doi.org/10.2527/jas.2006-656.
Stich B, Yu J, Maurer HP, Melchinger AE, Utz HF, Buckler ES. (2007) Power to detect higher-order epistatic interactions in a metabolic pathway using a new mapping strategy. Genetics 176:563-570. https://doi.org/10.1534/genetics.106.067033.
Gore M, Bradbury P, Hogers R, Kirst M, Verstege E, Oeveren JV, Peleman J, Buckler ES, Eijk MV. (2007) Evaluation of target preparation methods for single feature polymorphism detection in large complex plant genomes. The Plant Genome [A Supplement to Crop Science] 47:S135-148. https://doi.org/10.2135/cropsci2007.02.0085tpg.
Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635. https://doi.org/10.1093/bioinformatics/btm308.
Buckler ES, Gore M. (2007) An arabidopsis haplotype map takes root. Nature Genetics 39:1056-1057. https://doi.org/10.1038/ng0907-1056.
Hamblin MT, Warburton ML, Buckler ES. (2007) Empirical comparison of simple sequence repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness. PLoS ONE 2:e1367. https://doi.org/10.1371/journal.pone.0001367.
Esch E, Szymaniak JM, Yates H, Pawlowski WP, Buckler ES. (2007) Using crossover breakpoints in recombinant inbred lines to identify quantitative trait loci controlling the global recombination frequency. Genetics 177:1851-1858. https://doi.org/10.1534/genetics.107.080622.
Yu J, Holland JB, McMullen MD, Buckler ES. (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178:539-551. https://doi.org/10.1534/genetics.107.074245.
Stich B, Mohring J, Piepho H-P, Heckenberger M, Buckler ES, Melchinger AE. (2008) Comparison of Mixed-Model Approaches for Association Mapping. Genetics 178:1745-1754. https://doi.org/10.1534/genetics.107.079707.
Canaran P, Buckler ES, Glaubitz JC, Stein L, Sun Q, Zhao W, Ware D. (2008) Panzea: an update on new content and features. Nucleic Acids Research 36:D1041-D1043. https://doi.org/10.1093/nar/gkm1022.
Liang CZ, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T, Hurwitz B, McCouch S, Ni JJ, Pujar A, Ravenscroft D, Ren L, Spooner W, Tecle I, Thomason J, Tung CW, Wei XH, Yap I, Youens-Clark K, Ware D, Stein L. (2008) Gramene: a growing plant comparative genomics resource. Nucleic Acids Research 36:D947-D953. https://doi.org/10.1093/nar/gkm968.
Harjes CE, Rocheford TR, Bai L, Brutnell TP, Kandianis CB, Sowinski SG, Stapleton AE, Vallabhaneni R, Williams M, Wurtzel ET, Yan JB, Buckler ES. (2008) Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science 319:330-333. https://doi.org/10.1126/science.1150255.
Zhu C, Gore M, Buckler ES, Yu J. (2008) Status and prospects of association mapping in plants. Plant Genome 1:5-20. https://doi.org/10.3835/plantgenome2008.02.0089.
Weber AL, Briggs WH, Rucker J, Baltazar BM, Sanchez-Gonzalez JD, Feng P, Buckler ES, Doebley JF. (2008) The genetic architecture of complex traits in teosinte (Zea mays ssp. parviglumis): new evidence from association mapping. Genetics 180:1221-1232. https://doi.org/10.1534/genetics.108.090134.

2006 - 2005

Publication Title	PDF
Szalma SJ, Buckler ES, Snook ME, McMullen MD. (2005) Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks. Theoretical and Applied Genetics 110:1324-1333. https://doi.org/10.1007/s00122-005-1973-0.
Fukunaga K, Hill J, Vigouroux Y, Matsuoka Y, J Sanchez G, Liu K, Buckler ES, Doebley JF. (2005) Genetic diversity and population structure of teosinte. Genetics 169: 2241-2254. https://doi.org/10.1534/genetics.104.031393.
Vollbrecht E, Springer P, Goh L, Buckler ES, Martienssen RA. (2005) Architecture of floral branch systems in maize and related grasses. Nature 436:1119-1126. https://doi.org/10.1038/nature03892.
Flint-Garcia SA, Thuillet A-C, Yu JM, Pressoir G, Romero SM, Mitchell SE, Doebley J, Kresovich S, Goodman MM, Buckler ES. (2005) Maize association population: a high resolution platform for QTL dissection. Plant Journal 44:1054-1064. 10.1111/j.1365-313x.2005.02591.x .
Buckler ES, Goodman MM, Holtsford TP, Doebley JF, J Sanchez G. (2005) Phylogeography of the wild subspecies of Zea mays. Maydica 51:123-134.
Buckler ES, Stevens NM. (2005) Maize origins, domestication, and selection. In Darwin's Harvest (Motley TJ, Zerega N, Cross H, eds.) pp.67-90. Columbia University Press: New York
Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Holland JB, Kresovich S, Buckler ES. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics 38(2):203-208. https://doi.org/10.1038/ng1702.
Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S. (2006) Gramene: a bird's eye view of cereal genomes. Nucleic Acids Research 34:D717-723. https://doi.org/10.1093/nar/gkj154.
Zhao W, Canaran P, Jurkuta R, Fulton T, Glaubitz J, Buckler ES, Doebley JF, Gaut B, Goodman M, Holland J, Kresovich S, McMullen MD, Stein L, Ware D. (2006) Panzea: a database and resource for molecular and functional diversity in the maize genome. Nucleic Acids Research 34:D752-757. https://doi.org/10.1093/nar/gkj011.
Buckler ES, Gaut BS, McMullen MD. (2006) Molecular and functional diversity of maize. Current Opinions in Plant Biology 9:172-176. https://doi.org/10.1016/j.pbi.2006.01.013.
Yu J, Buckler ES. (2006) Genetic association mapping and genome organization of maize. Current Opinions in Biotechnology 17:155-160. https://doi.org/10.1016/j.copbio.2006.02.003.
Kirst M, Caldo R, Casati P, Tanimoto G, Walbot V, Wise RP, Buckler ES. (2006) Genetic diversity contribution to errors in short oligonucleotide microarray analysis. Plant Biotechnology Journal 4:489-498. https://doi.org/10.1111/j.1467-7652.2006.00198.x.
Tracy WF, Whitt SR, Buckler ES. (2006) Recurrent mutation and genome evolution: example of Sugary1 and the origin of sweet maize. The Plant Genome 46:S49-54. https://doi.org/10.2135/cropsci2006-03-0149tpg.

2004 - 2003

Publication Title	PDF
Flint-Garcia SA, Thornsberry JM, Buckler ES. (2003) Structure of linkage disequilibrium in plants. Annual Review of Plant Biology 54:357-374.ttps://doi.org/10.1146/annurev.arplant.54.031902.134907.
Whitt SR, Buckler ES. (2003) Using natural allelic diversity to evaluate gene function. In Plant Functional Genomics: Methods and Protocols (Grotewald E, ed). Humana Press. 236:123-140. https://doi.org/10.1385/1-59259-413-1:123.
Du C, Buckler ES, Muse SV. (2003) Development of a maize molecular evolutionary genomic database. Comparative and Functional Genomics 4:246–249. https://doi.org/10.1002/cfg.282.
Liu K, Goodman MM, Muse SV, Smith JS, Buckler ES, Doebley JF. (2003) Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165:2117-2128
Jaenicke-Despres V, Buckler ES, Smith BD, Gilbert MTP, Cooper A, Doebley JF, Pääbo S. (2003) Early allelic selection in maize as revealed by ancient DNA. Science 302:1206-1208. https://doi.org/10.1126/science.1089056.
Goode M, Buckler ES, Drummond A, Strimmer K, Rodrigo A. (2004) A brief introduction to the phylogentics analysis library V1.5. In Conference in Research and Practice in Information Technology (Chen P, ed) 29:175-179. https://dl.acm.org/doi/10.5555/976520.976544.
Casstevens TM, Buckler ES. (2004) GDPC: The genomic diversity and phenotype connection. Bioinformatics 20: 2839–2840. https://doi.org/10.1093/bioinformatics/bth277.
Wilson LM, Whitt SR, Ibanez-Carranza AM, Goodman MM, Rocheford TR, Buckler ES. (2004). Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16:2719-2733. https://doi.org/10.1105/tpc.104.025700.
Churchill GA, and the Complex Trait Consortium. (2004) The collaborative cross, a community resource for the genetic analysis of complex traits. Nature Genetics 36:1133-7. https://doi.org/10.1038/ng1104-1133.

2002 - 2001

Publication Title	PDF
Remington DL, Thornsberry J, Matsuoka Y, Wilson L, Rinehart-Whitt S, Doebley JF, Kresovich S, Goodman MM, Buckler ES. (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proceedings of the National Academy of Sciences of USA 98:11479-11484. https://doi.org/10.1073/pnas.201394398.
Bennetzen J, Buckler ES, Chandler V, Doebley JF, Dorweiler J, Gaut B, Freeling M, Hake S, Kellogg E, Poethig RS, Walbot V, Wessler S. (2001) Genetic evidence and the origin of maize. Latin American Antiquity 12:84-86. https://doi.org/10.2307/971759.
Thornsberry JM, Goodman MM, Doebley JF, Kresovich S, Nielsen D, Buckler ES. (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nature Genetics 28:286-289. https://doi.org/10.1038/90135.
Buckler ES, Thornsberry JM, Kresovich S. (2001) Molecular diversity, structure and domestication of grasses. Genetical Research 77:213-218. https://doi.org/10.1017/S0016672301005158.
Buckler ES, Thornsberry J. (2002) Plant molecular diversity and applications to genomics. Current Opinion in Plant Biology 5:107-111. https://doi.org/10.1016/s1369-5266(02)00238-8.
Matsuoka Y, Vigouroux Y, Goodman MM, Sanchez GJ, Buckler ES, Doebley JF. (2002) A single domestication for maize shown by multilocus microsatellite genotyping. Proceedings of the National Academy of Sciences of USA 99:6080-6084. https://doi.org/10.1073/pnas.052125199.
Rauh B, Basten C, Buckler ES. (2002) Quantitative trait loci analysis of growth response to varying nitrogen sources in Arabidopsis. Theoretical and Applied Genetics 104:743-750. https://doi.org/10.1007/s00122-001-0815-y.
Whitt SR, Wilson LM, Tenaillon MI, Gaut BS, Buckler ES. (2002) Genetic diversity and selection in the maize starch pathway. Proceedings of the National Academy of Sciences of USA 99:12959-12962. https://doi.org/10.1073/pnas.202476999.

1999 - 1994

Publication Title	PDF
Buckler ES, Pearsall DM, Holtsford TP. (1994) Zinc iodide and centrifugation allow rapid, inexpensive phytolith separation. Phytolitharien Newsletter 8:2-3.
Buckler ES, Holtsford TP. (1996) Zea ribosomal repeat evolution and mutation patterns. Molecular Biology and Evolution 13:612-622. https://doi.org/10.1093/oxfordjournals.molbev.a025622.
Buckler ES, Holtsford TP. (1996) Zea systematics: ribosomal ITS evidence. Molecular Biology and Evolution 13:623-632. https://doi.org/10.1093/oxfordjournals.molbev.a025621.
McCue KA, Buckler ES, Holtsford TP. (1996) A hierarchical view of genetic structure in the rare annual plant Clarkia springvillensis (Onagraceae). Conservation Biology 10:1425-1434. https://doi.org/10.1046/j.1523-1739.1996.10051425.x.
Buckler ES, Pearsall DM, Holtsford TP. (1998) Climate, plant ecology, and Central Mexican Archaic subsistence. Current Anthropology 39:152-164. https://doi.org/10.1086/204705.
Qing L, Buckler ES, Muse S, Walker JC. (1999) Molecular evolution of type 1 serine/threonine protein phosphatases. Molecular Phylogenetics and Evolution 12:57-66. https://doi.org/10.1006/mpev.1998.0560.
Lawton-Rauh AL, Buckler ES, Purugganan MD. (1999) Patterns of molecular evolution among paralogous floral homeotic genes. Molecular Biology and Evolution 16:1037-1045. https://doi.org/10.1093/oxfordjournals.molbev.a026193.
Buckler ES, Phelps TL, Keith-Buckler CS, Dawe RK, Doebley JF, Holtsford TP. (1999) Meiotic drive of chromosomal knobs reshaped the maize genome. Genetics 153:415-426.