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                    U.S. DEPARTMENT OF AGRICULTURE
 Plant, Soil and Nutrition Research: Ithaca, NY
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ARS Home Northeast Area Ithaca, New York Robert W. Holley Center for Agriculture & Health Plant, Soil and Nutrition Research People & Locations







Edward S Buckler IV

(Ed)
                        Plant, Soil and Nutrition Research

                        




                        
                        Research Geneticist (Plants)
                        Phone: (607) 255-4520
                        
                        
                        Fax: (607) 255-6249(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            ProjectsBreeding Insight Phase 2: Expansion to Support More Diverse Plant and Animal Use Cases
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 439262Breeding Insight 3
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 444969Creating a Circular Economy that Reimagines Agriculture Using Plant Diversity and Computational Modeling
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 445214CERCA - On-Farm Nitrogen Recycling
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 445490CERCA - On-Farm Nitrogen Recycling
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 445563CERCA - On-Farm Nitrogen Recycling
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 445599CERCA - On-Farm Nitrogen Recycling
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 445620CERCA - On-Farm Nitrogen Recycling
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 445621CERCA - On-Farm Nitrogen Recycling
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 445392Enabling Mechanistic Allele Mining to Accelerate Genomic Selection for New Agro-Ecosystems
                                                    In-House Appropriated
                                                                    (D)Accession Number: 445317Improving Maize and Sorghum Efficiency Using Grass Diversity and Computational Modeling
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 438558CERCA - Circular Economy that Reimagines Corn Agriculture (CERCA: On-Farm Nitrogen Recycling)
                                                    Trust Fund Cooperative Agreement
                                                                    (T)Accession Number: 445468**Publications**
                                                (Clicking on the reprint icon
                                                    Reprint Icon
                                                    will take you to the publication reprint.)2020-2021 Field seasons of maize G x E project within maize genomes to fields initiative
                                                        

- (Peer Reviewed Journal)Lima, D., Castro, A., Alpers, T., Perkins, A., De Leon, N., Kaeppler, S., Ertl, D., Romay, C., Gage, J., Holland, J.B., Thompson, A., Hirsch, C., Hooker, D., Buckler Iv, E.S., Schnable, J., Wallace, J., Edwards, J.W., Knoll, J.E., Singh, M., Bohn, M., Tuinstra, M., Thomison, P., Sekhon, R., Minyo, R., Murray, S., Flint Garcia, S.A., Weldekidan, T., Beissinger, T., Xu, W. 2023. 2020-2021 Field seasons of maize G x E project within maize genomes to fields initiative. BMC Research Notes. 16, 219 (2023). https://doi.org/10.1186/s13104-023-06430-y.Genomes to fields 2022 maize genotype by environment prediction competition
                                                        

- (Peer Reviewed Journal)Lima, D.C., Washburn, J.D., Varela, J.I., Chen, Q., Gage, J.L., Romay, M.C., Holland, J.B., Ertl, D., Lopez-Cruz, M., Aguate, F.M., De Los Campos, G., Kaeppler, S., Beissinger, T., Bohn, M., Buckler IV, E.S., Edwards, J.W., Flint Garcia, S.A., Gore, M.A., Hirsch, C.N., Knoll, J.E., Mckay, J., Minyo, R., Murray, S.C., Ortez, O.A., Schnable, J., Sekhon, R.S., Singh, M.P., Sparks, E.E., 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: Article 148. https://doi.org/10.1186/s13104-023-06421-z.Features that govern terminator strength in plants
                                                        

- (Pre-print Publication)Gorjifard, S., Jores, T., Tonnies, J., Mueth, N.A., Bubb, K., Wrightsman, T., Buckler IV, E.S., Fields, S., Cuperus, J.T., Queitsch, C. 2023. Features that Govern Terminator Strength in Plants. bioRxiv. https://doi.org/10.1101/2023.06.16.545379.Exploring the utility of regulatory network-based machine learning for gene expression prediction in maize
                                                        

- (Pre-print Publication)Ferebee, T.H., Buckler IV, E.S. 2023. Exploring the utility of regulatory network-based machine learning for gene expression prediction in maize. bioRxiv. 05/14/2023. https://doi.org/10.1101/2023.05.11.540406.A new Revolutio-N: radically rethinking nitrogen use in agriculture

- (Abstract Only)Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding
                                                        

- (Peer Reviewed Journal)Wu, Y., Li, D., Hu, Y., Li, H., Ramstein, G.P., Zhou, S., Zhang, X., Bao, Z., Zhang, Y., Song, B., Zhou, Y., Zhou, Y., Gagnon, E., Sarkinen, T., Knaap, S., Zhang, C., Stadler, T., Buckler IV, E.S., Huang, S. 2023. Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell. 186(11):2313-2328. https://doi.org/10.1016/j.cell.2023.04.008.A happy accident: a novel turfgrass reference genome
                                                        

- (Peer Reviewed Journal)Phillips, A.R., Seetharam, A.S., Albert, P.S., Aubuchon-Elder, T., Birchler, J.A., Buckler IV, E.S., Gillespie, L.J., Hufford, M.B., Romay, M., Soreng, R.J., Kellogg, E.A., Ross-Ibarra, J. 2023. A happy accident: a novel turfgrass reference genome. Genes, Genomes, Genetics. 13(6). Article jkad073. https://doi.org/10.1093/g3journal/jkad073.Genome-wide association study for root morphology and phosphorus acquisition efficiency in diverse maize panels
                                                        

- (Peer Reviewed Journal)Ribeiro, C.R., Tinoco, S.E., De Soouza, V., Negri, B., Gault, C., Pastina, M., Magalhaes, J., Guimaraes, L.I., De Barros, E.V., Buckler IV, E.S., Guimaraes, C.A. 2023. Genome-wide association study for root morphology and phosphorus acquisition efficiency in diverse maize panels. International Journal of Molecular Sciences. 24(7). Article 6233. https://doi.org/10.3390/ijms24076233.Elucidating the patterns of pleiotropy and its biological relevance in maize
                                                        

- (Peer Reviewed Journal)Khaipho-Burch, M., Ferebee, T., Giri, A., Ramstein, G., Monier, B., Yi, E., Romay, M., Buckler IV, E.S. 2023. Elucidating the patterns of pleiotropy and its biological relevance in maize. PLoS Genetics. PLoS Genet 19(3): e1010664. https://doi.org/10.1371/journal.pgen.1010664.Cross-species predictive modeling reveals conserved drought responses between maize and sorghum
                                                        

- (Peer Reviewed Journal)Pardo, J., Wai, C., Harman, M., Nguyen, A., Kremling, K.A., Romay, M., Lepak, N.K., Bauerle, T.L., Buckler IV, E.S., Thompson, A.M., Vanburen, R.M. 2023. Cross-species predictive modeling reveals conserved drought responses between maize and sorghum. Proceedings of the National Academy of Sciences (PNAS). 120(10). Article e2216894120. https://doi.org/10.1073/pnas.2216894120.Utilizing evolutionary conservation to detect deleterious mutations and improve genomic prediction in cassava
                                                        

- (Peer Reviewed Journal)Long, E.K., Romay, M., Ramstein, G., Buckler IV, E.S., Robbins, K.R. 2023. 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.Scale up trials to validate modified crops' benefits
                                                        

- (Peer Reviewed Journal)Khaipho-Burch, M., Cooper, M., Crossa, J., De Leon, N., Holland, J.B., Lewis, R., Mccouch, S., Murray, S., Rabbi, I., Ronald, P., Ross-Ibarra, J., Weigel, D., Buckler IV, E.S. 2023. Scale up trials to validate modified crops' benefits. Nature. 621:470-473. https://doi.org/10.1038/d41586-023-02895-w.Spatio-temporal modeling of high-throughput multi-spectral aerial images improves agronomic trait genomic prediction in hybrid maize
                                                        

- (Pre-print Publication)Morales, N., Anche, M.T., Kaczmar, N., Lepak, N.K., Ni, P., Romay, M., Santantonio, N., Buckler IV, E.S., Gore, M.A., Mueller, L.A., Robbins, K.R. 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.Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize
                                                        

- (Peer Reviewed Journal)Ramstein, G.P., Buckler IV, E.S. 2022. Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize. Genome Biology. 23. Article 183. https://doi.org/10.1186/s13059-022-02747-2.Elucidating the patterns of pleiotropy and its biological relevance in maize
                                                        

- (Pre-print Publication)Khaipho-Burch, M., Ferebee, T., Giri, A., Ramstein, G., Monier, B., Yi, E., Romay, M.C., Buckler IV, E.S. 2022. Elucidating the patterns of pleiotropy and its biological relevance in maize. bioRxiv. https://doi.org/10.1101/2022.07.20.500810.Mining alleles for tar spot complex resistance from CIMMYT's maize germplasm bank
                                                        

- (Peer Reviewed Journal)Willcox, M.C., Burgueño, J.A., Jeffers, D., Rodriguez-Chanona, E., Guadarrama-Espinoza, A., Kehel, Z., Chepetla, D., Shrestha, R., Swarts, K., Hearne, S., Buckler IV, E.S., Chen, N.C. 2022. Mining alleles for tar spot complex resistance from CIMMYT's maize germplasm bank. Frontiers in Sustainable Food Systems. 6:937200. https://doi.org/10.3389/fsufs.2022.937200.The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation.
                                                        

- (Peer Reviewed Journal)Bradbury, P.J., Casstevens, T., Jensen, S.E., Johnson, L.C., Miller, Z.R., Monier, B., Romay, M.C., Song, B., Buckler IV, E.S. 2022. The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac410.The practical haplotype graph, a platform for storing and using pangenomes for imputation
                                                        

- (Peer Reviewed Journal)Bradbury, P.J., Casstevens, T., Jensen, S.E., Johnson, L.E., Miller, Z.R., Monier, B., Romay, M., Song, B., Buckler IV, E.S. 2022. The practical haplotype graph, a platform for storing and using pangenomes for imputation. Bioinformatics. 38(15):3698-3702. https://doi.org/10.1093/bioinformatics/btac410.rTASSEL: An R interface to TASSEL for analyzing genomic diversity
                                                        

- (Peer Reviewed Journal)Monier, B., Casstevens, T.M., Bradbury, P., Buckler IV, E.S. 2022. rTASSEL: An R interface to TASSEL for analyzing genomic diversity. Journal of Open Source Software. https://doi.org/10.21105/joss.04530.Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks
                                                        

- (Peer Reviewed Journal)Wrightsman, T., Marand, A.P., Crisp, P.A., Springer, N.M., Buckler IV, E.S. 2022. Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks. The Plant Genome. 15(3):e20249. https://doi.org/10.1002/tpg2.20249.An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time
                                                        

- (Peer Reviewed Journal)Barnes, A.C., Rodríguez-Zapata, F., Juárez-Núñez, K.A., Gates, D.J., Janzen, G.M., Kur, A., Wang, L., Jensen, S.J., Estévez-Palmas, J.M., Crow, T.M., Kavi, H.S., Pil, H.D., Stokes, R.L., Knizner, K.T., Aguilar-Rangel, M.R., Demesa-Arévalo, E., Skopelitis, T., Pérez-Limón, S., Stutts, W.L., Thompson, P., Chiu, Y., Jackson, D., Muddiman, D.C., Fiehn, O., Runcie, D., Buckler Iv, E.S., Ross-Ibarra, J., Hufford, M.B., Sawers, R.J., Rellán-Álvarez, R. 2022. An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time. Proceedings of the National Academy of Sciences (PNAS). 119(27). Article e2100036119. https://doi.org/10.1073/pnas.2100036119.A happy accident: a novel turfgrass reference genome
                                                        

- (Pre-print Publication)Phillips, A.R., Seetharam, A.S., Aubuchon-Elder, T., Buckler IV, E.S., Gillespie, L.J., Hufford, M.B., Llaca, V., Romay, M.C., Soreng, R.J., Kellogg, E.A., Ross-Ibarra, J. 2022. A happy accident: a novel turfgrass reference genome. bioRxiv. https://doi.org/10.1101/2022.03.08.483531.Variation in upstream open reading frames contributes to allelic diversity in maize protein abundance
                                                        

- (Peer Reviewed Journal)Gage, J.L., Mali, S., McLoughlin, F., Khaipho-Burch, M., Monier, B., Bailey-Serres, J., Vierstra, R.D., Buckler IV, E.S. 2022. Variation in upstream open reading frames contributes to allelic diversity in maize protein abundance. Proceedings of the National Academy of Sciences (PNAS). 119(14). Article e2112516119. https://doi.org/10.1073/pnas.2112516119.Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte
                                                        

- (Peer Reviewed Journal)Samayoa, L., Olukolu, B.A., Yang, C.J., Chen, Q., Stetter, M.G., York, A.M., Sanchez-Gonzalez, J., Glaubitz, J.C., Bradbury, P., Cinta Romay, M., Sun, Q., Yang, J., Ross-Ibarra, J., Buckler IV, E.S., Doebley, J.F., Holland, J.B. 2021. Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte. PLoS Genetics. 2:1009797. https://doi.org/10.6084/m9.figshare.14750790.AnchorWave: sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication
                                                        

- (Peer Reviewed Journal)Song, B., Marco-Sola, S., Moreto, M., Johnson, L., Buckler IV, E.S., Stitzer, M.C. 2021. AnchorWave: sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication. Proceedings of the National Academy of Sciences (PNAS). 119(1). Article e2113075119. https://doi.org/10.1073/pnas.2113075119.Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks
                                                        

- (Pre-print Publication)Wrightsman, T., Marand, A.P., Crisp, P.A., Springer, N.M., Buckler IV, E.S. 2021. Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks. bioRxiv. https://doi.org/10.1101/2021.11.11.468292.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
                                                        

- (Peer Reviewed Journal)Oren, E., Tzuri, G., Dafna, A., Reese, E.R., Song, B., Freilich, S., Elkind, Y., Isaacson, T., Schaffer, A.A., Tadmor, Y., Burger, J., Buckler IV, E.S., 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. https://doi.org/10.1093/hr/uhab081.Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation
                                                        

- (Peer Reviewed Journal)Jordan, K., Bradbury, P., Miller, Z., Nyine, M., He, F., Guttieri, M.J., Brown Guedira, G.L., Buckler Iv, E.S., Jannink, J., Akhunov, E., Ward, B.P., Bai, G., Bowden, R.L., Fiedler, J.D., Faris, J.D. 2021. Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation. G3 Genes/Genomes/Genetics. https://doi.org/10.1101/2021.06.10.447944.Genome-wide imputation using the practical haplotype graph in the heterozygous crop cassava
                                                        

- (Peer Reviewed Journal)Long, E.M., Bradbury, P., Romay, C.M., Buckler IV, E.S., Robbins, K.R. 2021. 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.Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact
                                                        

- (Peer Reviewed Journal)Zhang, X., Zhu, Y., Kremling, K.A., Romay, C., Bukowski, R., Sun, Q., Gao, S., Buckler Iv, E.S., Lu, F. 2021. Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact. Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-021-03965-1.Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize
                                                        

- (Peer Reviewed Journal)Giri, A., Khaipho-Burch, M., Buckler IV, E.S., Ramstein, G.P. 2021. Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize. PLoS Genetics. https://doi.org/10.1371/journal.pgen.1009568.Prediction of evolutionary constraint by genomic annotations improves prioritization of causal variants in maize
                                                        

- (Pre-print Publication)Ramstein, G.P., Buckler IV, E.S. 2021. Prediction of evolutionary constraint by genomic annotations improves prioritization of causal variants in maize. bioRxiv. 2021.09.03.458856.  https://doi.org/10.1101/2021.09.03.458856.The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation
                                                        

- (Pre-print Publication)Bradbury, P., Casstevens, T., Jensen, S.E., Johnson, L.C., Miller, Z.R., Monier, B., Romay, M.C., Song, B., Buckler IV, E.S. 2021. The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. bioRxiv. 2021.08.27.457652. https://doi.org/10.1101/2021.08.27.457652.Predicting phenotypes from genetic, environment, management, and historical data using CNNs
                                                        

- (Peer Reviewed Journal)Washburn, J.D., Cimen, E., Ramstein, G., Reeves, T., O'Briant, P., McLean, G., Cooper, M., Hammer, G., Buckler IV, E.S. 2021. Predicting phenotypes from genetic, environment, management, and historical data using CNNs. Theoretical and Applied Genetics. 134:3997–4011. https://doi.org/10.1007/s00122-021-03943-7.AnchorWave: sensitive alignment of genomes with high diversity, structural polymorphism and whole-genome duplication variation
                                                        

- (Pre-print Publication)Song, B., Marco-Sola, S., Moreto, M., Johnson, L., Buckler IV, E.S., Stitzer, M.C. 2021. AnchorWave: sensitive alignment of genomes with high diversity, structural polymorphism and whole-genome duplication variation. bioRxiv. 2021.07.29.454331. https://doi.org/10.1101/2021.07.29.454331.Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes
                                                        

- (Peer Reviewed Journal)Pignon, C.P., Fernandes, S.B., Valluru, R., Bandillo, N., Lozano, R., Buckler IV, E.S., Gore, M.A., Long, S.P., Brown, P.J., Leakey, A. 2021. Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes. Plant Physiology. 184(4):2544-2562. https://doi.org/10.1093/plphys/kiab395.Pfam domain adaptation profiles reflect plant species’ evolutionary history
                                                        

- (Pre-print Publication)Jensen, S.E., Buckler IV, E.S. 2021. Pfam domain adaptation profiles reflect plant species’ evolutionary history. bioRxiv. https://doi.org/10.1101/2021.07.13.452250.Predicting protein domain temperature adaptation across the prokaryote-eukaryote divide
                                                        

- (Pre-print Publication)Jensen, S.E., Johnson, L.C., Casstevens, T., Buckler IV, E.S. 2021. Predicting protein domain temperature adaptation across the prokaryote-eukaryote divide. bioRxiv. 2021.07.13.452245. https://doi.org/10.1101/2021.07.13.452245.RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants
                                                        

- (Peer Reviewed Journal)Lozano, R., Booth, G.T., Omar, B., Li, B., Buckler IV, E.S., Lis, J.T., Pino Del Carpio, D., Jannink, J. 2021. RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants. Genes, Genomes, Genetics. jkab273. https://doi.org/10.1093/g3journal/jkab273.Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions
                                                        

- (Peer Reviewed Journal)Ferguson, J.N., Fernandes, S.B., Monier, B., Miller, N.D., Allan, D., Dmitrieva, A., Schmuker, P., Lozano, R., Valluru, R., Buckler IV, E.S., Gore, M.A., Brown, P.J., Spalding, E.P., Leakey, A.D. 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.Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation
                                                        

- (Pre-print Publication)Jordan, K., Bradbury, P., Miller, Z., Nyine, M., He, F., Guttieri, M.J., Brown Guedira, G.L., Buckler Iv, E.S., Jannink, J., Akhunov, E., Ward, B.P., Bai, G., Bowden, R.L., Fiedler, J.D., Faris, J.D. 2021. Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation. bioRxiv. https://doi.org/10.1101/2021.06.10.447944.A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants
                                                        

- (Other)Wu, Y., Johnson, L., Song, B., Romay, M., Stitzer, M., Siepel, A., Buckler IV, E.S., 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.Variation in upstream open reading frames contributes to allelic diversity in protein abundance
                                                        

- (Other)Gage, J.L., Mali, S., Mcloughlin, F., Khaipho-Burch, M., Monier, B., Bailey-Serres, J., Vierstra, R.D., Buckler IV, E.S. 2021. Variation in upstream open reading frames contributes to allelic diversity in protein abundance. bioRxiv. https://doi.org/10.1101/2021.05.25.445499.Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels
                                                        

- (Peer Reviewed Journal)Baseggio, M., Murray, M., Wu, D., Ziegler, G., Kaczmar, N., Chamness, J., Hamilton, J.P., Buell, R.C., Vatamaniuk, O.K., Buckler IV, E.S., Smith, M.E., Baxter, I., Tracy, W.F., Gore, M.A. 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). https://doi.org/10.1093/g3journal/jkab186.Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
                                                        

- (Peer Reviewed Journal)Song, B., Buckler IV, E.S., Wang, H., Wu, Y., Rees, E., Kellogg, E.A., Gates, D.J., Khaipho-Burch, M., Bradbury, P., Ross-Ibarra, J., Hufford, M.B., Romay, M. 2021. Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize. Genome Research. 31:1245-1257. https://doi.org/10.1101/gr.266528.120.Genome-wide imputation using the practical haplotype graph in the heterozygous crop cassava
                                                        

- (Other)Long, E.M., Bradbury, P., Romay, M., Buckler IV, E.S., Robbins, K.R. 2021. Genome-wide imputation using the practical haplotype graph in the heterozygous crop cassava. bioRxiv.  https://doi.org/10.1101/2021.05.12.443913.Underground heterosis for yield improvement in melon
                                                        

- (Peer Reviewed Journal)Dafna, A., Halperin, I., Oren, E., Isaacson, T., Tzuri, G., Meir, A., Schaffer, A.A., Burger, J., Tadmor, Y., Buckler IV, E.S., Gur, A. 2021. Underground heterosis for yield improvement in melon. Journal of Experimental Botany. 72(18):6205-6218. https://doi.org/10.1093/jxb/erab219.Somatic variations led to the selection of acidic and acidless orange cultivars
                                                        

- (Peer Reviewed Journal)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, R., Jiang, D., Ming, R., Buckler IV, E.S., 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.Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance
                                                        

- (Peer Reviewed Journal)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 IV, E.S., Dai, M. 2021. Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance. Genome Biology. 22(185):1-26. https://doi.org/10.1186/s13059-021-02377-0.Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes
                                                        

- (Other)Pignon, C.P., Fernandes, S.B., Valluru, R., Bandillo, N., Lozano, R., Buckler IV, E.S., Gore, M.A., Long, S.P., Brown, P.J., Leakey, A. 2021. Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes. bioRxiv. https://doi.org/10.1101/2021.05.06.442962.Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize
                                                        

- (Pre-print Publication)Giri, A., Khaipho-Burch, M., Buckler IV, E.S., Ramstein, G.P. 2021. Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize. bioRxiv. https://doi.org/10.1101/2021.04.30.442099.Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters
                                                        

- (Peer Reviewed Journal)Jores, T., Tonnies, J., Wrightsman, T., Buckler IV, E.S., Cuperus, J.T., 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.Underground heterosis for melons yield
                                                        

- (Pre-print Publication)Dafna, A., Halperin, I., Oren, E., Isaacson, T., Tzuri, G., Meir, A., Schaffer, A., Burger, J., Tadmor, Y., Buckler IV, E.S., Gur, A. 2021.  Underground heterosis for melons yield. bioRxiv. https://doi.org/10.1101/2021.03.04.434025.Joint analysis of days to flowering reveals independent temperate adaptations in maize
                                                        

- (Peer Reviewed Journal)Swarts, K., Bauer, E., Glaubitz, J.C., Ho, T., Johnson, L., Li, Y., Li, Y., Miller, Z., Schon, C., Wang, T., Zhang, Z., Buckler Iv, E.S., Bradbury, P. 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.A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants
                                                        

- (Peer Reviewed Journal)Wu, Y., Johnson, L., Song, B., Romay, M.C., Stitzer, M., Siepel, A., Buckler IV, E.S., Scheben, A. 2022. A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants. The Plant Genome. 15(2). Article e20204. https://doi.org/10.1002/tpg2.20204.Eleven biosynthetic genes explain the majority of natural variation in carotenoid levels in maize grain
                                                        

- (Peer Reviewed Journal)Diepenbrock, C.H., Ilut, D.C., Magallanes-Lundback, M., Kandianis, C.B., Lipka, A.E., Bradbury, P., Holland, J.B., Hamilton, J.P., Wooldridge, E., Vaillancourt, B., Góngora-Castillo, E., Wallace, J.G., Cepela, J., Mateos-Hernandez, M., Owens, B.F., Tiede, T., Buckler IV, E.S., Rocheford, T., Buell, C., Gore, M.A., Dellapenna, D. 2021. Eleven biosynthetic genes explain the majority of natural variation in carotenoid levels in maize grain. The Plant Cell. 33(4):882–900. https://doi.org/10.1093/plcell/koab032.Teosinte introgression modulates phosphatidylcholine levels and induces early maize flowering time
                                                        

- (Pre-print Publication)Rodriguez-Zapata, F., Barnes, A.C., Blocker-Juarez, K.A., Gates, D., Kur, A., Wang, L., Janzen, G.M., Jensen, S., Estevez-Palmas, J.M., Crow, T., Aguilar-Rangel, R., Demesa-Arevalo, E., Skopelitis, T., Perez-Limon, S., Stutts, W., Thompson, P., Chiu, Y., Jackson, D., Fiehn, O., Runcie, D., Buckler IV, E.S., Ross-Ibarra, J., Hufford, M.B., Sawers, R., Rellan-Alvarez, R. 2021. Teosinte introgression modulates phosphatidylcholine levels and induces early maize flowering time. bioRxiv. https://doi.org/10.1101/2021.01.25.426574.Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters
                                                        

- (Pre-print Publication)Jores, T., Tonnies, J., Wrightsman, T., Buckler IV, E.S., Cuperus, J.T., Fields, S., Queitsch, C. 2021. Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters. bioRxiv. https://doi.org/10.1101/2021.01.07.425784.Utility of climatic information via combining ability models to improve genomic prediction for yield within the genomes to fields maize project
                                                        

- (Peer Reviewed Journal)Jarquin, D., De Leon, N., Romay, M., Bohn, M., Buckler IV, E.S., Ciampitti, I., Edwards, J.W., Ertl, D., Flint Garcia, S.A., Gore, M.A., Graham, C., Hirsch, C.N., Holland, J.B., Hooker, D., Kaeppler, S.M., Knoll, J.E., Lee, E.S., Lawrence-Dill, C.J., Lynch, J.P., Moose, S.P., Murray, S.C., Nelson, R., Rocheford, T., Schnable, J.C., Schnable, P.S., Smith, M., Springer, N., Thomison, P., Tuinstra, M., Wisser, R.J., Xu, W., Lorenz, A. 2021. Utility of climatic information via combining ability models to improve genomic prediction for yield within the genomes to fields maize project. Frontiers in Genetics. 11:592769. https://doi.org/10.3389/fgene.2020.592769.Local adaptation contributes to gene expression divergence in maize
                                                        

- (Peer Reviewed Journal)Blanc, J., Kremling, K., Buckler IV, E.S., Josephs, E. 2021. Local adaptation contributes to gene expression divergence in maize. Genes, Genomes, Genetics. 11(2):jkab004. https://doi.org/10.1093/g3journal/jkab004.Decoding the regulatory architecture of the maize leaf
                                                        

- (Pre-print Publication)Tu, X., Mejia-Guerra, M.K., Valdes Franco, J.A., Tzeng, D., Chu, P., Dai, X., Li, P., Buckler IV, E.S., Zhong, S. 2020. Decoding the regulatory architecture of the maize leaf. bioRxiv. 54:34-41. https://doi.org/10.1101/2020.01.07.898056.Comparative evolutionary genetics of deleterious load in sorghum and maize
                                                        

- (Peer Reviewed Journal)Lozano, R., Gazave, E., Dos Santos, J., Valluru, R., Bandillo, N., Fernandes, S., Brown, P.J., Shakoor, N., Mockler, T., Ross-Ibarra, J., Buckler IV, E.S., Gore, M.A. 2021. Comparative evolutionary genetics of deleterious load in sorghum and maize. Nature Plants. (7):17-24. https://doi.org/10.1038/s41477-020-00834-5.Comparative evolutionary genetics of deleterious load in sorghum and maize
                                                        

- (Peer Reviewed Journal)Lozano, R., Gazave, E., Dos Santos, J., Stetter, M.G., Valluru, R., Bandillo, N., Fernandes, S., Brown, P.J., Shakoor, N., Mockler, T., Cooper, E., Perkins, T., Buckler IV, E.S., Ross-Ibarra, J., Gore, M.A. 2021. Comparative evolutionary genetics of deleterious load in sorghum and maize. Nature Plants. 7:17-24. https://doi.org/10.1038/s41477-020-00834-5.The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment
                                                        

- (Peer Reviewed Journal)Rogers, A.R., Dunne, J.C., Romay, C., Bohn, M., Buckler IV, E.S., Ciampitti, I.C., Edwards, J.W., Ertl, D., Flint Garcia, S.A., Gore, M.A., Graham, C., Hirsch, C.N., Hood, E., Hooker, D.C., Knoll, J.E., Lee, E.C., Lorenz, A., Lynch, J.P., Mckay, J., Moose, S.P., Murray, S.C., Nelson, R., Rocheford, T., Schnable, J.C., Schnable, P.S., Sekhon, R., Singh, M., Smith, M., Springer, N., Thelen, K., Thomison, P., Thompson, A., Tuinstra, M., Wallace, J., Wisser, R.J., Xu, W., Gilmour, A., Kaeppler, S.M., Deleon, N., Holland, J.B. 2021. The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment. Genes, Genomes, Genetics. https://doi.org/10.1093/g3journal/jkaa050.The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment
                                                        

- (Peer Reviewed Journal)Rogers, A.R., Dunne, J.C., Romay, M.C., Bohn, M., Buckler IV, E.S., Ciampitti, I.C., Edwards, J.W., Ertl, D., Flint Garcia, S.A., Gore, M.A., Graham, C., Hirsch, C.N., Hood, E.C., Hooker, D., Knoll, J.E., Lee, E.C., Lorenz, A., Lynch, J.P., Mckay, J., Moose, S.P., Murray, S.C., Nelson, R., Rocheford, T., Schnable, J.C., Schnable, P.S., Sekhon, R., Singh, M., Smith, M., Springer, N., Thelen, K., Thomison, P., Thompson, A., Tuinstra, M., Wallace, J., Wisser, R., Xu, W., Gilmour, A., Kaeppler, S.M., Deleon, N., Holland, J.B. 2021. The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment. Genes, Genomes, Genetics. 11(2):jkaa050. https://doi.org/10.1093/g3journal/jkaa050.Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions
                                                        

- (Pre-print Publication)Ferguson, J.N., Fernandes, S.B., Monier, B., Miller, N.D., Allan, D., Dmitrieva, A., Schmuker, P., Lozano, R., Valluru, R., Buckler IV, E.S., Gore, M.A., Brown, P., Spalding, E.P., Leakey, A. 2020. Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions. bioRxiv. https://doi.org/10.1101/2020.11.02.365213.Building a tRNA thermometer to estimate microbial adaptation to temperature
                                                        

- (Peer Reviewed Journal)Cimen, E., Jensen, S., Buckler IV, E.S. 2020. Building a tRNA thermometer to estimate microbial adaptation to temperature. Nucleic Acids Research. 48(21):12004-12045. https://doi.org/10.1093/nar/gkaa1030.Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors
                                                        

- (Peer Reviewed Journal)Tu, X., Majia-Guerra, M., Valdes Franco, J.A., Tzeng, D., Chu, P., Shen, W., Wei, Y., Dai, X., Li, P., Buckler IV, E.S., 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.Identification of miRNA-eQTLs in maize mature leaf by GWAS
                                                        

- (Peer Reviewed Journal)Chen, S., Mei-Hsiu, S., Kremling, K.A., Lepak, N.K., Romay, M.C., Sun, Q., Bradbury, P., Buckler IV, E.S., Ku, H. 2020. Identification of miRNA-eQTLs in maize mature leaf by GWAS. Biomed Central (BMC) Genomics. 21(689). https://doi.org/10.1186/s12864-020-07073-0.Genetic elucidation of interconnected antibiotic pathways mediating maize innate immunity
                                                        

- (Peer Reviewed Journal)Ding, Y., Weckwerth, P.R., Poretsky, E., Murphy, K.M., Sims, J., Saldivar, E., Christensen, S.A., Char, S., Yang, B., Tong, A., Shen, Z., Kremling, K.A., Buckler IV, E.S., Kono, T., Nelson, D.R., Bohlmann, J., Bakker, M.G., Vaughan, M.M., Khalil, A.S., Betsiashvili, M., Briggs, S.P., Zerbe, P., Schmelz, E.A., Huffaker, A. 2020. Genetic elucidation of interconnected antibiotic pathways mediating maize innate immunity. Nature Plants. (6):1375-1388. https://doi.org/10.1038/s41477-020-00787-9.A maize practical haplotype graph leverages diverse NAM assemblies
                                                        

- (Other)Valdes Franco, J.A., Gage, J.L., Bradbury, P., Johnson, L.C., Miller, Z.R., Buckler IV, E.S., Romay, M. 2020. A maize practical haplotype graph leverages diverse NAM assemblies. bioRxiv. https://doi.org/10.1101/2020.08.31.268425.Local adaptation contributes to gene expression divergence in maize
                                                        

- (Other)Blanc, J., Kremling, K.A., Buckler IV, E.S., Josephs, E.B. 2020. Local adaptation contributes to gene expression divergence in maize. bioRxiv. https://doi.org/10.1101/2020.08.01.231217.rTASSEL: an R interface to TASSEL for association mapping of complex traits
                                                        

- (Other)Monier, B., Casstevens, T.M., Buckler IV, E.S. 2020. rTASSEL: an R interface to TASSEL for association mapping of complex traits. bioRxiv. https://doi.org/10.1101/2020.07.21.209114.Constrained non-coding sequence provides insights into regulatory elements and loss of gene expression in maize
                                                        

- (Other)Song, B., Wang, H., Wu, Y., Rees, E., Gates, D.J., Burch, M., Bradbury, P., Ross-Ibarra, J., Kellogg, E.A., Hufford, M.B., Romay, C., Buckler IV, E.S. 2020. Constrained non-coding sequence provides insights into regulatory elements and loss of gene expression in maize. bioRxiv. https://doi.org/10.1101/2020.07.11.192575.Ten years of the maize Nested Association Mapping population: impact, limitations, and future directions
                                                        

- (Peer Reviewed Journal)Gage, J., Monier, B., Giri, A., Buckler IV, E.S. 2020. Ten years of the maize Nested Association Mapping population: impact, limitations, and future directions. The Plant Cell. https://doi.org/10.1105/tpc.19.00951.The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication

- (Peer Reviewed Journal)Chen, Q., Samayoa, L., Yang, C.J., Bradbury, P., Olukolu, B., Neumeyer, M.A., Tomay, M., Sun, Q., Lorant, A., Buckler IV, E.S., Ross-Ibarra, J., Holland, J.B., Doebley, J.F. 2020. The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication. PLoS Genetics. 16(5):e1008791.Genetic elucidation of complex biochemical traits mediating maize innate immunity
                                                        

- (Pre-print Publication)Ding, Y., Weckwerth, P., Poretsky, E., Murphy, K., Sims, J., Saldivar, E., Christensen, S.A., Char, S., Yang, B., Tong, A., Shen, Z., Kremling, K., Buckler IV, E.S., Kono, T., Nelson, D., Bohlmann, J., Bakker, M.G., Vaughan, M.M., Khalil, A., Betsiashvili, M., Briggs, S., Zerbe, P., Schmelz, E., Huffaker, A. 2020. Genetic elucidation of complex biochemical traits mediating maize innate immunity. bioRxiv. https://doi.org/10.1101/2020.03.04.977355.Deep learning for plant genomics and crop improvement
                                                        

- (Peer Reviewed Journal)Wang, H., Cimen, E., Singh, N., Buckler IV, E.S. 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.Dominance effects and functional enrichments improve prediction of agronomic traits in hybrid maize
                                                        

- (Peer Reviewed Journal)Ramstein, G.P., Larsson, S.J., Cook, J.P., Edwards, J.W., Ersoz, E.S., Flint Garcia, S.A., Gardner, C.A., Holland, J.B., Lorenz, A.J., Mcmullen, M.D., Millard, M.J., Rocheford, T.R., Tuinstra, M.R., Bradbury, P., Buckler IV, E.S., Romay, M.C. 2020. Dominance effects and functional enrichments improve prediction of agronomic traits in hybrid maize. Genetics. 215:215-230. https://doi.org/10.1534/genetics.120.303025.A sorghum practical haplotype graph facilitates genome-wide imputation and cost effective genomic prediction
                                                        

- (Peer Reviewed Journal)Jensen, S., Charles, J., Muleta, K., Bradbury, P., Casstevens, T., Deshpande, S.P., Gore, M.A., Gupta, R., Johnson, L., Lozano, R., Miller, Z., Ramu, P., Rathore, A., Upadhyaya, H.D., Varshney, R., Morris, G.P., Pressoir, G., Buckler IV, E.S., Ramstein, G. 2020. A sorghum practical haplotype graph facilitates genome-wide imputation and cost effective genomic prediction. The Plant Genome. 13(1). Article e20009. https://doi.org/10.1002/tpg2.20009.Novel bayesian networks for genomic prediction of developmental traits in biomass sorghum
                                                        

- (Peer Reviewed Journal)Dos Santos, J.P., Fernandes, S.B., Mccoy, S., Lozano, R., Brown, P.J., Leakey, A.D., Buckler IV, E.S., Garcia, A.A., Gore, M.A. 2020. Novel bayesian networks for genomic prediction of developmental traits in biomass sorghum. Genes, Genomes, Genetics. 10(2):769-781. https://doi.org/10.1534/g3.119.400759.Maize genomes to fields (G2F): 2014 –2017 field seasons: genotype, phenotype, climatic, soil and inbred ear image datasets
                                                        

- (Peer Reviewed Journal)Mcfarland, B.A., Alkhalifah, N., Bohn, M., Bubert, J., Buckler IV, E.S., Ciampitti, I., Edwards, J.W., Ertl, D., Gage, J.L., Falcon, C.M., Flint Garcia, S.A., Gore, M., Graham, C., Hirsch, C., Holland, J.B., Hood, E., Hooker, D., Jarquin, D., Kaeppler, S., Knoll, J.E., Kruger, G., Lauter, N.C., Lee, E.C., Lima, D.C., Lorenz, A., Lynch, J.P., Mckay, J., Miller, N.D., Moose, S.P., Murray, S.C., Nelson, R., Poudyal, C., Rocheford, T., Rodriguez, O., Romay, M., Schnable, J.C., Schnable, P.S., Scully, B.T., Sekhon, R., Silverstein, K., Singh, M., Smith, M., Spalding, E.P., Springer, N., Thelen, K., Thomison, P., Tuinstra, M., Wallace, J., Walls, R., Wills, D., Wisser, R.J., Xu, W., Yeh, C., De Leon, N. Maize genomes to fields (G2F): 2014 –2017 field seasons: genotype, phenotype, climatic, soil and inbred ear image datasets. BMC Research Notes. 13,71 (2020). https://doi.org/10.1186/s13104-020-4922-8.In-field whole plant maize architecture characterized by Subcanopy Rovers and Latent Space Phenotyping
                                                        

- (Peer Reviewed Journal)Gage, J.L., Richards, E., Lepak, N.K., Kaczmar, N., Soman, C., Chowdhary, G., Gore, M.A., Buckler IV, E.S. 2019. In-field whole plant maize architecture characterized by Subcanopy Rovers and Latent Space Phenotyping. The Plant Phenome Journal. 2(1):1-11. https://doi.org/10.1101/763342.Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn
                                                        

- (Peer Reviewed Journal)Baseggio, M., Murray, M., Magallanes-Lundback, M., Kaczmar, N., Chamness, J., Buckler IV, E.S., Smith, M.E., Dellapenna, D., Tracy, W.F., Gore, M.A. 2020. Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn. The Plant Genome. https://doi.org/10.1002/tpg2.20008.Widespread long-range cis-regulatory elements in the maize genome
                                                        

- (Peer Reviewed Journal)Ricci, W.A., Lu, Z., Ji, L., Marand, A.P., Ethridge, C.L., Murphy, N.G., Noshay, J.M., Galli, M., Mejia-Guerra, M.K., Colome-Tatche, M., Johannes, F., Rowley, M., Corces, V.G., Zhai, J., Scanlon, M.J., Buckler IV, E.S., Gallavotti, A., Springer, N.M., Schmitz, R.J., 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.Relative utility of agronomic, phenological, and morphological traits for assessing genotype-by-environment interaction in maize inbreds
                                                        

- (Peer Reviewed Journal)Falcon, C.M., Kaeppler, S.M., Spalding, E.P., Miller, N.D., Haase, N., Alkhalifah, N., Bohn, M., Buckler IV, E.S., Campbell, D.A., Ciampitti, I., Coffey, L., Edwards, J.W., Ertl, D., Flint Garcia, S.A., Gore, M.A., Graham, C., Hirsch, C.N., Holland, J.B., Jarquin, D., Knoll, J.E., Lauter, N.C., Lawrence-Dill, C.J., Lee, E.C., Lorenz, A., Lynch, J.P., Murray, S.C., Nelson, R., Romay, M., Rocheford, T., Schnable, P., Scully, B.T., Smith, M.C., Springer, N., Tuinstra, M., Walton, R., Weldekidan, T., Wisser, R.J., Xu, W., De Leon, N. Relative utility of agronomic, phenological, and morphological traits for assessing genotype-by-environment interaction in maize inbreds. Crop Science. 2020; 60:62-81. https://doi.org/10.1002/csc2.20035Multiple genes recruited from hormone pathways partition maize diterpenoid defences
                                                        

- (Peer Reviewed Journal)Ding, Y., Murphy, K., Poretsky, E., Mafu, S., Yang, B., Char, S., Christensen, S.A., Saldivar, E., Wu, M., Wang, Q., Ji, L., Schmitz, R., Kremling, K., Buckler IV, E.S., Shen, Z., Briggs, S., Bohlmann, J., Sher, A., Castro-Falcon, G., Hughes, C., Huffaker, A., Zerbe, P., Schmelz, E. 2019. Multiple genes recruited from hormone pathways partition maize diterpenoid defences. Nature Plants. https://doi.org/10.1038/s41477-019-0509-6.Transcriptome-wide association supplements genome-wide association in Zea mays
                                                        

- (Peer Reviewed Journal)Kremling, K., Diepenbrock, C., Gore, M., Buckler IV, E.S., Bandillo, N. 2019. Transcriptome-wide association supplements genome-wide association in Zea mays. Genes, Genomes, Genetics. 9(9):3023-3033. https://doi.org/10.1534/g3.119.400549.Single-gene resolution of locally adaptive genetic variation in Mexican maize
                                                        

- (Other)Gates, D., Runcie, D., Janzen, G., Romero Navarro, A., Willcox, M., Sonder, K., Snodgrass, S., Rodriqyez-Zapata, F., J.H. Sawers, R., Buckler IV, E.S., Hearne, S., Hufford, M., Ross-Ibarra, J. 2019. Single-gene resolution of locally adaptive genetic variation in Mexican maize. bioRxiv. https://doi.org/10.1101/706739.Novel bayesian networks for genomic prediction of developmental traits in biomass sorghum
                                                        

- (Peer Reviewed Journal)Dos Santos, J.P., Fernandes, S.B., Lozano, R., Brown, P.K., Buckler IV, E.S., Garcia, A.A., Gore, M.A. 2019. Novel bayesian networks for genomic prediction of developmental traits in biomass sorghum. bioRxiv. https://doi.org/10.1101/677179.Metabolome-scale genome-wide association studies reveal chemical diversity and genetic control of maize specialized metabolites
                                                        

- (Review Article)Shaoqun, Z., Kremling, K.A., Bandillo, N., Richter, A., Zhang, Y.K., Ahern, K.R., Artyukhin, A.B., Hui, J.X., Younkin, G.C., Schroeder, F.C., Buckler IV, E.S., Jander, G. 2019. Metabolome-scale genome-wide association studies reveal chemical diversity and genetic control of maize specialized metabolites. The Plant Cell. 31:937-955.  https://doi.org/10.1105/tpc.18.00772.The multi-allelic APRR2 Gene is associated with fruit pigment accumulation in melon and watermelon
                                                        

- (Peer Reviewed Journal)Oren, E., Tzuri, G., Vexler, L., Dafna, A., Meir, A., Faigenboim, A., Kenigswald, M., Portnoy, V., Schaffer, A.A., Levi, A., Buckler IV, E.S., Katzir, N., Burger, J., Tadmor, Y., Gur, A. 2019. The multi-allelic APRR2 Gene is associated with fruit pigment accumulation in melon and watermelon. Journal of Experimental Botany. https://doi.org/10.1093/jxb/erz182.k-mer grammar uncovers maize regulatory architecture
                                                        

- (Review Article)Mejia-Guerra, M., Buckler IV, E.S. 2019. k-mer grammar uncovers maize regulatory architecture. Biomed Central (BMC) Plant Biology. 19:103. https://doi.org/10.1186/s12870-019-1693-2.The genetic architecture of teosinte catalyzed and constrained maize domestication

- (Peer Reviewed Journal)Yang, C., Samayoa, L., Bradbury, P., Olukolu, B.A., Xue, W., York, A.M., Tuholski, M.R., Wang, W., Daskalska, L.L., Neumeyer, M.A., Sanchez-Gonzales, J., Romay, M.C., Glaubitz, J.C., Sun, Q., Buckler IV, E.S., Holland, J.B., Doebley, J.F. 2019. The genetic architecture of teosinte catalyzed and constrained maize domestication. Proceedings of the National Academy of Sciences. 116:5643-5652.Evolutionarily informed deep learning methods: Predicting transcript abundance from DNA sequence
                                                        

- (Review Article)Washburn, J.D., Mejia Guerra, M., Ramstein, G., Kremling, K., Valluru, R., Buckler IV, E.S., Wang, H. 2019. Evolutionarily informed deep learning methods: Predicting transcript abundance from DNA sequence. Proceedings of the National Academy of Sciences. 116(12):5542-5549. https://doi.org/10.1073/pnas.1814551116.Deleterious mutation burden and its association with complex traits in sorghum (sorghum bicolor)
                                                        

- (Peer Reviewed Journal)Valluru, R., Gazave, E., Fernandes, S., Ferguson, J., Lazano, R., Hirannaiah, P., Zuo, T., Brown, P., Leakey, A., Gore, M., Buckler IV, E.S., Bandillo, N. 2019. Deleterious mutation burden and its association with complex traits in sorghum (sorghum bicolor). Genetics. 211(3):1075-1087. https://doi.org/10.25386/genetics.7638122.Breaking the curse of dimensionality to identify causal variants in Breeding 4
                                                        

- (Review Article)Ramstein, G.P., Jensen, S.E., Buckler IV, E.S. 2019. Breaking the curse of dimensionality to identify causal variants in Breeding 4. Theoretical and Applied Genetics. 132(3):559-567. https://doi.org/10.1007/s00122-018-3267-3.On the road to breeding 4.0: unraveling the good, the bad, and the boring of crop quantitative genomics
                                                        

- (Peer Reviewed Journal)Wallace, J.G., Rodgers-Melnick, E., Buckler IV, E.S. 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(1)421-444. https://doi.org/10.1146/annurev-genet-120116-024846.Ethylene signaling regulates natural variation in the abundance of antifungal acetylated diferuloylsucroses and Fusarium graminearum resistance in maize seedling roots
                                                        

- (Review Article)Zhou, S., Zhang, Y., Kremling, K., Ding, Y., Bennett, J., Bae, J., Kim, D., Kolomiets, M., Schmelz, E., Schroeder, F., Buckler Iv, E.S., 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. 221(4):2096-2111. https://doi.org/10.1111/nph.15520.Co-regulation of ribosomal RNA with hundreds of genes contributes to phenotypic variations
                                                        

- (Peer Reviewed Journal)Li, B., Kremling, K., Wu, P., Bukowski, R., Romay, M., Xie, E., Buckler IV, E.S., Chen, M. 2018. Co-regulation of ribosomal RNA with hundreds of genes contributes to phenotypic variations. Genome Research. https://doi.org/10.1101/gr.229716.117.Quantitative genetics of the maize leaf microbiome
                                                        

- (Review Article)Wallace, J., Kremling, K., Buckler IV, E.S. 2019. Quantitative genetic analysis of the maize leaf microbiome. Phytobiomes Journal. 2(4):208-224. https://doi.org/10.1094/PBIOMES-02-18-0008-R.Genome-wide association and genomic prediction models of tocochromanols in fresh sweet corn kernels
                                                        

- (Review Article)Baseggio, M., Murray, M., Magallanes-Lundback, M., Kaczmar, N., Chamness, J., Buckler IV, E.S., Smith, M.E., Dellapenna, D., Tracy, W.F., Gore, M.A. 2018. Genome-wide association and genomic prediction models of tocochromanols in fresh sweet corn kernels. The Plant Genome. 12:180038. https://doi.org/10.3835/plantgenome2018.06.0038.RNA polymerase mapping in plants identifies enhancers enriched in causal variants

- (Review Article)Lozano, R., Booth, G.T., Omar, B.Y., Li, B., Buckler IV, E.S., Lis, J.T., Jannink, J., Pino Del Carpio, D. 2018. RNA polymerase mapping in plants identifies enhancers enriched in causal variants. bioRxiv. https://doi.org/10.1101/376640.Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy
                                                        

- (Review Article)Gault, C., Kremling, K., Buckler IV, E.S. 2018. Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy. The Plant Genome. https://doi.org/10.1101/267682.Leveraging mutational burden for complex trait prediction in sorghum
                                                        

- (Review Article)Valluru, R., Gazave, E.E., Fernandes, S.B., Ferguson, J.N., Lozano, R., Hirannaiah, P., Zuo, T., Brown, P.J., Leakey, A.D., Gore, M., Buckler IV, E.S., Bandillo, N. 2018. Leveraging mutational burden for complex trait prediction in sorghum. bioRxiv. https://doi.org/10.1101/357418.Maize genomes to fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets
                                                        

- (Peer Reviewed Journal)Alkhalifah, N., Campbell, D., Falcon, C., Miller, N., Romay, M., Walls, R., Walton, R., Yeh, C., Bohn, M., Buckler IV, E.S., Ciampitti, I., Flint Garcia, S.A., Gore, M., Graham, C., Hirsch, C., Holland, J.B., Hooker, D., Kaeppler, S., Knoll, J.E., Lauter, N.C., Lee, E., Lorenz, A., Lynch, J., Moose, S., Murray, S., Nelson, R., Rocheford, T., Rodriguez, O., Schnable, J., Scully, B.T., Smith, M., Springer, N., Thomison, P., Tuinstra, M., Wisser, R., Xu, W., Ertl, D., Schnable, P., De Leon, N., Spalding, E., Edwards, J.W., Lawrence-Dill, C. 2018. Maize genomes to fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets. Biomed Central (BMC) Plant Biology. 11:452. https://doi.org/10.1186/s13104-018-3508-1.Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes
                                                        

- (Peer Reviewed Journal)Sun, S., Zhou, Y., Chen, J., Shi, J., Zhao, H., Zhao, H., Song, W., Zhang, M., Cui, Y., Dong, X., Liu, H., Ma, X., Yinping, J., Bo, W., Wei, X., Stein, J., Glaubitz, J., Lu, F., Yu, G., Liang, C., Fengler, K., Li, B., Rafalski, A., Schnable, P., Ware, D., Buckler IV, E.S., 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.Large-scale replicated field study of maize rhizosphere identifies heritable microbes

- (Peer Reviewed Journal)Walters, W.A., Jin, Z., Youngblut, N., Wallace, J.G., Sutter, J., Zhang, W., González-Peña, A., Peiffer, J., Koren, O., Shi, Q., Knight, R., Glavina Del Rio, T., Tringe, S.G., Buckler IV, E.S., Dangl, J.L., Ley, R.E. 2018. Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Proceedings of the National Academy of Sciences. 115(28):7368-7373.Increased experimental conditions and marker densities identified more genetic loci associated with southern and northern leaf blight resistance in maize
                                                        

- (Peer Reviewed Journal)Li, Y., Chen, L., Bradbury, P., Shi, Y., Song, Y., Zhang, D., Zhang, Z., Buckler IV, E.S., 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. Nature Scientific Reports. (8):6848. https://doi.org/10.1038/s41598-018-25304-z.The maize W22 genome provides a foundation for functional genomics and transposon biology
                                                        

- (Peer Reviewed Journal)Springer, N., Anderson, S., Andorf, C.M., Ahern, K., Bai, F., Barad, O., Barbazuk, W., Bass, H.W., Baruch, K., Gen-Zvi, G., Buckler IV, E.S., Bukowski, R., Campbell, M.S., Cannon, E.K., Chomet, P., Dawe, R., Davenport, R., Dooner, H.K., He Du, L., Du, C., Easterling, K., Gault, C., Guan, J., Jander, G., Hunter III, C.T., Jiao, Y., Koch, K.E., Kol, G., Kudo, T., Li, Q., Lu, F., Mayfield-Jones, D., Mei, W., McCarty, D.R., Noshay, J., Portwood II, J.L., Ronen, G., Settles, M.A., Shem-Tov, D., Shi, J., Soifer, I., Stein, J.C., Suzuki, M., Vera, D.L., Vollbrecht, E., Vrebalov, J.T., Ware, D., Wei, X., Wimalanathan, K., Woodhouse, M.R., Xiong, W., Brutnell, T.P. 2018. The maize W22 genome provides a foundation for functional genomics and transposon biology. Nature Genetics. 50:1282-1288. https://doi.org/10.1038/s41588-018-0158-0.Construction of the third generation Zea mays haplotype map

- (Peer Reviewed Journal)Bukowski, R., Guo, X., Lu, Y., Zou, C., He, B., Rong, Z., Yang, B., Wang, B., Xu, D., Xie, C., Fan, L., Gao, S., Xy, X., Zhang, G., Li, Y., Jiao, Y., Doebley, J., Ross-Ibarra, J., Buffalo, V., Romay, C., Buckler IV, E.S., Wu, Y., Lai, J., Ware, D., Sun, Q. 2018. Construction of the third generation Zea mays haplotype map. Gigascience. 7(4):1-12.Expanding the BLUP alphabet for genomic prediction adaptable to the genetic architectures of complex traits
                                                        

- (Peer Reviewed Journal)Wang, J., Zhou, Z., Li, H., Liu, D., Zhang, Q., Bradbury, P., Buckler IV, E.S., Zhang, Z. 2018. Expanding the BLUP alphabet for genomic prediction adaptable to the genetic architectures of complex traits. Heredity. https://doi.org/10.1038/s41437-018-0075-0.Dysregulation of expression correlates with rare allele burden and fitness loss in maize
                                                        

- (Peer Reviewed Journal)Kremling, K., Chen, S., Su, M., Jannink, J., Romay, M., Swarts, K., Lu, F., Lorant, A., Bradbury, P., Buckler IV, E.S. 2018. Dysregulation of expression correlates with rare allele burden and fitness loss in maize. Nature. 555:520-523. https://doi.org/10.1038/nature25966.Diverse chromosomal locations of quantitative trait loci for tolerance to maize chlorotic mottle in five maize populations
                                                        

- (Peer Reviewed Journal)Jones, M.W., Penning, B., Jamann, T.M., Glaubitz, J.C., Romay, C., Buckler IV, E.S., Redinbaugh, M.G. 2017. Diverse chromosomal locations of quantitative trait loci for tolerance to maize chlorotic mottle in five maize populations. Phytopathology. 108(6):748-758. https://doi.org/10.1094/PHYTO-09-17-0321-R.Genomic features shaping the landscape of meiotic double-strand break hotspots in maize

- (Peer Reviewed Journal)He, Y., Wang, M., Dukowic-Schulze, S., Zhou, A., Tiang, C., Shilo, S., Sidh Sidhu, G., Eichten, S., Bradbury, P., Springer, N., Buckler IV, E.S., Levy, A., Sun, Q., Pillardy, J., Kianian, P., Kianian, S., Chen, C., Pawlowski, W. 2017. Genomic features shaping the landscape of meiotic double-strand break hotspots in maize. Proceedings of the National Academy of Sciences. 114(46):12231-12236.Novel loci underlie natural variation in vitamin E levels in maize grain
                                                        

- (Peer Reviewed Journal)Diepenbrock, C., Kandianis, C., Lipka, A., Magallanes-Lundback, M., Vaillancourt, B., Gongora-Castillo, E., Wallace, J., Cepela, J., Mesberg, A., Bradbury, P., Ilut, D., Mateos-Hernandez, M., Hamilton, J., Owens, B., Tiede, T., Buckler IV, E.S., Rocheford, T., Buell, R., Gore, M., Dellapenna, D. 2017. Novel loci underlie natural variation in vitamin E levels in maize grain. The Plant Cell. 29(10):2374-2392. DOI: https://doi.org/10.1105/tpc.17.00475The effect of artificial selection on phenotypic plasticity in maize
                                                        

- (Peer Reviewed Journal)Gage, J., Jarquin, D., Romay, M., Lorenz, A., Buckler IV, E.S., Kaeppler, S., Alkhalifah, N., Bohn, M., Campbell, D., Edwards, J.W., Ertl, D., Flint Garcia, S.A., Gardiner, J., Good, B., Hirsch, C., Holland, J.B., Hooker, D., Knoll, J.E., Kolkman, J., Kruger, G., Lauter, N.C., Lawrence-Dill, C., Lee, E., Lynch, J., Murray, S., Nelson, R., Petzoldt, J., Rocheford, T., Schnable, J., Schnable, P., Scully, B.T., Smith, M., Springer, N., Srinivasan, S., Walton, R., Weldekidan, T., Wisser, R., Xu, W., Yu, J., De Leon, N. 2017. The effect of artificial selection on phenotypic plasticity in maize. Nature Communications. 8:1348. https://doi.org/10.1038/S41467-017-01450-2.Genetic analysis of lodging in diverse maize hybrids
                                                        

- (Review Article)Larsson, S.J., Peiffer, J.A., Edwards, J.W., Ersoz, E.S., Flint Garcia, S.A., Holland, J.B., Mcmullen, M.D., Tuinstra, M.R., Romay, M.C., Buckler Iv, E.S. 2017. Genetic analysis of lodging in diverse maize hybrids. bioRxiv. https://doi.org/10.1101/185769.Non-mendelian single-nucleotide polymorphism inheritance and atypical meiotic configurations are prevalent in hop
                                                        

- (Peer Reviewed Journal)Zhang, D., Easterling, K., Pitra, N., Coles, M., Buckler IV, E.S., Bass, H., Matthews, P. 2017. Non-mendelian single-nucleotide polymorphism inheritance and atypical meiotic configurations are prevalent in hop. The Plant Genome. 10(3). https://doi.org/10.3835/plantgenome2017.04.0032.Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize
                                                        

- (Peer Reviewed Journal)Yang, J., Mezmouk, S., Baumgarten, A., Buckler IV, E.S., Guill, K.E., McMullen, M., Mumm, R., Ross-Ibarra, J. 2017. Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize. PLoS Genetics. https://doi.org/10.1371/journal.pgen.1007019.Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

- (Peer Reviewed Journal)Varshney, R., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., Srivastava, R., Chitikineni, A., Fan, G., Bajaj, P., Punnuri, S., Gupta, S., Wang, H., Jiang, Y., Couderc, M., Katta, M., Paudel, D., Mungra, K., Chen, W., Harris-Shultz, K.R., Garg, V., Desai, N., Doddamani, D., Kane, N., Conner, J., Ghatak, A., Chaturvedi, P., Subramaniam, S., Yadav, O., Berthouly-Salazar, C., Hamidou, F., Wang, J., Liang, X., Clotault, J., Upadhyaya, H., Cubry, P., Rhoné, B., Gueye, M., Sunkar, R., Dupuy, C., Sparvoli, F., Cheng, S., Mahala, R., Singh, B., Yadav, R., Lyons, E., Datta, S., Hash, C., Devos, K., Buckler IV, E.S., Bennetzen, J., Paterson, A.H., Ozias-Akins, P., Grando, S., Wang, J., Mohapatra, T., Weckwerth, W., Reif, J.C., Liu, X., Vigouroux, Y., Xu, X. 2017. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nature Communications. 35(10):969.Maize YABBY Genes drooping leaf1 and drooping leaf2 regulate plant architecture

- (Peer Reviewed Journal)Strable, J., Wallace, J., Briggs, S., Unger-Wallace, E., Bradbury, P., Buckler IV, E.S., Volbrecht, E. 2017. Maize YABBY genes drooping leaf1 and drooping leaf2 affect agronomic traits by regulating leaf architecture. The Plant Cell. doi: 10.1105/tpc.16.00477.Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America

- (Peer Reviewed Journal)Swartz, K., Gutaker, R.M., Benz, B., Blake, M., Bukowski, R., Holland, J.B., Kruse-Peeples, M., Lepak, N.K., Prim, L., Romay, M.C., Ross-Ibarra, J., Sanchez-Gonzalez, J., Schmidt, C., Schuenemann, V.J., Krause, J., Matson, R.G., Weigel, D., Buckler IV, E.S., Burbano, H.A. 2017. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science. 357:512-515.Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments
                                                        

- (Peer Reviewed Journal)Shi, C., Thudi, M., Mariac, C., Wallace, J., Zhang, H., Ghatak, A., Chaturvedi, P., Zhao, Y., Wang, X., Rathore, A., Wang, J., Srivastava, R., Chitikineni, A., Fan, G., Punnuri, S., Gupta, S., Jiang, Y., Couderc, M., Bajaj, P., Katta, M., Paudel, D., Mungra, K., Chen, W., Harris-Shultz, K.R., Garg, V., Desai, N., Doddamani, D., Kane, N., Conner, J., Subramaniam, S., Yadav, O., Berthouly-Salazar, C., Hamidu, F., Liang, X., Clotault, J., Gueye, M., Sunkar, R., Dupuy, C., Sparvoli, F., Cheng, S., Mahala, R., Singh, B., Yadav, R., Lyons, E., Datta, S., Hash, C., Devos, K., Buckler Iv, E.S., Bennetzen, J., Paterson, A., Ozias-Akins, P., Grando, S., Wang, J., Reif, J., Weckwerth, W., Liu, X., Vigouroux, Y., Xu, X. 2017. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nature Biotechnology. 35:969-976. https://doi.org/10.1038/nbt.3943.Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize

- (Other)Patterns of genomic and phenomic diversity in wine and table grapes
                                                        

- (Peer Reviewed Journal)Migicovsky, Z., Sawler, J., Gardner, K., Aradhya, M.K., Prins, B.H., Schwaninger, H.R., Bustamente, C., Buckler, E.S., Zhong, G., Brown, P., Myles, S. 2017. Patterns of genomic and phenomic diversity in wine and table grapes. Horticulture Research. 4:17035. doi: 10.1038/hortres.2017.35.Rapid cycling genomic selection in a multiparental tropical maize population

- (Peer Reviewed Journal)Zhang, X., Perez-Rodriguez, P., Burgueno, J., Olsen, M., Buckler IV, E.S., Atlin, G., Prasanna, B., Vargas, M., San Vincente, F., Crossa, J. 2017. Rapid cycling genomic selection in a multiparental tropical maize population. Genes, Genomes, and Genomics. 7(7):2315-2326.Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

- (Peer Reviewed Journal)Ramu, P., Esuma, W., Kawuki, R., Rabbi, I., Egesi, C., Bredeson, J., Bart, R., Verma, J., Buckler IV, E.S., Lu, F. 2017. Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation. Nature Genetics. 49:959-963.A study of allelic diversity underlying flowering-time adaptation in maize landraces

- (Peer Reviewed Journal)Romero-Navarro, A., Wilcox, M., Burgueno, J., Romay, M., Swarts, K., Trachsel, S., Preciado, E., Terron, A., Delgado, H.O., Vidal, V., Ortega, A., Ortiz-Monasterio, I., San Vicente, F., Atlin, G., Wenzl, P., Hearne, S., Buckler IV, E.S. 2017. A study of allelic diversity underlying flowering-time adaptation in maize landraces. Nature Genetics. 46:476-480.A large scale joint analysis of flowering time reveals independent temperate adaptations in maize

- (Other)Swarts, K., Bauer, E., Glaubitz, J., Ho, T., Johnson, L., Li, Y., Li, Y., Miller, Z., Romay, M., Schoen, C., Wang, T., Zhang, Z., Buckler IV, E.S., Bradbury, P. 2016. A large scale joint analysis of flowering time reveals independent temperate adaptations in maize. bioRxiv. https://doi.org/10.1101/086082.Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

- (Peer Reviewed Journal)Hirsch, C., Hirsch, C., Brohammer, A., Bowman, M., Soifer, I., Barad, O., Shem-Tov, D., Baruch, K., Lu, F., Hernandez, A., Fields, C., Wright, C., Koehler, K., Springer, N., Buckler IV, E.S., Buell, R., De Leon, N., Kaeppler, S., Childs, K., Mikel, M. 2016. Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize. The Plant Cell. 28(11):2700-2714.Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations

- (Peer Reviewed Journal)Li, C., Sun, B., Li, Y., Liu, C., Wu, X., Zhang, D., Shi, Y., Song, Y., Buckler IV, E.S., Zhang, Z., Wang, T., Li, Y. 2016. Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations. Biomed Central (BMC) Genomics. 17:894.Characterization of biosynthetic pathways for the production of the volatile homoterpenes DMNT and TMTT in Zea mays

- (Peer Reviewed Journal)Richter, A., Schaff, C., Zhang, Z., Lipka, A., Tian, F., Kollner, T., Schnee, C., Preib, S., Irmisch, S., Jander, G., Boland, W., Gershenzon, J., Buckler IV, E.S., Degenhardt, J. 2016. Characterization of biosynthetic pathways for the production of the volatile homoterpenes DMNT and TMTT in Zea mays. The Plant Cell. 28:2651-2665.Genome-wide association mapping of provitamin A carotenoid content in cassava

- (Peer Reviewed Journal)Esuma, W., Herselman, L., Labuschagne, M., Ramu, P., Lu, F., Baguma, Y., Buckler IV, E.S., Kawuki, R. 2016. Genome-wide association mapping of provitamin A carotenoid content in cassava. Euphytica. DOI: 10.1007/s10681-016-1772-5.Non-mendelian inheritance of SNP markers reveals extensive chromosomal translocations in dioecious hops (humulus lupulus L.)

- (Other)Zhang, D., Pitra, N., Coles, M., Buckler IV, E.S., Matthews, P. 2016. Non-mendelian inheritance of SNP markers reveals extensive chromosomal translocations in dioecious hops (humulus lupulus L.). bioRxiv. Available: http://dx.doi.org/10.1101/069849.Fast-flowering mini-maize: seed to seed in 60 days

- (Peer Reviewed Journal)Mccaw, M.E., Wallace, J.G., Albert, P.S., Buckler IV, E.S., Birchler, J.A. 2016. Fast-flowering mini-maize: seed to seed in 60 days. Genetics. 204:35.Correlation-based network analysis of metabolite and enzyme profiles reveals a role of citrate biosynthesis in modulating N and C metabolism in zea mays

- (Peer Reviewed Journal)Toubiana, D., Xue, W., Zhang, N., Kremling, K., Gur, A., Pilosof, S., Gibon, Y., Sitt, M., Buckler IV, E.S., Fernie, A., 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.Biosynthesis of 8-O-methylated benzoxazinoid defense compounds in maize

- (Peer Reviewed Journal)Handrick, V., Robert, C., Ahem, K., Zhou, S., Machado, R., Maag, D., Glauser, G., Fernandez-Penny, F., Chandran, J., Rodgers-Melnick, E., Schneider, B., Buckler IV, E.S., Boland, W., Gershenzon, J., Jander, G., Erb, M., Kollner, T. 2016. Biosynthesis of 8-O-methylated benzoxazinoid defense compounds in maize. The Plant Cell. 28(7):1682-1700.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

- (Peer Reviewed Journal)Wallace, J., Zhang, X., Beyene, Y., Semagn, K., Olsen, M., Prasanna, B., Buckler IV, E.S. 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. 56:2365.Analysis of recombination QTLs, segregation distortion, and epistasis for fitness in maize multiple populations using ultra-high-density markers

- (Peer Reviewed Journal)Li, C., Li, Y., Shi, Y., Song, Y., Zhang, D., Buckler IV, E.S., Zhang, Z., Li, Y., 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. 129(9):1775-1784.Open chromatin reveals the functional maize genome

- (Peer Reviewed Journal)Rodgers-Melnick, E., Vera, D.L., Kellogg, E.A., Bass, H.W., Buckler IV, E.S. 2016. Open chromatin reveals the functional maize genome. Proceedings of the National Academy of Sciences. 113(22):E3177-E3184.Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population

- (Peer Reviewed Journal)Li, Y., Li, C., Bradbury, P., Liu, X., Romay, C., Glaubitz, J., Wu, X., Peng, B., Shi, Y., Song, Y., Zhang, D., Buckler IV, E.S., Zhang, Z., Li, Y., Wang, T. 2016. Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population. Plant Journal. 86(5):391-402.A proposal regarding best practices for validating the identity of genetic stocks and the effects of genetic variants

- (Other)Bergelson, J., Buckler IV, E.S., Ecler, J., 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.Development of high-density linkage map and tagging leaf spot resistance in pearl millet using genotyping-by-sequencing markers

- (Peer Reviewed Journal)Punnuri, S.M., Wallace, J.G., Knoll, J.E., Hyma, K.E., Mitchell, S.E., Buckler IV, E.S., Varshney, R.K., Singh, B.P. 2016. Development of high-density linkage map and tagging leaf spot resistance in pearl millet using genotyping-by-sequencing markers. The Plant Genome. 9(2):1-13. doi: 10.3835/plantgenome2015.10.0106.Development of a high-density linkage map and tagging leaf spot resistance in pearl millet uysing genotyping-by-sequencing markers

- (Peer Reviewed Journal)Punnuri, S.M., Wallace, J.G., Knoll, J.E., Hyma, K.E., Mitchell, S.E., Buckler IV, E.S., Varshney, R.K., Singh, B.P. 2016. Development of a high-density linkage map and tagging leaf spot resistance in pearl millet uysing genotyping-by-sequencing markers. The Plant Genome. 9(2):1-13.Sequence, assembly and annotation of the maize W22 genome

- (Abstract Only)Andorf, C.M., Ahem, K., Bai, F., Barad, O., Barbazuk, B.W., Bass, H.W., Baruch, K., Ben-Zvi, G., Buckler Iv, E.S., Bukowski, R., Davenport, R., Dooner, H.K., He Du, L., Du, C., Easterling, K.A., Gault, C.M., Guan, J., Jander, G., Jiao, Y., Koch, K., Kol, G., Kudo, T., Li, Q., Lu, F., Mayfield-Jones, D., Mei, W., McCarty, D., Portwood II, J.L., Ronen, G., Settles, M.A., Shem-Tov, D., Soifer, I., Springer, N.M., Suzuki, M., Vera, D., Vollbrecht, E., Vrebalov, J.T., Ware, D., Wimalanathan, K., Xiong, W., Brutnell, T. 2016. Sequence, assembly and annotation of the maize W22 genome. In: 58th Annual Maize Genetics Conference, March 17-20, 2016, Jacksonville, Florida. p. 91.GAPIT version 2: an enhanced integrated tool for genomic association and prediction

- (Peer Reviewed Journal)Tang, Y., Liu, X., Wang, J., Li, M., Wang, Q., Tian, F., Su, Z., Pan, Y., Liu, D., Lipka, A., Buckler IV, E.S., Zhang, Z. 2016. GAPIT version 2: an enhanced integrated tool for genomic association and prediction. The Plant Genome. 7(7):2315-2326.Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies

- (Peer Reviewed Journal)Liu, X., Huang, M., Fan, B., Buckler IV, E.S., Zhang, Z. 2016. Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies. PLoS Genetics. 12(3):e1005957.Joint-linkage mapping and GWAS reveal extensive genetic loci that regulate male inflorescence size in maize

- (Peer Reviewed Journal)Wu, X., Li, Y., Shi, Y., Song, Y., Zhang, D., Li, C., Buckler IV, E.S., 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.Genome-wide associations with flowering time in switchgrass

- (Abstract Only)Grabowski, P.P., Buckler IV, E.S., Casler, M.D. 2016. Genome-wide associations with flowering time in switchgrass [abstract]. Plant and Animal Genome XXIV. Paper No. P0001.Expanding maize genetic resources with predomestication alleles: maize-teosinte introgression populations
                                                        

- (Peer Reviewed Journal)Liu, Z., Cook, J., Melia-Hancock, S., Guill, K.E., Bottoms, C., Garcia, A., Ott, O., Nelson, R., Recker, J., Balint-Kurti, P.J., Larsson, S., Lepak, N.K., Buckler, E.S., Trimble, L., Tracy, W., McMullen, M.D., Flint-Garcia, S.A. 2016. Expanding maize genetic resources with predomestication alleles: maize-teosinte introgression populations. The Plant Genome. 9(1). doi:10.3835/plantgenome2015.07.0053.Expanding maize genetic resources with predomestication alleles: Maize–teosinte introgression populations

- (Peer Reviewed Journal)Liu, Z., Cook, J., Melia-Hancock, S., Guill, K.E., Bottoms, C., Garcia, A., Ott, O., Nelson, R., Reckerd, J., Balint Kurti, P.J., Larsson, S., Lepak, N.K., Buckler IV, E.S., Trimble, L., Tracy, W., McMullen, M.D., Flint Garcia, S.A. 2016. Expanding maize genetic resources with predomestication alleles: Maize–teosinte introgression populations. The Plant Genome. (9):1.Construction of high-quality recombination maps with low-coverage genomic sequencing for joint linkage analysis in maize

- (Peer Reviewed Journal)Li, C., Li, Y., Bradbury, P., Wu, X., Shi, Y., Song, Y., Zhang, D., Rodgers-Melnick, E., Buckler IV, E.S., Zhang, Z., Li, Y., Wang, T. 2015. Construction of high-quality recombination maps with low-coverage genomic sequencing for joint linkage analysis in maize. Biomed Central (BMC) Plant Biology. 13:78.Population genetics and structure of a global foxtail millet germplasm collection

- (Peer Reviewed Journal)Upadhyaya, H.D., Vetriventhan, M., Deshpande, S.P., Sivasubramani, S., Wallace, J.G., Buckler IV, E.S., Hash, T.C., Ramu, P. 2015. Population genetics and structure of a global foxtail millet germplasm collection. The Plant Genome. DOI: 10.385/plantgenome2015.07.0054.Independent molecular basis of convergent highland adaptation in maize

- (Peer Reviewed Journal)Takuno, S., Ralph, P., Swarts, K.L., Elshire, R.J., Glaubitz, J.C., Buckler IV, E.S., Hufford, M.B., Ross-Ibarra, J. 2015. Independent molecular basis of convergent highland adaptation in maize. Genetics. 200(4):1297.Genome-environment associations in sorghum landraces predict adaptive traits

- (Peer Reviewed Journal)Lasky, J.R., Upadhyaya, H.D., Ramu, P., Deshpande, S., Hash, T.C., Bonnette, J., Juenger, T., Hyma, K., Acharya, C., Mitchell, S.E., Buckler IV, E.S., Brenton, Z., Kresovich, S., Morris, G.P. 2015. Genome-environment associations in sorghum landraces predict adaptive traits. Life Science Advances. 1(6):e1400218.Genome-wide association study of carbon and nitrogen metabolism in the maize nested association mapping population

- (Peer Reviewed Journal)Zhang, N., Gibon, Y., Lepak, N.K., Pinghua, L., Dedow, L., Chen, C., So, Y., Brutnell, T., Sitt, M., Buckler Iv, E.S., Wallace, J.G., Kremling, K., Bradbury, P. 2015. Genome-wide association study of carbon and nitrogen metabolism in the maize nested association mapping population. Plant Physiology. doi: 10.1104/pp.15.0025.High-resolution genetic mapping of maize pan-genome sequence anchors
                                                        

- (Peer Reviewed Journal)Lu, F., Romay, M.C., Glaubitz, J.C., Bradbury, P., Elshire, R.J., Wang, T., Li, Y., Li, Y., Semagn, K., Zhang, X., Hernandez, A.G., Mikel, M.A., Soifer, I., Barad, O., Buckler IV, E.S. 2015. High-resolution genetic mapping of maize pan-genome sequence anchors. Nature Communications. 6:694.Genome-wide association analysis based on multiple imputation with low-depth GBS data: application to biofuel traits in reed canarygrass
                                                        

- (Peer Reviewed Journal)Ramstein, G., Lu, F., Lipka, A., Costich, D., Cherney, J., Casler, M.D., Buckler IV, E.S. 2015. Genome-wide association analysis based on multiple imputation with low-depth GBS data: application to biofuel traits in reed canarygrass. G3, Genes/Genomes/Genetics. 5(5):891-909.Genetic mapping in grapevine using a SNP microarray: intensity values

- (Peer Reviewed Journal)Myles, S., Brooks, S., Harriman, J.V., Reisch, B., Ramming, D.W., Owens, C.L., Li, L., Buckler Iv, E.S., Cadle Davidson, L.E. 2015. Genetic mapping in grapevine using a SNP microarray: intensity values. Molecular Breeding. 35:88.Recombination in maize is stable, predictable, and associated with genetic load: a joint study of the US and Chinese maize NAM populations
                                                        

- (Peer Reviewed Journal)Rodgers-Melnick, E., Bradbury, P., Elshire, R.J., Glaubitz, J.C., Archarya, C.B., Mitchell, S.E., Li, C., Li, Y., Buckler IV, E.S. 2015. Recombination in maize is stable, predictable, and associated with genetic load: a joint study of the US and Chinese maize NAM populations. Proceedings of the National Academy of Sciences. 112(12):3823.The genetic makeup of a global barnyard millet germplasm collection

- (Peer Reviewed Journal)Wallace, J.G., Upadhyaya, H.D., Vetriventhan, M., Buckler IV, E.S., Hash, T.C., Ramu, P. 2015. The genetic makeup of a global barnyard millet germplasm collection. The Plant Genome. 8(1):1-39.Genome-wide association study of Fusarium ear rot disease in the U.S.A. maize inbred line collection

- (Peer Reviewed Journal)Zila, C., Ogut, F., Romay, M.C., Gardner, C.A., Buckler IV, E.S., Holland, J.B. 2014. Genome-wide association study of Fusarium ear rot disease in the U.S.A. maize inbred line collection. Biomed Central (BMC) Plant Biology. 14:372.VitisGen on the road: mapping the way to the next generation of grapes
                                                        

- (Abstract Only)Yang, S., Fresnedo, J., Takacs, E., Barba, P., Hyma, K., Lillis, J.A., Acharya, C., Fisher, A., Cote, L., Manns, D., Ryona, I., Gadoury, D., Seem, B., Sacks, G., Mansfield, A., Ledbetter, C.A., Luby, J., Hemstad, P., Fennell, A., Hwang, C., Walker, A., Riaz, S., Cousins, P., Londo, J.P., Buckler Iv, E.S., Mitchell, S., Schweitzer, P., Sun, Q., Cadle Davidson, L.E., Reisch, B. 2015. VitisGen on the road: mapping the way to the next generation of grapes. Annual International Plant & Animal Genome Conference. P0873: 15597.Association mapping across numerous traits reveals patterns of functional variation in maize

- (Peer Reviewed Journal)Wallace, J., Bradbury, P., Zhang, N., Gibon, Y., Stitt, M., Buckler IV, E.S. 2014. Association mapping across numerous traits reveals patterns of functional variation in maize. PLoS Genetics. 10(2). doi: 10.1371/journal.pgen.1004845.Accelerating the switchgrass (Panicum virgatum L.) breeding cycle using genomic selection approaches
                                                        

- (Peer Reviewed Journal)Lipka, A.E., Lu, F., Cherney, J.H., Buckler IV, E.S., Casler, M.D., Costich, D.E. 2014. Accelerating the switchgrass (panicum virgatum L.) breeding cycle using genomic selection approaches. PLoS One. 9(11):e112227.Genomic prediction in bi-parental tropical maize populations in water-stressed and well-watered environments using low density and GBS SNPs
                                                        

- (Peer Reviewed Journal)Zhang, X., Perez-Rodriquez, P., Kassa, S., Beyene, Y., Babu, R., Lopez Cruz, M., San Vicente, F., Olsen, M., Buckler IV, E.S., Jannink, J., Prasanna, B.M., Crossa, J. 2014. Genomic prediction in bi-parental tropical maize populations in water-stressed and well-watered environments using low density and GBS SNPs. Heredity. 114:291-299.Enrichment of statistical power for genome-wide association studies

- (Peer Reviewed Journal)Li, M., Liu, X., Bradbury, P., Yu, J., Zhang, Y., Todhunter, R., Buckler IV, E.S., Zhang, Z. 2014. Enrichment of statistical power for genome-wide association studies. Biomed Central (BMC) Plant Biology. 12:73.A super powerful method for genome wide association study

- (Peer Reviewed Journal)Wang, Q., Tian, F., Pan, Y., Buckler IV, E.S., Zhang, Z. 2014. A super powerful method for genome wide association study. PLoS One. 9(9):e107684.Novel methods to optimize genotypic imputation for low-coverage, next-generation sequence data in crop plants

- (Peer Reviewed Journal)Swarts, K., Li, H., Navarro, J., An, D., Romay, M., Hearne, S., Acharya, C., Glaubitz, J.C., Mitchell, S., Elshire, R.J., Buckler Iv, E.S., Bradbury, P. 2014. Novel methods to optimize genotypic imputation for low-coverage, next-generation sequence data in crop plants. The Plant Genome. 7(3). DOI: 10.3835/plantgenome2014.05.0023.Insights into the effects of long-term artificial selection on seed size in maize
                                                        

- (Peer Reviewed Journal)Hirsch, C.N., Flint Garcia, S.A., Beissinger, T.M., Eichten, S.R., Deshpande, S., Barry, K., Mcmullen, M.D., Holland, J.B., Buckler IV, E.S., Springer, N., Buell, R.C., de Leon, N., Kaeppler, S.M. 2014. Insights into the effects of long-term artificial selection on seed size in maize. Genetics. 198(1):409-421.The genetic architecture of maize height
                                                        

- (Peer Reviewed Journal)Peiffer, J.A., Romay, M.C., Gore, M.A., Flint Garcia, S.A., Zhang, Z., Millard, M.J., Gardner, C.A., McMullen, M.D., Holland, J.B., Bradbury, P., Buckler IV, E.S. 2014. The genetic architecture of maize height. Genetics. 196:1337-1356.TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline

- (Peer Reviewed Journal)Glaubitz, J.C., Casstevens, T.M., Lu, F., Harriman, J., Elshire, R.J., Sun, Q., Buckler Iv, E.S. 2014. TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One. 9(2):e90346.A modern ampelography: A genetic basis for leaf shape and venation patterning in grape
                                                        

- (Peer Reviewed Journal)Chitwood, D.H., Ranjan, A., Martinez, C.C., Headland, L.R., Thiem, T., Kumar, R., Covington, M.F., Hatcher, T, Naylor, D.T., Zimmerman, S., Downs, N., Raymundo, N., Buckler IV, E.S., Maloof, J.N., Aradhya, M.K., Prins, B.H., Li, L., Myles, S., Sinha, N.R. 2013. A modern ampelography: A genetic basis for leaf shape and venation patterning in grape. Plant Physiology. 164(1):259-272.Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls
                                                        

- (Peer Reviewed Journal)Miller, A., Matasci, N., Schwaninger, H.R., Aradhya, M.K., Prins, B.H., Zhong, G., Simon, C., Buckler IV, E.S., Myles, S. 2013. Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls. PLoS One. doi: 10.1371/journal.pone.0078680.Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits

- (Peer Reviewed Journal)Morris, G.P., Rhodes, D.H., Brenton, Z., Ramu, P., Thayil, V.L., Deshpande, S., Hash, T.C., Acharya, C., Mitchell, S.E., Buckler IV, E.S., Yu, J., Kresovich, S. 2013. Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits. Genes, Genomes, Genetics. 3(11):2085-2094.Genomic prediction in maize breeding populations with genotyping-by-sequencing

- (Peer Reviewed Journal)Crossa, J., Beyene, Y., Segman, K., Perez, P., Hickey, J.M., Chen, C., De Los Campos, G., Burgueno, J., Windhausen, V.S., Buckler IV, E.S., Jannink, J., Lopez Crua, M.A., Babu, R. 2013. Genomic prediction in maize breeding populations with genotyping-by-sequencing. Genes, Genomes, Genetics. DOI: 10.1534/g3.113.008227.Mining conifers’ mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform

- (Peer Reviewed Journal)Charles, C., Mitchell, S., Elshire, R.J., Buckler IV, E.S., El-Kassaby, Y.A. 2013. Mining conifers’ mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform. Tree Genetics and Genomes. 9(6):1537-1544.Natural variation in maize aphid resistance is associated with 2,4-Dihydroxy-7-Methoxy-1,4-Benzoxazin-3-One Glucoside Methyltransferase activity

- (Peer Reviewed Journal)Meihls, L.N., Handrick, V., Glauser, G., Barbier, H., Kaur, H., Haribal, M.M., Lipka, A.E., Gershenzon, J., Buckler IV, E.S., Erb, M., Kollner, T.G., 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.Comprehensive genotyping of the USA national maize inbred seed bank

- (Peer Reviewed Journal)Romay, M.C., Millard, M.J., Glaubitz, J.C., Peiffer, J.A., Swarts, K.L., Casstevens, T.M., Elshire, R.J., Acharya, C.B., Mitchell, S.E., Flint Garcia, S.A., McMullen, M.D., Holland, J.B., Buckler IV, E.S., Gardner, C.A. 2013. Comprehensive genotyping of the US national maize inbred seed bank. Genome Biology. 14(6):1-18.Genome-wide association study and pathway level analysis of tocochromanol levels in maize grain

- (Peer Reviewed Journal)Lipka, A.E., Gore, M., Magallanes-Lundback, M., Mesberg, A., Lin, H., Tiede, T., Chen, C., Buell, R.C., Buckler IV, E.S., Rocheford, T., Dellapenna, D. 2013. Genome-wide association study and pathway level analysis of tocochromanol levels in maize grain. Genes, Genomes, Genetics. DOI: 10.1534/g3.113.006148.The genetic architecture of maize stalk strength
                                                        

- (Peer Reviewed Journal)Peiffer, J.A., Flint Garcia, S.A., De Leon, N.N., McMullen, M.D., Kaeppler, S.M., Buckler IV, E.S. 2013. The genetic architecture of maize stalk strength. PLoS One. 8(6):e67066. Available: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067066#pone-0067066-g005.Diversity and heritability of the maize rhizosphere microbiome under field conditions

- (Peer Reviewed Journal)Peiffer, J.A., Spor, A., Koren, O., Jin, Z., Tringe, S., Dangl, J.L., Buckler IV, E.S., Ley, R.E. 2013. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proceedings of the National Academy of Sciences. 110(16):6548-6553.Aluminum tolerance is associated with higher MATE1 gene copy-number in maize
                                                        

- (Peer Reviewed Journal)Maron, L., Guimareas, C., Matias, K., Albert, P.S., Birchler, J.A., Bradbury, P., Buckler IV, E.S., Coluccio, A.E., Danilova, T.V., Kudrna, D., Magalhaes, J.V., Pineros, M., Schatz, M.C., Wing, R., Kochian, L.V. 2013. Aluminum tolerance is associated with higher MATE1 gene copy-number in maize. Proceedings of the National Academy of Sciences. 110(13):5241-5246.Compare Identity By Sequence Relationships of the Ames Diversity Panel using TYPSimSelector [abstract]
                                                        

- (Abstract Only)Mauch, E., Andorf, C.M., Millard, M.J., Romay, C., Buckler Iv, E.S., Gardner, C.A., Lawrence, C.J. 2013. Compare Identity By Sequence Relationships of the Ames Diversity Panel using TYPSimSelector [abstract]. In: Maize Genetics Conference, St. Charles, IL.  Mar. 14-17, 2013. p. 55.Entering the second century of maize quantitative genetics

- (Review Article)Wallace, J.G., Larsson, S.J., Buckler IV, E.S. 2013. Entering the second century of maize quantitative genetics. Heredity. DOI: 10.1038/hdy.2013.6.Lessons from dwarf8 on the strengths and weaknesses of structured association mapping
                                                        

- (Peer Reviewed Journal)Larson, S., Lipka, A.E., Buckler IV, E.S. 2013. Lessons from dwarf8 on the strengths and weaknesses of structured association mapping. PLoS Genetics. 9(2):e1003246.Population genomic and genome-wide association studies of agroclamatic traits in sorghum
                                                        

- (Peer Reviewed Journal)Morris, G.P., Ramu, P., Deshpande, S.P., Hash, T.C., Shah, T., Upadhyaya, H.D., Riera-Lizarazu, O., Brown, P., Acharya, C.B., Mitchell, S.E., Harriman, J., Glaubitz, J.C., Buckler IV, E.S., Kresovich, S. 2013. Population genomic and genome-wide association studies of agroclamatic traits in sorghum. Proceedings of the National Academy of Sciences. 110(2):453-458.Can genomics boost productivity of orphan crops?
                                                        

- (Other)Varshney, R.K., Ribaut, J., Buckler IV, E.S., Tuberosa, R., Rafalski, A.J., Langridge, P. 2012. Can genomics boost productivity of orphan crops?. Nature Biotechnology. 30:1172-1176.Switchgrass genomic diversity, ploidy and evolution: novel insights from a network-based SNP discovery protocol

- (Peer Reviewed Journal)Lu, F., Lipka, A.E., Glaubitz, J.C., Elshire, R., Cherney, J.H., Casler, M.D., Buckler IV, E.S., Costich, D. 2013. Switchgrass genomic diversity, ploidy and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genetics. 9(1):e1003215. DOI:10.1371/journal.pgen.1003215.PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants

- (Peer Reviewed Journal)Charles, C., Declerck, G., Tian, F., Spooner, W., Mccouch, S., Buckler IV, E.S. 2012. PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants. PLoS One. 7(11): e46596.Genetic analysis of visually scored orange kernel color in maize

- (Peer Reviewed Journal)Chandler, K., Lipka, A.E., Owens, B.F., Li, H., Buckler IV, E.S., Rocheford, T., Gore, M.A. 2012. Genetic analysis of visually scored orange kernel color in maize. Crop Science. 53:189-200.SNP discovery with EST and NextGen sequencing in switchgrass (panicum virgatum L.)

- (Peer Reviewed Journal)Ersoz, E.S., Wright, M.H., Pangilinan, J.L., Sheehan, M.J., Tobias, C.M., Casler, M.D., Buckler IV, E.S., Costich, D. 2012. SNP discovery with EST and NextGen sequencing in switchgrass (panicum virgatum L.). PLoS One. 7(9):e44112.GAPIT: genome association and prediction integrated tool

- (Peer Reviewed Journal)Lipka, A.E., Feng, T., Wang, Q., Peiffer, J., Li, M., Bradbury, P., Gore, M.A., Buckler IV, E.S., Zhang, Z. 2012. GAPIT: genome association and prediction integrated tool. Bioinformatics. 28(18):2397-2399.Using High-Throughput Genotyping Information for Management of a Large Maize Collection

- (Abstract Only)Gardner, C.A., Romay-Alvarez, M.C., Millard, M.J., Flint Garcia, S.A., Holland, J.B., Buckler Iv, E.S. 2012. Using High-Throughput Genotyping Information for Management of a Large Maize Collection. Agronomy Society of America, Crop Science Society of America, Soil Science Society of America Meeting. Abstract 375-3.ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize

- (Peer Reviewed Journal)Hung, H., Shannon, L.M., Tian, F., Bradbury, P., Chen, C., Flint Garcia, S.A., McMullen, M.D., Ware, D., Buckler IV, E.S., Doebley, J.F., Holland, J.B. 2012. ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize. Proceedings of the National Academy of Sciences. 109:E1913–E1921.Genic and non-genic contributions to natural variation of quantitative traits in maize

- (Peer Reviewed Journal)Li, X., Zhu, C., Yeh, C., Wu, W., Takacs, E.M., Petsch, K.A., Tian, F., Bai, G., Buckler Iv, E.S., Muehlbauer, G.J., Timmermans, M., Scanlon, M.J., Schnable, P.S., Yu, J. 2012. Genic and non-genic contributions to natural variation of quantitative traits in maize. Genome Research. 22:2436-2444.Maize HapMap2 identifies extant variation from a genome in flux

- (Peer Reviewed Journal)Chia, J., Song, C., Bradbury, P., Costich, D., De Leon, N., Doebley, J., Elshire, R., Gaut, B., Geller, L., Glaubitz, J., Gore, M.A., Guill, K., Holland, J., Hufford, M., Lai, J., Li, M., Liu, X., Lu, Y., McCombie, R., Nelson, R., Poland, J.A., Prasanna, B., Phyajarvi, T., Rong, T., Sekhon, R., Sun, Q., Tenaillon, M., Tian, F., Wang, J., Xu, X., Zhang, Z., Kaeppler, S.M., Ross-Ibarra, J., McMullen, M.D., Buckler IV, E.S., Zhang, G., Xu, Y., Ware, D. 2012. Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics. 40:803-807. DOI: 10.1038/ng.2313.Comparative population genomics of maize domestication and improvement

- (Peer Reviewed Journal)Hufford, M., Xu, X., Van Heerwaarden, J., Pyhajarvi, T., Chia, J., Cartwright, R., Elshire, R., Glaubitz, J., Guill, K.E., Kaeppler, S., Lai, J., Morrell, P., Shannon, L., Song, C., Springer, N., Swanson-Wagner, R., Tiffin, P., Wang, J., Zhang, G., Doebley, J., McMullen, M.D., Ware, D., Buckler IV, E.S., Yang, S., Ross-Ibarra, J. 2012. Comparative population genomics of maize domestication and improvement. Nature Genetics. 44:808-811. DOI: 10.1038/ng.2309.Construction of genomic library of Theobroma cacao using genotyping by sequencing (GBS)

- (Abstract Only)Takrama, J., Kuhn, D.N., Gutierrez, O.A., Schnell, R.J., Fulton, T., Elshire, R.J., Buckler Iv, E.S., Mitchell, S.E. 2012. Construction of genomic library of Theobroma cacao using genotyping by sequencing (GBS). Meeting Abstract. Available: https://pag.confex.com/pag/xx/webprogram/Paper2082.html.Crop genomics: advances and applications

- (Review Article)Morrell, P.L., Buckler IV, E.S., Ross-Ibarra, J. 2011. Crop genomics: advances and applications. Nature Reviews Genetics. 13:85-96.Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels

- (Peer Reviewed Journal)Cook, J.P., McMullen, M.D., Holland, J.B., Tian, F., Bradbury, P., Ross-Ibarra, J., Buckler IV, E.S., Flint-Garcia, S.A. 2012. Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels. Plant Physiology. 158:824-834.A large maize (Zea Mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome

- (Peer Reviewed Journal)Ganal, M.W., Durstewitz, G., Polley, A., Berard, A., Buckler IV, E.S., Charcosset, A., Clarke, J.D., Graner, E., Mcmullen, M.D., 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. DOI: 10.1371/journal.pone.0028334.Distinct genetic architectures for male and female inflorescence traits of maize

- (Peer Reviewed Journal)Brown, P.J., Upadyayula, N., Mahone, G.S., Tian, F., Bradbury, P., Myles, S., Holland, J.B., Flint Garcia, S.A., McMullen, M.D., Buckler IV, E.S., Rocheford, T.R. 2011. Distinct genetic architectures for male and female inflorescence traits of maize. PLoS Genetics. 7(11):e1002383.The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population

- (Peer Reviewed Journal)Hung, H., Browne, C.J., Guill, K.E., Coles, N., Eller, M., Garcia, A., Lepak, N.K., Melia-Hancock, S., Oropeza-Rosas, M., Salvo, S., Upadyayula, N., Buckler IV, E.S., Flint Garcia, S.A., Mcmullen, M.D., Rocheford, T., Holland, J.B. 2012. The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population. Heredity. 108:490-499.A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species

- (Peer Reviewed Journal)Elshire, R.J., Glaubitz, J.C., Sun, Q., Poland, J.A., Kawamoto, K., Buckler IV, E.S., Mitchell, S.E. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 123:307-326.Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize

- (Peer Reviewed Journal)Poland, J.A., Bradbury, P., Buckler IV, E.S., Nelson, R. 2011. Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proceedings of the National Academy of Sciences. 108:6893-6898.Population genetics of genomics-based crop improvement methods

- (Review Article)Hamblin, M., Buckler Iv, E.S., Jannink, J. 2011. Population genetics of genomics-based crop improvement methods. Trends in Genetics. 27:98-106.Joint QTL linkage mapping for multiple-cross mating design sharing one common parent

- (Peer Reviewed Journal)Li, H., Bradbury, P., Buckler IV, E.S., Ersoz, E., Wang, J. 2011. Joint QTL linkage mapping for multiple-cross mating design sharing one common parent. PLoS One. 6:e17573.Genome-wide association study of maize identifies genes affecting leaf architecture

- (Peer Reviewed Journal)Tian, F., Bradbury, P., Brown, P., Sun, Q., Flint Garcia, S.A., Rocheford, T.R., McMullen, M.D., Holland, J.B., Buckler IV, E.S. 2011. Genome-wide association study of maize identifies genes affecting leaf architecture. Nature Genetics. 43:159-162.Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population

- (Peer Reviewed Journal)Kump, K., Bradbury, P., Buckler IV, E.S., Belcher, A., Oropeza-Rosas, M., Wisser, R., Zwonitzer, J., Kresovich, S., McMullen, M.D., Ware, D., Balint Kurti, P.J., Holland, J.B. 2011. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nature Genetics. 43:163-168.Genetic structure and domestication history of the grape

- (Peer Reviewed Journal)Myles, S., Boyko, A., Owens, C.L., Brown, P., Fabrizio, G., Aradhya, M.K., Prins, B.H., Reynolds, A., Chia, J., Ware, D., Bustamante, C., Buckler IV, E.S. 2011. Genetic structure and domestication history of the grape. Proceedings of the National Academy of Sciences. 10.1073/pnas.1009363108.Fine quantitative trait loci mapping of carbon and nitrogen metabolism enzyme activities and seedling biomass in the intermated maize IBM mapping population

- (Peer Reviewed Journal)Zhang, N., Gibon, Y., Gur, A., Chen, C., Lepak, N.K., Hohne, M., Zhang, Z., Kroon, D., Tschoep, H., Sitt, M., Buckler IV, E.S. 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.Response-Additional Implications of Perennial Bioenergy Crops: Hydrology and Climate

- (Research Notes)Glover, J.D., Reganold, J.P., Bell, L.W., Borevitz, J., Brummer, E.C., Buckler Iv, E.S., Cox, C.M., Cox, T.S., Crews, T.E., Culman, S.W., Dehann, L.R., Eriksson, D., Gill, B.S., Holland, J.B., Hu, F., Hulke, B.S., Ibrahim, A., Jackson, W., Jones, S.S., Murray, S.C., Paterson, A.H., Ploschuk, E., Sacks, E.J., Snapp, S., Tao, D., Van Tassel, D.L., Wade, L.J., Wyse, D.L., Xu, Y. 2010. Perennial questions of hydrology and climate - response. Science. 330:33-34.Genome-wide and fine resolution association studies of 14 agronomic traits in rice land races

- (Peer Reviewed Journal)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., Zhang, L., Buckler IV, E.S., Qian, Q., Zhang, Q., Li, J., Han, B. 2010. Genome-wide and fine resolution association studies of 14 agronomic traits in rice land races. Nature Genetics. 42:961-967.Genetic Association Mapping Identifies Single Nucleotide Polymorphisms in Genes that Affect Abscisic Acid Levels in Maize Floral Tissues During Drought

- (Peer Reviewed Journal)Setter, T.L., Yan, J., Warburton, M.L., Ribaut, J., Xu, Y., Sawkins, M., Buckler, E.S., Zhang, Z., Gore, M.A. 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. 62:701-716. doi:10.1093/jxb/erq308.Genome-size variation in switchgrass (Panicum virgatum):  flow cytometry and cytology reveal rampant aneuploidy

- (Peer Reviewed Journal)Costich, D., Friebe, B., Sheehan, M.J., Casler, M.D., Buckler IV, E.S. 2010. Genome-size variation in switchgrass (Panicum virgatum): flow cytometry and cytology reveal rampant aneuploidy. The Plant Genome. 3:130-141.Increasing food and ecosystem security through perennial grains

- (Peer Reviewed Journal)Glover, J.D., Reganold, J.P., Bell, L.W., Borevitz, J., Brummer, E.C., Buckler Iv, E.S., Cox, C.M., Cox, T., Crews, T.E., Culman, S.W., Dehann, L.R., Eriksson, D., Gill, B., Holland, J.B., Hu, F.Y., Hulke, B.S., Ibrahim, A., Jackson, W., Jones, S., Murray, S., Paterson, A.H., Ploschuk, E., Sacks, E.J., Snapp, S., Tao, D.Y., Van Tassel, D., Wade, L., Wyse, D., Xu, Y. 2010. Increasing food and ecosystem security through perennial grains. Science. 328:1638-1639.Association and linkage analysis of aluminum tolerance genes in maize

- (Peer Reviewed Journal)Krill, A.M., Kirst, M., Kochian, L.V., Buckler Iv, E.S., Hoekenga, O. 2010. Association and linkage analysis of aluminum tolerance genes in maize. PLoS One. 5(4):e9958. DOI: 10.1371/journal.pone.0009958.Rare Genetic Variation at Zea mays crtRB1 Increases B-Carotene in Maize Grain

- (Peer Reviewed Journal)Yan, J., Kandianis, C.B., Haries, C.E., Bai, L., Kim, E., Yang, X., Skinner, D., Fu, Z., Mitchell, S., Li, Q., Fernandez, M., Zaharieva, M., Babu, R., Fu, Y., Palacios, N., Li, J., DellaPenna, D., Brutnell, T., Buckler, E.S., Warburton, M.L., Rocheford, T. 2010. Rare Genetic Variation at Zea mays crtRB1 Increases B-carotene in Maize Grain. Nature Genetics. 42:322-329.Mixed linear model approach adapted for genome-wide association studies

- (Peer Reviewed Journal)Zhang, Z., Ersoz, E., Lai, C., Todhunter, R., Tiwari, H.K., Gore, M.A., Bradbury, P., Yu, J., Arnett, D., Ordovas, J.M., Buckler IV, E.S. 2010. Mixed linear model approach adapted for genome-wide association studies. Nature Genetics. 42:355-360.Genetic analysis of central carbon metabolism unveils an amino acid substitution that alters maize NAD-dependent isocitrate dehydrogenase activity

- (Peer Reviewed Journal)Zhang, N., Gur, A., Gibbon, Y., Sulpice, R., Flint Garcia, S.A., Mcmullen, M.D., Stitt, M., Buckler IV, E.S. 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.DNA Markers and Sequences Reveal Geographic Races of Reed Canarygrass (Phalaris arundinacea)

- (Abstract Only)Jakubowski, A., Casler, M.D., Denton, M., Costich, D., Buckler Iv, E.S., Phillips, M., Jackson, R., Krohn, A. 2010. DNA Markers and Sequences Reveal Geographic Races of Reed Canarygrass (Phalaris arundinacea) [abstract]. Proceedings of the 6th International Symposium on the Molecular Breeding of Forage and Turf, March 15-19, 2010, Buenos Aires, Argentina. Abstract P-44: p.98.Rapid genomic characterization of the genus Vitis

- (Peer Reviewed Journal)Myles, S., Chia, J., Hurwitz, B., Simon, C.J., Zhong, G., Buckler IV, E.S., Ware, D. 2010. Rapid genomic characterization of the genus Vitis. PLoS One. 5(1):e8219.Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers

- (Peer Reviewed Journal)Yan, J., Shah, T., Warburton, M.L., Buckler IV, E.S., McMullen, M.D., Crouch, J. 2009. Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers. PLoS One. 4:1-14.A first generation haplotype map of maize

- (Peer Reviewed Journal)Gore, M.A., Chia, J., Elshire, R.J., Sun, Q., Ersoz, E.S., Hurwitz, B.L., Peiffer, J.A., Mcmullen, M.D., Grills, G.S., Ross-Ibarra, J., Ware, D., Buckler Iv, E.S. 2009. A first generation haplotype map of maize. Science. 326(5956):1115-1117.Software engineering the mixed model for genome-wide association studies on large samples

- (Peer Reviewed Journal)Zhang, Z., Buckler IV, E.S., Casstevens, T., Bradbury, P. 2009. Software engineering the mixed model for genome-wide association studies on large samples. Briefings in Bioinformatics. 10(6):664-675.Heterosis is Prevalent for Multiple Traits in Diverse Maize Germplasm

- (Peer Reviewed Journal)Flint Garcia, S.A., Buckler IV, E.S., Tiffin, P., Ersoz, E., Springer, N.M. 2009. Heterosis is Prevalent for Multiple Traits in Diverse Maize Germplasm. PLoS One. 4:e7433.Joint linkage association analysis of aluminum tolerance in maize

- (Proceedings)Hoekenga, O., Buckler Iv, E.S., Kirst, M., Krill, A., Lyi, S., Magalhaes, J., Maron, L., Kochian, L.V. 2009. Joint linkage association analysis of aluminum tolerance in maize. Symposium Proceedings. Proceedings of the 7th International Symposium on Plant-Soil Interaction at Low pH, October 5-10, 2009, Guangzhou, China. p. 136-137.Association mapping: critical considerations shift from genotyping to experimental design

- (Peer Reviewed Journal)Buckler IV, E.S., Myles, S., Peiffer, J., Brown, P., Ersoz, E., Zhang, Z., Costich, D. 2009. Association mapping: critical considerations shift from genotyping to experimental design. The Plant Cell. 10.1105/tpc.109.068437.Genetic Properties of the Maize Nested Association Mapping Population

- (Peer Reviewed Journal)Mcmullen, M.D., Kresovich, S., Sanchez-Villeda, H., Bradbury, P., Li, H., Sun, Q., Flint Garcia, S.A., Thornsberry, J., Acharya, C., Bottoms, C., Brown, P., Browne, C.J., Eller, M.S., Guill, K.E., Harjes, C., Kroon, D., Lepak, N.K., Mitchell, S., Peterson, B.E., Pressoir, G., Romero, S.M., Oropeza Rosas, M., Salvo, S.A., Yates, H., Hanson, M., Jones, E., Smith, S., Glaubitz, J., Goodman, M., Ware, D., Holland, J.B., Buckler Iv, E.S. 2009. Genetic Properties of the Maize Nested Association Mapping Population. Science. 325:737-740.The Genetic Architecture of Maize Flowering Time

- (Peer Reviewed Journal)Buckler Iv, E.S., Holland, J.B., Mcmullen, M.D., Kresovich, S., Acharya, C., Bradbury, P., Brown, P., Browne, C.J., Eller, M.S., Ersoz, E., Flint Garcia, S.A., Garcia, A., Glaubitz, J.C., Goodman, M., Haries, C., Guill, K.E., Kroon, D., Larsson, S., Lepak, N.K., Li, H., Mitchell, S.E., Pressoir, G., Peiffer, J., Oropeza Rosas, M., Rocheford, T., Romay, C., Romero, S., Salvo, S.A., Sanchez Villeda, H., Sun, Q., Tian, F., Upadyayula, N., Ware, D., Yates, H., Yu, J., Zhang, Z. 2009. The Genetic Architecture of Maize Flowering Time. Science. 325(5941):714-718.Status and Prospects of Association Mapping in Plants

- (Review Article)Buckler Iv, E.S., Gore, M., Zhu, C., Yu, J. 2009. Status and Prospects of Association Mapping in Plants. The Plant Genome. 1(1):5-20.Tracking footprints of maize domestication and evidence for a massive selective sweep on chromosome 10

- (Peer Reviewed Journal)Buckler IV, E.S., Tian, F., Stevens, N.M. 2009. Tracking footprints of maize domestication and evidence for a massive selective sweep on chromosome 10. Proceedings of the National Academy of Sciences. 106:9979-9986Applications of Linkage Disequilibrium and Association Mapping in Maize

- (Book / Chapter)Buckler Iv, E.S., Ersoz, E.S., Jianming, Y. 2009. Applications of Linkage Disequilibrium and Association Mapping in Maize. In: A.L. Kriz, B.A. Larkins, editors. Molecular Genetic Approaches to Maize Improvement, New York, NY: Springer-Verlag Berlin Heidelberg. p. 173.Discovery and mapping of single feature polymorphisms in wheat using affymetrix arrays

- (Peer Reviewed Journal)Bernardo, A.N., Bradbury, P., Ma, H., Hu, S., Bowden, R.L., Buckler Iv, E.S., Bai, G. 2009. Discovery and mapping of single feature polymorphisms in wheat using affymetrix arrays. Biomed Central (BMC) Genomics. 10:251.Large-scale enrichment and discovery of gene-associated SNPs

- (Peer Reviewed Journal)Buckler Iv, E.S., Gore, M., Wright, M., Ersoz, E., Bouffard, P., Jarvie, T., Hurwitz, B., Narechania, A., Harkins, T., Grills, G., Ware, D. 2009. Large-scale enrichment and discovery of gene-associated SNPs. The Plant Genome. 2:121-133.Simulation appraisal of the adequacy of numbers of background markers for relationship estimation in association mapping

- (Peer Reviewed Journal)Buckler Iv, E.S., Yu, J., Zhang, Z., Tabanao, D.A., Gail, P., Kresovich, S., Todhunter, R.J. 2009. Simulation appraisal of the adequacy of numbers of background markers for relationship estimation in association mapping. The Plant Genome. 2:63-77.Natural variation in maize architecture is mediated by allelic differences at the PINOID co-ortholog barren inflorescence2

- (Peer Reviewed Journal)Pressoir, G., Brown, P.J., Zhu, W., Upadyayula, N., Rocheford, T., Buckler IV, E.S., Kresovich, S. 2009. Natural variation in maize architecture is mediated by allelic differences at the PINOID co-ortholog barren inflorescence2. Plant Journal. 58:618-628.Panzea: An Update on New Content and Features

- (Peer Reviewed Journal)Canaran, P., Buckler Iv, E.S., Glaubitz, J., Stein, L., Sun, Q., Zhao, W., Ware, D. 2009. Panzea: An Update on New Content and Features. Nucleic Acids Research. 36:D1041-D1043.Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness

- (Peer Reviewed Journal)Buckler Iv, E.S., Hamblin, M.T., Warburton, M.L. 2008. Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness. PLoS One. 2(12):e1367.The Genetic Architecture of Complex Traits in Teosinte (Zea mays ssp. parviglumis): New Evidence from Association Mapping

- (Peer Reviewed Journal)Buckler Iv, E.S., Weber, A.L., Briggs, W.H., Rucker, J., Baltazar, B.M., Sanchez-Gonzalez, J.D., Feng, P., Doebley, J.F. 2008. The Genetic Architecture of Complex Traits in Teosinte (Zea mays ssp.parviglumis): New Evidence from Association Mapping. Genetics. 180(2):1221-1232.An Arabidopsis haplotype map takes root

- (Review Article)Buckler Iv, E.S., Gore, M. 2008. An Arabidopsis haplotype map takes root. Nature Genetics.39:1056-1057.Comparison of Mixed-Model Approaches for Association Mapping

- (Peer Reviewed Journal)Stich, B., Mohring, J., Piepho, H., Heckenberger, M., Buckler Iv, E.S., Melchinger, A.E. 2008. Comparison of Mixed-Model Approaches for Association Mapping. Genetics. 178(3):1748-1754.Natural genetic variation in the lycopene epsilon cyclase gene can enhance provitamin A biofortification of maize

- (Peer Reviewed Journal)Buckler Iv, E.S., Harjes, C., Rocheford, T., Bai, L., Brutnell, T., Kandianis, C.B., Sowinski, S.G., Stapleton, A.E., Vallabhaneni, R., Williams, M., Wurtzel, E., Jianbing, Y. 2008. Natural genetic variation in the lycopene epsilon cyclase gene can enhance provitamin A biofortification of maize. Science. 319(5861):330-333.GENOME-WIDE COMPLEX TRAIT DISSECTION THROUGH NESTED ASSOCIATION MAPPING

- (Peer Reviewed Journal)Buckler Iv, E.S., Yu, J., Holland, J.B., Mcmullen, M.D. 2008. Genome-wide complex trait dissection through nested association mapping. Genetics. 178:539-551.Genetic and biochemical analysis of iron bioavailability in maize

- (Abstract Only)Hoekenga, O., Mwaniki, A., Buckler Iv, E.S., Glahn, R.P., Kochian, L.V. 2007. Genetic and biochemical analysis of iron bioavailability in maize (abstract). Agronomy Society of America, Crop Science Society of America, Soil Science Society of America Meeting.  Session 176:4Genetic and biochemical analysis of iron bioavailability in maize

- (Abstract Only)Hoekenga, O., Mwankini, A., Buckler Iv, E.S., Glahn, R.P., Kochian, L.V. 2007. Genetic and biochemical analysis of iron bioavailability in maize. American Society of Agronomy Meetings.  Volume 52:102.Gramene: a growing plant comparative genomics resource

- (Peer Reviewed Journal)Jaiswal, P., Avraham, S., Buckler Iv, E.S., Casstevens, T., Hebbard, C., Liang, C., Ni, J., Ravenscroft, D., Ren, L., Stein, L., Spooner, W., Tecle, I., Thomason, J., Wei Xuehong, Ware, D., Youens-Clark, K., Yap, I., Mccouch, S., Tung, C. 2008. Gramene: a growing plant comparative genomics resource. Nucleic Acids Research. 36:D947-D953.Using Crossover Breakpoints in Recombinant Inbred Lines to Identify Quantitative Trait Loci Controlling the Global Recombination Frequency

- (Peer Reviewed Journal)Buckler Iv, E.S., Esch, E., Szymaniak, J., Yates, H., Wojciech, P. 2007. Using Crossover Breakpoints in Recombinant Inbred Lines to Identify Quantitative Trait Loci Controlling the Global Recombination Frequency. Genetics. 177:1851-1858.TASSEL: Software for Association Mapping of Complex Traits in Diverse Samples

- (Peer Reviewed Journal)Bradbury, P., Zhang, Z., Kroon, D., Casstevens, T., Ramdoss, Y., Buckler Iv, E.S. 2007. Tassel: software for association mapping of complex traits in diverse samples. Bioinformatics. 23:2633-2635.Gramene: a bird's eye view of cereal genomes

- (Peer Reviewed Journal)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, T., Buckler Iv, E.S., Stein, L., Mccouch, S. 2007. Gramene: a bird's eye view of cereal genomes. Nucleic Acids Research. 34:D717-D723. Available: http://nar.oxfordjournals.org/Evaluation of Target Preparation Methods for Single Feature Polymorphism Detection in Large Complex Plant Genomes

- (Peer Reviewed Journal)Gore, M., Bradbury, P., Hogers, R., Kirst, M., Verstege, E., Van Oeveren, J., Peleman, J., Buckler Iv, E.S., Van Eijk, M. 2007. Evaluation of Target Preparation Methods for Single Feature Polymorphism Detection in Large Complex Plant Genomes. Crop Science. 47:S135-S148.APPLICATIONS OF LINKAGE DISEQUILIBRIUM AND ASSOCIATION MAPPING IN CROP PLANTS

- (Review Article)Buckler Iv, E.S., Ersoz, E., Yu, J. 2007. Applications of linkage disequilibrium and association mapping in crop plants. Book Chapter. In: Genomics Assisted Crop Improvement Vol. 1: Genomics Approaches and Platforms,  R.K. Varshney and R. Ruberosa, editors. pp 97-119. Publisher: Springer, Dordrecht, The NetherlandsPanzea: A Database and Resource for Molecular and Functional Diversity in the Maize Genome

- (Peer Reviewed Journal)Zhao, W., Canaran, P., Jurkuta, R., Fulton, T., Glaubitz, J., Buckler Iv, E.S., Doebley, J., Gaut, B., Goodman, M., Holland, J.B., Kresovich, S., Mcmullen, M.D., Stein, L., Ware, D. 2007. Panzea: A Database and Resource for Molecular and Functional Diversity in the Maize Genome. Nucleic Acids Research. 34:D752-D757.POWER TO DETECT HIGHER-ORDER EPISTATIC INTERACTIONS IN A METABOLIC PATHWAY USING NESTED ASSOCIATION MAPPING AND DIALLEL ASSOCIATION MAPPING

- (Peer Reviewed Journal)Buckler Iv, E.S., Stich, B., Yu, J., Maurer, H.P., Melchinger, A.E., Utz, H. 2007. Power to detect higher-order epistatic interactions in a metabolic pathway using nested association mapping and diallel association mapping. Genetics. Vol. 176:563-570Joint linkage-association analysis of aluminum tolerance in maize

- (Abstract Only)Hoekenga, O., Buckler Iv, E.S., Maron, L., Magalhaes, J., Kirst, M., Krill, A., Lyi, M., Rose, J., Thannhauser, T.W., Kochian, L.V. 2007. Joint linkage-association analysis of aluminum tolerance in maize [abstract]. Plant and Animal Genome VX Conference Abstracts. p. 55.Technical note: Use of marker-based relationships with multiple-trait derivative-free restricted maximal likelihood

- (Peer Reviewed Journal)Zhang, Z., Todhunter, R.J., Buckler Iv, E.S., Van Vleck, L.D. 2007. Technical note: Use of marker-based relationships with multiple-trait derivative-free restricted maximal likelihood. Journal of Animal Science. 85:881-885.CONTRIBUTION OF GENETIC DIVERSITY TO TYPE I ERRORS IN SHORT-OLIGONUCLEOTIDE MICROARRAY ANALYSIS

- (Peer Reviewed Journal)Kirst, M., Caldo, R., Casati, P., Tanimoto, G., Walbot, V., Wise, R.P., Buckler Iv, E.S. 2006. Contribution of genetic diversity to type 1 errors in short-oligonucleotide microarray analysis. Plant Biotechnology Journal. 4:489-498.RECURRENT MUTATION AND GENOME EVOLUTION: EXAMPLE OF SUGARY1 AND THE ORIGIN OF SWEET MAIZE

- (Peer Reviewed Journal)Tracy, W.F., Whitt, S.R., Buckler Iv, E.S. 2006. Recurrent mutation and genome evolution: example of sugary1 and the origin of sweet maize. The Plant Genome. 1:1-6.GENETIC ASSOCIATION MAPPING AND GENOME ORGANIZATION OF MAIZE

- (Review Article)Yu, J., Buckler Iv, E.S. 2006. Genetic association mapping and genome organization of maize. Current Opinion in Biotechnology. 17:155-160.MOLECULAR AND FUNCTIONAL DIVERSITY OF MAIZE

- (Review Article)Buckler Iv, E.S., Gaut, B.S., Mcmullen, M.D. 2006. Molecular and functional diversity of maize. Current Opinion in Plant Biology. 9:172-176.INTERDISCIPLINARY ANALYSIS OF ALUMINUM TOLERANCE IN MAIZE

- (Abstract Only)Hoekenga, O., Buckler Iv, E.S., Maron, L., Magalhaes, J., Isaacson, T., Kirst, M., Krill, A., Lyi, S.M., Rose, J., Thannhauser, T.W., Kochian, L.V. 2006. Interdisciplinary analysis of aluminum tolerance in maize [abstract]. Plant and Animal Genome VX Conference Abstracts. p. 226.ARCHITECTURE OF FLORAL BRANCH SYSTEMS IN MAIZE AND RELATED GRASSES

- (Peer Reviewed Journal)Vollbrecht, E., Springer, P.S., Goh, L., Buckler Iv, E.S., Martienssen, R. 2005. Architecture of floral branch systems in maize and related grasses. Nature. 436:1119-1126.A UNIFIED MIXED-MODEL METHOD FOR ASSOCIATION MAPPING ACCOUNTING FOR MULTIPLE LEVELS OF RELATEDNESS

- (Peer Reviewed Journal)Yu, J., Pressoir, G., Briggs, W., Vroh, B., Yamasaki, M., Doebley, J.F., Mcmullen, M.D., Gaut, B.S., Holland, J.B., Kresovich, S., Buckler Iv, E.S. 2006. A unified mixed-model method for association mapping accounting for multiple levels of relatedness. Nature Genetics. 38:203-208.MAIZE ASSOCIATION POPULATION: A HIGH RESOLUTION PLATFORM FOR QUANTITATIVE TRAIT LOCUS DISSECTION

- (Peer Reviewed Journal)Flint Garcia, S.A., Thuillet, A., Yu, J., Pressoir, G., Romero, S.M., Mitchell, S.E., Doebley, J., Kresovich, S., Goodman, M.M., Buckler Iv, E.S. 2005. Maize association population: a high resolution platform for quantitative trait locus dissection. Plant Journal. 44:1054-1064.BRIDGING MOLECULAR DIVERSITY AND FUNCTIONAL DIVERSITY: COMPLEX TRAITS DISSECTION IN MAIZE

- (Abstract Only)Yu, J., Pressoir, G., Holland, J.B., Kresovich, S., Buckler Iv, E.S. 2005. Bridging molecular diversity and functional diversity: complex traits dissection in maize. Agronomy Abstracts.ASSOCIATION ANALYSIS OF CANDIDATE GENES FOR MAYSIN AND CHLOROGENIC ACID ACCUMULATION IN MAIZE SILKS

- (Peer Reviewed Journal)Szalma, S.J., Buckler Iv, E.S., Snook, M.E., Mcmullen, M.D. 2005. Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks. Journal of Theoretical and Applied Genetics. 110(7):1324-1333.GENETIC DIVERSITY AND POPULATION STRUCTURE OF TEOSINTE

- (Peer Reviewed Journal)Fukunaga, K., Hill, J., Vigouroux, Y., Matsuoka, Y., G, J.S., Liu, K., Buckler Iv, E.S., Doebley, J. 2005. Genetic diversity and population structure of teosinte. Genetics. 169:2241-2254.THE COLLABORATIVE CROSS, A COMMUNITY RESOURCE FOR THE GENETIC ANALYSIS OF COMPLEX TRAITS

- (Peer Reviewed Journal)Churchill, G.A., Airey, D.C., Allayee, H., Angel, J.M., Attie, A.D., Beatty, J., Beavis, W.D., Belknap, J.K., Bennett, B., Buckler Iv, E.S.,  2005. The collaborative cross, a community resource for the genetic analysis of complex traits. Nature Genetics. 36(11):1133-1137.MOLECULAR AND FUNCTIONAL DIVERSITY IN THE MAIZE GENOME

- (Abstract Only)Briggs, W., Buckler Iv, E.S., Canaran, P., Doebley, J., Fulton, T., Gaut, B., Goodman, M., Holland, J.B., Kresovich, S., Mcmullen, M.D., Stein, L., Ware, D., Wright, S., Zhao, W. 2005. Molecular and functional diversity in the maize genome [abstract]. Maize Genetics Conference. Paper No. 177. p. 126.SNP GENOTYPING FOR DIVERSITY AND MAPPING STUDIES IN MAIZE AND TEOSINTE

- (Abstract Only)Briggs, W., Vroh, B., Yamasaki, M., Pressoir, G., Mcmullen, M.D., Gaut, B., Kresovich, S., Buckler Iv, E.S., Doebley, J. 2005. Snp genotyping for diversity and mapping studies in maize and teosinte [abstract]. Maize Genetics Conference. Paper No. 182. p. 129.MOLECULAR AND FUNCTIONAL DIVERSITY IN THE MAIZE GENOME

- (Abstract Only)Doebley, J., Buckler Iv, E.S., Fulton, T., Gaut, B., Goodman, M., Holland, J.B., Kresovich, S., Mcmullen, M., Stein, L., Ware, D., Zhao, W. 2005. Molecular and functional diversity in the maize genome. Plant and Animal Genome XIII. [Abstracts].DISSECTION OF MAIZE KERNEL COMPOSITION AND STARCH PRODUCTION BY CANDIDATE GENE ASSOCIATION

- (Peer Reviewed Journal)Wilson, L.M., Whitt, S.R., Ibanez, A.M., Rocheford, T.R., Goodman, M.M., Buckler Iv, E.S. 2004. Dissection of maize kernel composition and starch production by candidate gene association. The Plant Cell. 16:2719-2733.PHYLOGEOGRAPHY OF THE WILD SUBSPECIES OF ZEA MAYS

- (Peer Reviewed Journal)Buckler Iv, E.S., Goodman, M.M., Holtsford, T.P., Doebley, J.F., G, J.S. 2006. Phylogeography of the wild subspecies of zea mays. Maydica. 51:123-134.GDPC: THE GENOMIC DIVERSITY AND PHENOTYPE CONNECTION

- (Peer Reviewed Journal)Casstevens, T.M., Buckler Iv, E.S. 2004. GDPC: The Genomic Diversity and Phenotype Connection.  Bioinformatics. 20:2839-2840.DARWIN'S HARVEST: NEW APPROACHES TO THE ORIGINS, EVOLUTION, AND CONSERVATION OF CROPS

- (Book / Chapter)Buckler Iv, E.S., Stevens, N.M. 2006. Darwin's harvest: new approaches to the origins, evolution, and conservation of crops. In: Motley, T.J., Zerega, N., Cross, H. (eds.) Maize Origins, Domestication, and Selection. New York: Columbia University Press. p. 67-90.GENETIC STRUCTURE AND DIVERSITY AMONG MAIZE INBRED LINES AS INFERRED FROM DNA MICROSATELLITES

- (Peer Reviewed Journal)Liu, K., Goodman, M., Muse, S., Smith, J.S., Buckler Iv, E.S., Doebley, J. 2003. Genetic structure and diversity among maize inbred lines as inferred from dna microsatellites. Genetics. 165:2117-2128.A BRIEF INTRODUCTION TO THE PHYLOGENETIC ANALYSIS LIBRARY, VERSION 1.5

- (Peer Reviewed Journal)Goode, M., Strimmer, K., Drummond, A., Buckler Iv, E.S., Rodrigo, A. 2004. A brief introduction to the phylogenetic analysis library, version 1.5. Conferences in Research and Practice in Information Technology. 29:175-179.EARLY ALLELIC SELECTION IN MAIZE AS REVEALED BY ANCIENT DNA

- (Peer Reviewed Journal)JAENICKE, V., BUCKLER IV, E.S., SMITH, B.D., GILBERT, T.P., COOPER, A., DOEBLEY, J., PAABO, S. EARLY ALLELIC SELECTION IN MAIZE AS REVEALED BY ANCIENT DNA. SCIENCE. 2003. v. 302. p. 1206-1208.STRUCTURE OF LINKAGE DISEQUILIBRIUM IN PLANTS

- (Review Article)FLINT-GARCIA, S.A., THORNSBERRY, J.M., BUCKLER IV, E.S. STRUCTURE OF LINKAGE DISEQUILIBRIUM IN PLANTS. ANNUAL REVIEWS OF PLANT BIOLOGY. 2003. v. 54. p. 357-374.DEVELOPMENT OF A MAIZE MOLECULAR EVOLUTIONARY GENOMIC DATABASE

- (Peer Reviewed Journal)DU, C., BUCKLER IV, E.S., MUSE, S. DEVELOPMENT OF A MAIZE MOLECULAR EVOLUTIONARY GENOMIC DATABASE. COMPARATIVE AND FUNCTIONAL GENOMICS. 2003. v. 4. p. 246-249.USING NATURAL ALLELIC DIVERSITY TO EVALUATE GENE FUNCTION.

- (Other)ASSOCIATIONS BETWEEN GLOSSY15 POLYMORPHISMS AND VARIATION IN JUVENILE LEAF NUMBER

- (Abstract Only)LIU, D., FROST, J., SZALMA, S., ANDALUZ, S., MUSKET, T., BUCKLER IV, E.S., MCMULLEN, M.D., DAVIS, G. ASSOCIATIONS BETWEEN GLOSSY15 POLYMORPHISMS AND VARIATION IN JUVENILE LEAF NUMBER. MAIZE GENETICS CONFERENCE. 2002. ABSTRACT. P. 118.MAIZE DOMESTICATION AND DIVERSIFICATION INFERRED FROM MICROSATELLITE DNA

- (Proceedings)PLANT MOLECULAR DIVERSITY AND APPLICATIONS TO GENOMICS

- (Peer Reviewed Journal)STRUCTURE OF LINKAGE DISEQUILIBRIUM AND PHENOTYPIC ASSOCIATIONS IN THE     MAIZE GENOME.

- (Peer Reviewed Journal)MOLECULAR DIVERSITY, STRUCTURE AND DOMESTICATION OF GRASSES

- (Peer Reviewed Journal)DWARF8 POLYMORPHISMS ASSOCIATE WITH VARIATION IN FLOWERING TIME.

- (Peer Reviewed Journal)QUANTITATIVE TRAIT LOCI ANALYSIS OF GROWTH RESPONSE TO VARYING NITROGEN    SOURCES IN ARABIDOPSIS THALIANA.

- (Peer Reviewed Journal)
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                                                The Goal: Finding--and Using--Key Grape Genes


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