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United States Department of Agriculture

Agricultural Research Service

Research Project: DISSECTING COMPLEX TRAITS IN MAIZE AND BIOFUEL GRASSES BY APPLYING GENOMICS, BIOINFORMATICS, AND GENETIC RESOURCES

Location: Plant, Soil and Nutrition Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

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.
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.
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     Reprint Icon - (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.
Can genomics boost productivity of orphan crops?     Reprint Icon - (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.
SNP discovery with EST and NextGen sequencing in switchgrass (panicum virgatum L.)     Reprint Icon - (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     Reprint Icon - (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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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. 106:9979-9986
Applications 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.
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.
Last Modified: 7/28/2014
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