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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 » Peter Bradbury

Peter J Bradbury
Plant, Soil and Nutrition Research
Computational Biologist

Phone: (607) 255-5392
Fax:
Room 741

USDA-ARS-NAA
ROBERT W. HOLLEY CENTER - TOWER ROAD
ITHACA, NY 14853
Projects
Improving Crop Efficiency Using Genomic Diversity and Computational Modeling
In-House Appropriated (D)
  Accession Number: 434435
Database Tools for Managing and Analyzing Big Data Sets to Enhance Small Grains Breeding
In-House Appropriated (D)
  Accession Number: 434608
Improving Maize and Sorghum Efficiency Using Grass Diversity and Computational Modeling
Non-Assistance Cooperative Agreement (S)
  Accession Number: 438558
Profiling of Diverse Maize and Tripsacum to Identify Functional Variants
Non-Assistance Cooperative Agreement (S)
  Accession Number: 431405

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
A maize practical haplotype graph leverages diverse NAM assemblies Reprint Icon ()
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.
Maize introgression library provides evidence for the involvement of liguleless1 in resistance to northern leaf blight Reprint Icon - (Peer Reviewed Journal)
Kolkman, J.M., Strable, J., Harline, K., Kroon, D.E., Wiesner-Hanks, T., Bradbury, P., Nelson, R.J. 2020. Maize introgression library provides evidence for the involvement of liguleless1 in resistance to northern leaf blight. Genes, Genomes, Genetics. https://doi.org/10.1534/g3.120.401500.
Eleven biosynthetic genes explain the majority of natural variation for carotenoid levels in maize grain Reprint Icon ()
Diepenbrock, C.H., Llut, D.C., Magallanes-Lundback, M., Kandianis, C.B., Lipka, A.E., Bradbury, P., Holland, J.B., Hamilton, J.P., Wooldridge, E., Vaillancourt, B., Gongora-Castillo, E., Wallace, J.G., Capela, J., Mateos-Hernandez, M. 2020. Eleven biosynthetic genes explain the majority of natural variation for carotenoid levels in maize grain. bioRxiv. https://doi.org/10.1101/2020.07.15.203448.
Constrained non-coding sequence provides insights into regulatory elements and loss of gene expression in maize Reprint Icon ()
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.
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.
Dominance effects and functional enrichments improve prediction of agronomic traits in hybrid maize Reprint Icon - (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 strategy for building and using a human reference pangenome Reprint Icon ()
Llamas, B., Narzisi, G., Schneider, V., Audano, P.A., Biederstedt, E., Blauvelt, L., Bradbury, P., Chang, X., Chin, C., Fungtammasan, A., Clarke, W.E., Cleary, A., Ebler, J., Eizenga, J.M., Sibbesen, J.A., Markello, C.J., Garrison, E., Lazo, G.R., Lin, M.F., Mahmoud, M., Marschall, T., Minkin, L., Monlong, J., Musunuri, R.L., Sagayaradj, S., Novak, A.M., Rautiainen, M., Regier, A., Sedlazeck, F.J., Siren, J., Souilmi, Y., Souilmi, Y., Wrightsman, T., Yokoyama, T., Zeng, Q., Zook, J.M., Paten, B., Busby, B. 2019. A strategy for building and using a human reference pangenome. F1000Research. 8:1751. https://doi.org/10.12688/f1000research.19630.1.
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.
Increased experimental conditions and marker densities identified more genetic loci associated with southern and northern leaf blight resistance in maize Reprint Icon - (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.
Expanding the BLUP alphabet for genomic prediction adaptable to the genetic architectures of complex traits Reprint Icon - (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 Reprint Icon - (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.
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 Reprint Icon - (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.17.00475
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.
A large scale joint analysis of flowering time reveals independent temperate adaptations in maize ()
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.
Genetic architecture of domestication-related traits in maize - (Peer Reviewed Journal)
Xue, S., Bradbury, P., Casstevens, T., Holland, J.B. 2016. Genetic architecture of domestication-related traits in maize. Genetics. 204:99-113.
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.
The triticeae toolbox: combining phenotype and genotype data to advance small-grains breeding - (Peer Reviewed Journal)
Blake, V., Birkett, C.L., Matthews, D.E., Hane, D., Bradbury, P., Jannink, J. 2015. The triticeae toolbox: combining phenotype and genotype data to advance small-grains breeding. The Plant Genome. doi: 10.3835/PlantGenome2014.12.0099.
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.
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 Reprint Icon - (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.
From association to prediction: statistical methods for the dissection and selection of complex traits in plants ()
Lipka, A.E., Kandianis, C.E., Hudson, M.E., Yu, J., Drnevich, J., Bradbury, P., Gore, M. 2015. From association to prediction: statistical methods for the dissection and selection of complex traits in plants. Current Opinion in Plant Biology. 24:110-118.
Recombination in maize is stable, predictable, and associated with genetic load: a joint study of the US and Chinese maize NAM populations Reprint Icon - (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.
Joint-multiple family linkage analysis predicts within-family variation better than single-family analysis of the maize nested association mapping population - (Peer Reviewed Journal)
Ogut, F., Bradbury, P., Holland, J.B., Bian, Y. 2015. Joint-multiple family linkage analysis predicts within-family variation better than single-family analysis of the maize nested association mapping population. Heredity. 114(4):552-563.
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.
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.
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.
A genome-wide association study of the maize hypersensitive defense response identifies genes that cluster in related pathways - (Peer Reviewed Journal)
Olukolu, B., Wang, G., Vontimitta, V., Venkata, B.P., Marla, S., Ji, J., Gachomo, E., Chu, K., Negeri, A., Benson, J., Nelson, R., Bradbury, P., Nielsen, D., Holland, J.B., Balint Kurti, P.J., Johal, G. 2014. A genome-wide association study of the maize hypersensitive defense response identifies genes that cluster in related pathways. PLoS Genetics. 10(8): e1004562. doi: 10.1371/journal.pgen.1004562.
The genetic architecture of maize height Reprint Icon - (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.
Aluminum tolerance is associated with higher MATE1 gene copy-number in maize Reprint Icon - (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.
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.
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.
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.
Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels Reprint Icon - (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.
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.
Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize Reprint Icon - (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.
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.
Assessment of power and false discovery in genome-wide association studies using the BarleyCAP germplasm - (Peer Reviewed Journal)
Bradbury, P., Parker, T., Hamblin, M.T., Jannink, J. 2010. Assessment of power and false discovery in genome-wide association studies using the BarleyCAP germplasm. Crop Science. 51:52-59.
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.
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.
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.
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.
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.
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.
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