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United States Department of Agriculture

Agricultural Research Service

Related Topics

Peter J Bradbury
Plant, Soil and Nutrition Research
General Biological Science

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

USDA-ARS-NAA
ROBERT W. HOLLEY CENTER - TOWER ROAD
ITHACA , NY 14853

Projects
Enhancing Breeding of Small Grains through Improved Bioinformatics
In-House Appropriated (D)
  Accession Number: 424887
Development and Application of Genetic, Genomic, and Bioinformatic Resources in Maize
In-House Appropriated (D)
  Accession Number: 424894
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.)
Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population -
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 -
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 -
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 -
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 -
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 -
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 QTL analysis predicts within-family variation better than single family analysis of the maize nested association mapping population -
Ogut, F., Bradbury, P., Holland, J.B., Bian, Y. 2015. Joint multiple family QTL analysis predicts within-family variation better than single family analysis of the maize nested association mapping population. Heredity. 114:552-563.
Association mapping across numerous traits reveals patterns of functional variation in maize -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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.
ARS News Articles
Last Modified: 5/2/2016
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