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United States Department of Agriculture

Agricultural Research Service

Research Project: Development and Application of Genetic, Genomic, and Bioinformatic Resources in Maize

Location: Plant, Soil and Nutrition Research

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

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.
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 - (Review Article)
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.
Accelerating the switchgrass (Panicum virgatum L.) breeding cycle using genomic selection approaches     Reprint Icon - (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.
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.
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     Reprint Icon - (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.
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.
Population genomic and genome-wide association studies of agroclamatic traits in sorghum     Reprint Icon - (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.
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.
Last Modified: 7/23/2016
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