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United States Department of Agriculture

Agricultural Research Service

Related Topics

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.)

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.

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.

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.

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.

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 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.

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.

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: 2/23/2016
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