Location: Corn Insects and Crop Genetics Research
2019 Annual Report
Accomplishments
1. Publication of the genome sequence for cowpea. Cowpea is a highly nutritious food, used both for its seed and leaves. It is relatively tolerant of drought and heat and is a vital food source in many countries; particularly in Sub-Saharan Africa, where cowpea originated. Cowpea is also valuable for its ability, shared with many legume crops, to fix atmospheric nitrogen into a form of fertilizer that is directly useable by plants, enabling cowpea to be grown on relatively nutrient-poor soils. ARS researchers in Ames, Iowa, through a collaboration with researchers at the University of California, Davis, reported the complete genome sequence and predicted genes for cowpea. This research identifies a large genomic change in a chromosomal region that is responsible for resistance to a parasitic plant (Striga or "witchweed") that is a serious problem in cowpea fields in Africa. The research also identifies a probable genetic factor that is responsible for the desirable traits of large seed and pod size in cowpea. This work will assist breeders and other scientists to more rapidly develop improved cowpea varieties, to benefit both small-holder farmers and consumers worldwide.
2. Publication of the genome sequence for peanut. Peanut is a major crop in the U.S. and in many countries around the world. It is particularly important as a subsistence crop in many developing countries, where its high protein and oil content and its edibility without cooking make it especially valuable. Working with a large international research consortium, including ARS collaborators in Stoneville, Mississippi, and Tifton, Georgia, ARS researchers in Ames, Iowa reported the complete genome sequence for a variety of peanut that is important in the U.S. The genome sequence consists of all of the DNA letters for all of the chromosomes. It provides a valuable road map for breeders and plant biologists. The genome sequence contains all the genes that control the characteristics of the plant. The sequence can also be used to identify genetic markers that plant breeders use to more efficiently target and improve traits of interest. Among the new findings from this research is an explanation for a unique way in which new variation arises to generate new peanut varieties: sequences exchange between sets of corresponding chromosomes. This mechanism is uncommon. It is seen in peanut because domesticated peanut contains two complete sets of chromosomes that are highly similar, but not identical. The similarity allows occasional pairings and exchanges between the similar chromosomes. The genome sequence of peanut will help breeders and other researchers improve this important crop and develop varieties with improved nutrition and better response to environmental stresses.
3. Publication of the genome sequence for wild soybean. Plant breeders and scientists work to identify what genes are responsible for important traits (yield, nutrition, etc.) and where these genes are located within the species of interest’s DNA. Sequencing a species’ genome, down to the level of individual DNA bases, helps researchers link genes with traits. The soybean genome sequence, developed from one variety, has been available for the last eight years and has enabled many discoveries about gene function. However, more rapid progress could be made if multiple genome sequences, for distinct soybean varieties, could be examined to see how DNA changes alter particular traits. The work reported by ARS researchers in Ames, Iowa, conducted as part of a collaboration with researchers at the Chinese University of Hong Kong, is the complete, high-resolution sequence of approximately one billion DNA bases for the closest wild relative of soybean (Glycine soja). This sequence will allow researchers to determine how changes during domestication occurred. For example, identifying genes that changed wild soybean from a vine with small, hard seeds, into domesticated soybean, a robust, short plant with larger, softer seeds. The genome sequence for wild soybean is also of use because it will help researchers more finely pinpoint regions responsible for valuable traits, and assist breeders to more efficiently move desirable genes into cultivated varieties, to benefit farmers and consumers worldwide.
Review Publications
Min, X., Yik-Lok, C., Man-Wah, L., Fuk-Ling, W., Xin, W., Ailin, L., Zhili, W., King-Yung, A., Tin-Hang, W., Suk-Wah, I., Zhixia, X., Kejing, F., Ming-Sin, N., Linfeng, Y., Tianquan, D., Lijuan, H., Lu, C., Aisi, F., Qiong, D., Junxian, H., Gyuhwa, C., Sachiko, I., Babu, V., Nguyen, H., Cannon, S.B., Foyer, C.H., Ting-Fung, C., Hon-Ming, L. 2019. A reference-grade wild soybean genome. Nature Communications. 10:1216. https://doi.org/10.1038/s41467-019-09142-9.
Stai, J.S., Yadav, A., Sinou, C., Bruneau, A., Doyle, J.J., Fernandez-Baca, D., Cannon, S.B. 2019. Cercis: A non-polyploid genomic relic within the generally polyploid legume family. Frontiers in Plant Science. 10:345. https://doi.org/10.3389/fpls.2019.00345.
Ren, L., Huang, W., Cannon, S.B. 2019. Reconstruction of ancestral genome reveals chromosome evolution history for selected legume species. New Phytologist. https://doi.org/10.1111/nph.15770.
Assefa, T., Rubyogo, J., Mahama, A.A., Brown, A.V., Cannon, E., Blair, M.W., Cannon, S.B. 2019. A review of breeding objectives, genomic resources, and marker-assisted methods in common bean (Phaseolus vulgaris L.). Molecular Breeding. 39:20. https://doi.org/10.1007/s11032-018-0920-0.
Bertioli, D.J., Jenkins, J., Clevenger, J., Dudchenko, O., Gao, D., Seijo, G., Leal-Bertioli, S., Ren, L., Farmer, A., Pandey, M., Samoluk, S.S., Abernathy, B., Agarwal, G., Ballen-Taborda, C., Cameron, C., Campbell, J., Chavarro, C., Chitikineni, A., Chu, Y., Dash, S., El Baidouri, M., Guo, B., Huang, W., Kim, K.D., Korani, W., Lanciano, S., Lui, C.G., Mirouze, M., Moretzsohn, M.C., Pham, M., Shin, J.H., Shirasawa, K., Sinharoy, S., Sreedasyam, A., Weeks, N.T., Zhang, X., Zheng, Z., Sun, Z., Froenicke, L., Aiden, E.L., Michelmore, R., Varshney, R.K., Holbrook Jr, C.C., Cannon, E.K., Scheffler, B.E., Grimwwood, J., Ozias-Akins, P., Cannon, S.B., Jackson, S.A., Schmutz, J. 2019. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nature Genetics. 51:877-884. https://doi.org/10.1038/s41588-019-0405-z.
Brown, A.V., Campbell, J.D., Assefa, T., Grant, D.M., Nelson, R., Weeks, N.T., Cannon, S.B. 2018. Ten quick tips for sharing open genomic data. PLoS Computational Biology. https://doi.org/10.1371/journal.pcbi.1006472.
Lonardi, S., Munoz-Amatriain, M., Liang, Q., Shu, S., Wanamaker, S., Lo, S., Tanskanen, J., Zhu, T., Schulman, A.H., Luo, M., Alhakami, H., Ounit, R., Abid, H., Verdier, J., Roberts, P.A., Santos, J., Ndeve, A., Dolezel, J., Vrana, J., Hokin, S.A., Farmer, A.D., Cannon, S.B., Close, T.J. 2019. The genome of cowpea (Vigna unguiculata [L.] Walp.). Plant Journal. 98(5)767-782. https://doi.org/10.1111/tpj.14349.
