Location: Soybean Genomics & Improvement Laboratory
2020 Annual Report
Accomplishments
1. Three new reference-quality genome assemblies for soybean. Plant breeders and scientists use plant DNA genome sequences to identify genes that are important for yield, disease resistance, and plant growth characteristics. For soybean, a genome sequence assembly for the widely-used Williams 82 variety has been available for about ten years, but there were numerous known gaps and errors in the sequence assembly. USDA-ARS scientists at Beltsville, Maryland, and researchers at the Department of Energy Joint Genome Institute, Hudson-Alpha Institute for Biotechnology, University of Missouri, Iowa State University, University of Minnesota, University of Georgia, University of Australia, Chinese University of Hong Kong, and The International Crops Research Institute for the Semi-Arid Tropics (CRISAT), India, made major improvements to the Williams 82 reference genome sequence, as well as built new genome assemblies for two other soybean varieties: one for the most important U.S. southern cultivar 'Lee', and another for the closest wild relative of soybean, Glycine soja. These three genome sequences are available to the public and can be used to identify similarities and differences that underpin important agricultural traits.
2. Soybean cyst nematode resistance gene function. Soybean cyst nematode (SCN) is the most damaging soybean pathogen, causing significant yield and quality losses. Resistance to SCN is conferred by genes at two main soybean DNA regions, Rhg1 and Rhg4, at chromosome 18 and 8, respectively. The molecular mechanisms through which Rhg1 mediates SCN resistance is known, but the function of Rhg4 remains to be elucidated. The Rhg4 locus contains only one gene encoding serine hydroxymethyltransferase (GmSHMT08). USDA-ARS scientists at Beltsville, Maryland, and researchers at University of Tennessee and Southern Illinois University studied the function of GmSHMT08 in establishing DNA methylation landscapes of soybean roots during SCN infection. They observed that the susceptible soybean exhibited reduced DNA methylation levels in both protein-coding genes and transposable elements, whereas the resistant line showed the opposite response in response to SCN infection. This trend was observed in all DNA methylation contexts, suggesting that GmSHMT08's function is vital for cellular methyltransferase activity, possibly regulating soybean DNA through methylation. Scientists at universities, government agencies, and private institutes will be able to use this knowledge to help shape soybean defense responses upon SCN infection.
Review Publications
Qin, J., Shi, A., Song, Q., Li, S., Wang, F., Cao, Y., Ravelombola, W., Yang, C., Zhang, M. 2019. Genome wide association study and genomic selection of amino acid concentrations in soybean seeds. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2019.01445.
Murube, E., Campa, A., Song, Q., Mcclean, P., Ferreira, J.J. 2019. Toward validation of QTLs associated with pod and seed size in common bean using two nested recombinant inbred line populations. Molecular Breeding. 40:7. https://doi.org/10.1007/s11032-019-1085-1.
Leitao, S., Malosetti, M., Song, Q., Eeuwijk, F., Rubiales, D., Patto, M. 2020. Natural variation in Portuguese common bean germplasm reveals new sources of resistance against Fusarium oxysporum f. sp. phaseoli and resistance-associated candidate genes. Phytopathology. 110(3):663-647.
Rambani, A., Pantalone, V., Yang, S., Rice, H., Song, Q., Mazarei, M., Arelli, P.R., Meksem, K., Stewart, N., Hewezi, T. 2020. Identification of introduced and stably inherited DNA methylation variants in soybean associated with soybean cyst nematode parasitism. New Phytologist. 227(1):168-184. https://doi.org/10.1111/nph.16511.
Beche, E., Gillman, J.D., Song, Q., Nelson, R.L., Beissinger, T., Decker, J., Shannon, G., Scaboo, A.M. 2020. Nested association mapping of important agronomic traits in three interspecific soybean populations. Theoretical and Applied Genetics. 133:1039-1054. https://doi.org/10.1007/s00122-019-03529-4.
Ma, G.J., Song, Q., Underwood, W., Zhang, Z.W., Fiedler, J.D., Xuehui, L., Qi, L. 2019. Molecular dissection of resistance gene cluster and candidate gene identification of Pl17 and Pl19 in sunflower by whole-genome resequencing. Scientific Reports. 9:14974. https://doi.org/10.1038/s41598-019-50394-8.
Valliyodan, B., Cannon, S.B., Bayer, P.E., Shu, S., Brown, A.V., Ren, L., Jenkins, J., Chung, C.Y.L., Chan, T.F., Daum, C.G., Plott, C., Hastie, A., Baruch, K., Barry, K.W., Huang, W., Gunvant, P., Varshney, R.K., Hu, H., Batley, J., Yuan, Y., Song, Q., Stupar, R.M., Goodstein, D.M., Stacey, G., Lam, H.M., Jackson, S.A., Schmutz, J., Grimwood, J., Edwards, D., Nguyen, H.T. 2019. Construction and comparison of three new reference-quality genome assemblies for soybean. Plant Journal. 100(5):1066-1082. https://doi.org/10.1111/tpj.14500.
Islam, N., Stupar, R., Luthria, D.L., Garrett, W.M., Stec, A.O., Roessler, J., Natarajan, S.S. 2019. Genomic changes and biochemical alterations of seed protein and oil content in a subset of fast neutron induced soybean mutants. Biomed Central (BMC) Plant Biology. 19(1):420. https://doi.org/10.1186/s12870-019-1981-x.
Tan, R., Collins, P.J., Wang, J., Wen, Z., Boyse, J.F., Laurenz, R., Gu, C., Jacobs, J.L., Song, Q., Chilvers, M.I., Wang, D. 2018. Different loci associated with root and foliar resistance to sudden death syndrome (Fusarium virguliforme) in soybean. Theoretical and Applied Genetics. 132:501-513. https://doi.org/10.1007/s00122-018-3237-9.
La, T., Large, E., Taliercio, E.W., Song, Q., Gillman, J.D., Xu, D., Nguyen, H., Shannon, G., Scaboo, A. 2018. Characterization of a USDA core collection of wild soybean (Glycine soja Siebold & Zucc.) accessions for seed composition and agronomic traits. Frontiers in Plant Science. https://doi.org/10.2135/cropsci2017.08.0514.
