Location: Corn Insects and Crop Genetics Research
2020 Annual Report
Accomplishments
1. White paper describing needs and priorities for legume genetic data. ARS researchers in Ames, Iowa, worked with a group of two dozen international collaborators to publish a white paper, "The future of legume genetic data resources: challenges, opportunities, and priorities" (LGDWG, 2019). The whitepaper presents the conclusions of an international working group of legume researchers about objectives and methods in legume genomic science. The working group consisted of researchers who were convened by this ARS project and by the associated National Science Foundation Legume Federation project in March, 2019, to evaluate the needs for data management and methodologies, in order to best utilize this information for crop improvement and for basic research in this important group of species. The workshop identified various needs and recommendations: (a) Develop strategies to effectively store, integrate, and relate genetic resources collected in different projects. (b) Leverage information collected across many legume species by standardizing data formats and terms, improving the state of information about datasets, and increasing use of the FAIR data principles (FAIR: data should be Findable, Accessible, Interoperable, Reusable). (c) Advocate for the critical role that curators exercise in integrating complex datasets into databases and adding high value information that enable downstream analytics and facilitate practical applications. (d) Implement standardized software and database development practices to best leverage limited developer time and expertise gained from the various legume (and other) species. (e) Develop tools and databases that can manage genetic information for the world's plant genetic resources, enabling efficient incorporation of important traits into breeding programs. (f) Centralize information on databases, tools, and training materials and establish funding streams to support training and outreach.This white paper is expected to help guide and inform research priorities and activities for the coming decade.
2. Genome sequence assemblies for three soybean accessions. Genome sequence assemblies for three soybean accessions. ARS researchers in Ames, Iowa, and Beltsville, Maryland, along with other soybean researchers in the U.S. and internationally, published the genome sequence for three accessions of 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 ten 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 here describes the complete, high-resolution sequence of approximately one billion DNA bases for two widely used soybean cultivars and for one wild soybean (Glycine soja). These assemblies and annotations have been integrated into SoyBase, making them available to researchers for browsing and searching. Having the genome sequences for these two widely used soybean accessions will be helpful in identifying genes that are important in identifying the genetic control of traits such as early maturity. The genome sequence for the wild soybean accession will help researchers to determine how changes during domestication occurred, and to find genes that may not have been transferred from wild to cultivated soybean. This work will assist breeders and other scientists to more rapidly develop improved soybean varieties, to benefit farmers and consumers worldwide.
Review Publications
Bauchet, G., Bett, K.E., Cameron, C.T., Campbell, J.D., Cannon, E., Cannon, S.B., Carlson, J., Chan, A., Cleary, A., Close, T., Cook, D., Cooksey, A., Coyne, C.J., Dash, S., Dickstein, R., Farmer, A., Fernandez-Baca, D., Hokin, S., Jones, E., Kang, Y., Monteros, M., Munoz-Amatriain, M., Mysore, K., Pislariu, C., Richards, C.M., Shi, A., Town, C., Udvardi, M., Wettberg, E., Young, N., Zhao, P. 2019. The future of legume genetic data resources: Challenges, opportunities, and priorities. Legume Science. 1(1):e16. https://doi.org/10.1002/leg3.16.
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.
