Location: Plant Genetics Research
2019 Annual Report
Accomplishments
1. Developing a large resource of single nucleotide variants for soybean genetic improvement. With the advent of next-generation sequencing technologies, soybean researchers have generated more than 15 terabytes of genome sequencing data from 1,519 diverse wild and cultivated accessions in the past-decade. ARS researchers in St. Louis, Missouri, demonstrated that the 1,519 diverse soybean accessions represent almost the entire genetic diversity of over 20,000 wild and cultivated soybean accessions in the U.S. soybean collection. They analyzed the entire set of DNA sequencing data, and further identified, validated and annotated a total of 29.5 million single nucleotide variants. The large set of the single nucleotide variants could serve as an important resource for U.S. soybean research and product development and plays an important role in translating U.S. soybean genomic research into soybean improvement.
2. Development of a highly effective in-silico genotyping approach for soybean research. With the advent of next-generation sequencing technologies, soybean researchers have re-sequenced genomes of over 1,500 diverse soybean accessions and generated a huge amount of the genome sequencing data. ARS researchers in St. Louis, Missouri, have developed a bioinformatic algorithm to examine the nucleotide sequences of a given gene or a deoxyribonucleic acid region such as a quantitative trait locus interval in those diverse sequenced soybean accessions. This allows soybean researchers to genotype known quantitative trait locus gene alleles, discover new quantitative trait locus alleles, and identify soybean accessions containing novel trait alleles that can be used as new genetic materials for soybean breeding. The in-silico approach increases soybean genotyping efficiency by orders of magnitude in comparison with traditional wet-lab approaches and should greatly enhance translating soybean genome research into soybean improvement.
Review Publications
Bartels, A., Han, Q., Nair, P., Stacey, L., Gaynier, H., Mosley, M., Huang, Q., Pearson, J., Hsieh, T., An, Y., Xiao, W. 2018. Dynamic DNA methylation in plant growth and development. International Journal of Molecular Sciences. 19(7):2144. https://doi.org/10.3390/ijms19072144.
Diers, B.W., Specht, J., Rainey, K., Cregan, P., Song, Q., Ramasubramanian, V., Graef, G., Nelson, R., Schapaugh, W., Wang, E., Shannon, G., McHale, L., Kantartzi, S., Xavier, A., Mian, R.M., Stupar, R., Michno, J., An, Y., Goettel, W., Ward, R., Fox, C., Lipka, A.E., Hyten, D., Cary, T., Beavis, W.D. 2018. Genetic architecture of soybean yield and agronomic traits. G3, Genes/Genomes/Genetics. 8(10):3367-3375. https://doi.org/10.1534/g3.118.200332.
