Location: Soybean Genomics & Improvement Laboratory
2021 Annual Report
Accomplishments
1. Creation of a series of efficient tools for soybean genetics and breeding research. Although high-throughput sequencing technology can genotype a large number of breeding materials in plants, the information provided by sequencing is often too detailed for researchers, costing them a large amount of money and time to analyze the data. In many cases, a small set of informative, high-quality markers of a unique pattern is enough to screen breeding lines in early generations, perform genomic prediction, and map genes controlling traits. ARS-USDA scientists at Beltsville, Maryland, developed two assays, BARCSoySNP3K and SoySNP1K, containing 3K and 1K DNA markers, respectively. The 3K was commercialized by Illumina Inc, and the 1K was commercialized by Agriplex Genomics, Cleveland, Ohio. These affordable assays are expected to shorten breeding cycles and accelerate soybean trait mapping and improvement, significantly impacting private and public soybean breeding programs.
2. Identification of the gene controlling a major protein content locus in soybean. Soybean, one of the most important crops globally, was domesticated from wild soybean and has been further improved as a dual-use seed crop to provide highly valuable oil and protein for human consumption and animal feed. Previously, several studies have reported a major locus controlling protein and oil content on Chromosome 15, however, the corresponding gene for the locus is unknown. In this study, USDA-ARS scientists at Beltsville, Maryland, and St. Louis, Missouri, analyzed 631 soybean whole genome sequences and determined that the sucrose transporter gene controls seed protein and oil content as well as seed weight in soybean. This is the first report of the gene responsible for the major locus controlling protein and oil content on chromosome 15. The comprehensive knowledge on the molecular basis controlling the traits on Chromosome 15 is valuable for scientists to design new strategies for soybean seed quality improvement through breeding and biotechnological approaches.
3. Soybean gene restricting nitrogen-fixing identified. Nitrogen is the most critical nutrient requirement for crop production. Legume crops like soybean can derive most of the nitrogen required for optimal growth and yield with nitrogen-fixing bacteria known as rhizobia. Despite knowing how rhizobia establish connections to form symbiotic root nodules in plants, scientists still do not understand why this is possible. USDA-ARS scientists, in collaboration with researchers at Huazhong Agricultural University, China, analyzed the DNA genomes of soybean and found a gene, GmNNL1, responsible for the numbers of root nodules formed by rhizobia. These findings will be helpful to soybean scientists and breeders at government agencies, universities, and private institutes who want to improve soybean cultivation with less fertilizer application.
Review Publications
Rosso, L., Shang, C., Escamilla, D.M., Gillenwater, J., Song, Q., Zhang, B. 2021. Development of breeder-friendly KASP markers for low concentration of kunitz trypsin inhibitor in soybean seeds. International Journal of Molecular Sciences. 22:2675. https://doi.org/10.3390/ijms22052675.
Zhang, H., Goettel, W., Song, Q., Jiang, H., Hu, Z., Wang, M.L., An, Y. 2020. Selection of GmSWEET39 for oil and protein improvement in soybean. PLoS Genetics. 16(11).e1009114. https://doi.org/10.1371/journal.pgen.1009114.
Zhang, B., Wang, M., Sun, Y., Zhao, P., Liu, C., Qing, K., Hu, X., Zhong, Z., Cheng, J., Wang, H., Pemg, Y., Shi, J., Zhuang, L., Du, S., He, M., Wu, H., Liu, M., Chen, S., Wang, H., Chen, X., Fan, W., Tian, K., Wang, Y., Chen, Q., Wang, S., Dong, F., Yang, C., Zhang, M., Song, Q., Li, Y., Wang, X. 2021. Glycine max NNL1 restricts symbiotic compatibility with widely distributed bradyrhizobia via root hair infection. Nature Plants. 7:73-86. https://doi.org/10.1038/s41477-020-00832-7.
Soler-Garzon, A., Oladzadabbasabadi, A., Beaver, J., Beebe, S., Lee, R., Lobaton, J., Macea, E., Mcclean, P., Raatz, B., Rosas, J.C., Song, Q., Miklas, P.N. 2021. NAC candidate gene marker for bgm-1 and interaction with QTL for resistance to Bean golden yellow mosaic virus in common bean. Frontiers in Plant Science. 12. Article 628443. https://doi.org/10.3389/fpls.2021.628443.
Costa, L.C., Nalin, R.S., Dias, M.A., Ferreira, M.E., Song, Q., Pastor Corrales, M.A., Hurtado-Gonzales, O.P., Souza, E.A. 2020. Different loci control resistance to different isolates of the same race of Colletotrichum lindemuthianum in common bean. Theoretical and Applied Genetics. 134:543-556. https://doi.org/10.1007/s00122-020-03713-x.
Clevinger, E., Biyashev, R., Lerch, E., Yu, H., Quigley, C.V., Song, Q., Dorrance, A., Robertson, A., Maroof, S. 2021. Identification of quantitative disease resistance Loci towards four Pythium species in soybean. Frontiers in Plant Science. 12:514. https://doi.org/10.3389/fpls.2021.644746.
Beche, E., Gillman, J.D., Song, Q., Nelson, R.L., Beissinger, T., Decker, J., Shannon, G., Scaboo, A.M. 2021. Genomic prediction using training population design in interspecific soybean populations. Molecular Breeding. 41. Article e15. https://doi.org/10.1007/s11032-021-01203-6.
Valliyodan, B., Brown, A.V., Wang, J., Patil, G., Liu, Y., Otyama, P.I., Nelson, R., Vuong, T., Song, Q., Musket, T.A., Wagner, R., Marri, P., Reddy, S., Sessions, A., Wu, X., Grant, D.M., Bayer, P., Roorkiwal, M., Varshney, R.K., Liu, X., Edwards, D., Xu, D., Joshi, T., Cannon, S.B., Nguyen, H.T. 2020. Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Scientific Data. 8. Article 50. https://doi.org/10.1038/s41597-021-00834-w.
Ma, G., Song, Q., Li, X., Qi, L. 2020. High-density mapping and candidate gene analysis of Pl18 and Pl20 in sunflower by whole-genome resequencing. International Journal of Molecular Sciences. 21(24):9571. https://doi.org/10.3390/ijms21249571.
Ma, G., Long, Y., Song, Q., Talukder, Z.I., Shamimuzzaman, M., Qi, L. 2021. Map and sequence-based chromosome walking towards cloning of the male fertility restoration gene Rf5 linked to R11 in sunflower. Scientific Reports. https://doi.org/10.1038/s41598-020-80659-6.
Gilio, T., Hurtado-Gonzales, O.P., Goncalves-Vidigal, M.C., Valentini, G., Ferreira Elias, J.C., Song, Q., Pastor Corrales, M.A. 2020. Fine mapping of an anthracnose-resistance locus in Andean common bean cultivar Amendoim Cavalo. PLOS ONE. 15(10):0239763. https://doi.org/10.1371/journal.pone.0239763.
Liu, J.Y., Zhang, Y.W., Han, X., Zuo, J.F., Zhang, Z.B., Shang, H.H., Song, Q., Zhang, Y.M. 2020. Evolutionary population structure model reveals pleiotropic effects of GmPDAT for seed oil- and size-related traits in soybean. Journal of Experimental Botany. 71(22):6988-7002. https://doi.org/10.1093/jxb/eraa426.
Song, Q., Yan, L., Quigley, C.V., Fickus, E.W., Wei, H., Chen, L., Dong, F., Arya, S., Liu, J., Hyten, D., Pantalone, V., Nelson, R.L. 2020. Soybean BARCSoySNP6K - An assay for soybean genetics and breeding research. Plant Journal. https://doi.org/10.1111/tpj.14960.
Zhu, Q., Escamilla, D.M., Wu, X., Song, Q., Li, S., Rosso, L., Lord, N., Xie, F., Zhang, B. 2020. Identification and validation of major QTLs associated with low seed coat deficiency of natto soybean seeds (Glycine max L.). Theoretical and Applied Genetics. 133(1):3165-3176. https://doi.org/10.1007/s00122-020-03662-5.
Bornowski, N., Song, Q., Kelly, J. 2020. QTL Mapping of Post-Processing Color Retention in Two Black Bean Populations. Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-020-03656-3.
Goncalves-Vidigal, M.C., Gilio, T., Valentini, G., Vaz-Bisneta, M., Vidigal Filho, P.S., Song, Q., Oblessuc, P.R., Melotto, M. 2020. New Andean source of resistance to anthracnose and angular leaf spot: fine-mapping of disease-resistance genes in California Dark Red Kidney common bean cultivar. PLoS One. 15(6):e0235215. https://doi.org/10.1371/journal.pone.0235215.
