Genome wide association study and genomic selection of amino acid concentrations in soybean seeds

Authors: QIN, JUN - Hebei Academy Of Agriculture & Forestry; SHI, AINONG - University Of Arkansas; Song, Qijian; LI, SONG - Virginia Tech; WANG, FENGMIN - Beijing University Of Agriculture; CAO, YINGHAO - Hebei Academy Of Agriculture & Forestry; RAVELOMBOLA, WALTRAM - University Of Arkansas; YANG, CHUNYAN - Hebei Academy Of Agriculture & Forestry; ZHANG, MENGCHEN - Hebei Academy Of Agriculture & Forestry

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/17/2019
Publication Date: 11/15/2019
Citation: 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.
DOI: https://doi.org/10.3389/fpls.2019.01445

Interpretive Summary: Soybean is a major source of protein for human consumption and livestock feed in the world. It is estimated that more than 70% of the world's total protein meal comes from soybean. Although soybean seeds are a major source of protein, soybean seed protein is deficient in lysine, threonine, methionine, and cysteine amino acids that are nutritionally important. Thus, the genetic improvement of soybean seed amino acid composition is needed. Researchers at USDA-ARS, University of Arkansas, Virginia Tech, and Hebei Province Academy of Agricultural and Forestry Sciences investigated soybean seed amino acid composition and sequenced DNA of a set of 249 genetically diverse soybean cultivars from China, Japan, Korea and the United States. The scientists determined amino acid concentration variation in the populations and identified soybean cultivars with high concentrations of individual amino acids. They also detected DNA markers associated with the concentration of individual amino acids and a group of amino acids. The scientists then tested these markers for selecting plants with improved amino acid content. The results from this study will help breeders in industry, the government or at universities better choose soybeans for breeding and accelerate the development of new soybeans with improved protein quality.

Technical Abstract: Soybean is a major source of protein for human consumption and animal feed. Breeding new cultivars with high nutritional value is one of the major goals in soybean breeding. Genome-wide association study of amino acids was conducted based on 249 soybean accessions from China, US, Japan, and South Korea. The accessions were evaluated for 15 amino acids and genotyped by sequencing. Significant genetic variation was observed for amino acids among the accessions. Of the 231 SNPs significantly associated with 15 amino acids, a total of 15 were from 14 genes involving in amino acid metabolism. The amino acids were classified into two groups with five in one group and seven in the other. Correlation coefficients among the amino acids within each group were high and positive, but the correlation coefficients of amino acids between the two groups were negative. Twenty-five SNP markers associated with several amino acids provided a possibility to simultaneously improve multi-amino acid concentration in soybean. Genomic selection analysis of amino acid concentration based on RR-BLUP in rrBLUP and CMLM in GAPIT showed that selection efficiency of amino acids based on the markers significantly associated with 15 amino acids was higher than that based on genome-wide random markers or markers only associated with individual amino acid. The identified markers could facilitate selection of soybean varieties with improved nutrition.