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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Plant Sci. | doi: 10.3389/fpls.2019.01445

Genome Wide Association Study and Genomic Selection of Amino Acid Concentrations in Soybean Seeds

  • 1National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture. Laboratory of Crop Genetics and Breeding of Hebei.Cereal & Oil Crop Institute, Hebei Academy of Agriculture and Forestry Sciences (HAAFS), China
  • 2Department of Horticulture, Bumpers College, University of Arkansas, United States
  • 3Soybean Genomics & Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, United States
  • 4Department of Crop and Soil Environmental Sciences, College of Agriculture and Life Sciences, Virginia Tech, United States
  • 5Other, China

Soybean is a major source of protein for human consumption and animal feed. Releasing new cultivars with high nutritional value is one of the major goals in soybean breeding. To achieve this goal, genome-wide association studies of seed amino acid contents were 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. Among the 231 SNPs significantly associated with variations in amino acid contents, fifteen SNPs localized near 14 candidate genes involving in amino acid metabolism. The amino acids were classified into two groups with five in one group and seven amino acids 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 multiple amino acids can be used to simultaneously improve multi-amino acid concentration in soybean. Genomic selection analysis of amino acid concentration showed that selection efficiency of amino acids based on the markers significantly associated with all 15 amino acids was higher than that based on random markers or markers only associated with individual amino acid. The identified markers could facilitate selection of soybean varieties with improved seed quality.

Keywords: Glycine max, Soybean, Seed amino acid contents, Genome-Wide Association Study, genomic selection, Genotyping by sequencing, Single nucleotide polymorphism

Received: 30 Apr 2019; Accepted: 17 Oct 2019.

Copyright: © 2019 Qin, Shi, Song, Li, Wang, Cao, Ravelombola, Song, Yang and Zhang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Mengchen Zhang, Hebei Academy of Agriculture and Forestry Sciences (HAAFS), National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture. Laboratory of Crop Genetics and Breeding of Hebei.Cereal & Oil Crop Institute, Shijiazhuang, 050000, Hebei Province, China, mengchenzhang@hotmail.com