A Genome-Wide Association Study of Protein, Oil, and Amino Acid Content in Wild Soybean (Glycine soja)

Abstract

Soybean (Glycine max L.) is a globally important source of plant proteins, oils, and amino acids for both humans and livestock. Wild soybean (Glycine soja Sieb. and Zucc.), the ancestor of cultivated soybean, could be a useful genetic source for increasing these components in soybean crops. In this study, 96,432 single-nucleotide polymorphisms (SNPs) across 203 wild soybean accessions from the 180K Axiom® Soya SNP array were investigated using an association analysis. Protein and oil content exhibited a highly significant negative correlation, while the 17 amino acids exhibited a highly significant positive correlation with each other. A genome-wide association study (GWAS) was conducted on the protein, oil, and amino acid content using the 203 wild soybean accessions. A total of 44 significant SNPs were associated with protein, oil, and amino acid content. Glyma.11g015500 and Glyma.20g050300, which contained SNPs detected from the GWAS, were selected as novel candidate genes for the protein and oil content, respectively. In addition, Glyma.01g053200 and Glyma.03g239700 were selected as novel candidate genes for nine of the amino acids (Ala, Asp, Glu, Gly, Leu, Lys, Pro, Ser, and Thr). The identification of the SNP markers related to protein, oil, and amino acid content reported in the present study is expected to help improve the quality of selective breeding programs for soybeans.

Integrating Genome-Wide Association Study, Transcriptome and Metabolome Reveal Novel QTL and Candidate Genes That Control Protein Content in Soybean

“…Meantime, LysoPE(0:0/18:2(9Z,12Z)) belonged to glycerophospholipid metabolism. It was reported that a negative correlation existed between the soybean oil content and the PC [ 40 ]. We also found that Glyma.08G042800 and Glyma.12G094400 were positively associated with Nicotianamine (r > 0.93, p < 1.90 × 10 −9 and r > 0.5, p < 0.02).…”

Genome-Wide Association Study for Agronomic Traits in Gamma-Ray-Derived Mutant Kenaf (Hibiscus cannabinus L.)

“…While linkage mapping methods use bi-parental populations, GWAS is an approach that exploits diverse natural populations [ 24 , 25 , 26 ]. This approach has been applied to a variety of crops, including rice [ 27 ], soybean [ 28 ], maize [ 29 ], and sorghum [ 20 ], and it is being used in breeding programs. To date, no GWAS analyses of kenaf have been reported.…”