Genetic Diversity of Wild Soybean and its Exploitation for Efficient Discovery of Novel Allelic Variants

Wild soybean (Glycine soja) is the closest extant wild relative species of the domesticated soybean (G. max), and grows naturally in East Asia. As G. soja is cross-compatible with soybean, and the two yield fertile hybrids, the former represents a promising source of novel genes and alleles for soybean breeding and improvement. More than 2,000 G. soja accessions are distributed publicly by US and Japanese research institutes. In this study, the genetic diversity of the G. soja germplasm was analyzed with the genotypes of 80 SSR markers. Four SSR markers per chromosome were selected based on the polymorphism information content (PIC) and the position on 20 chromosomes. The number of alleles and PIC values of the respective marker loci in the germplasm showed much greater variation than those in the soybean of NIAS Japanese and world core collections (Kaga et al., 2012). Most of the variation at the respective soybean loci was reflected in those of G. soja. The phylogenetic tree based on the SSR marker loci indicated that the germplasm included soybean in several clusters, and its diversity extended beyond the domesticated variety. Exploiting this wide diversity to verify the presence of novel genes and alleles, we screened a novel allele at the Sg-1 locus. The Sg-1 locus encodes a glycosyltransferase and regulates the terminal sugar species located on the C-22 sugar chain of soyasaponin. A novel allele was discovered in the germplasm through length polymorphism analysis of the Sg-1 coding region.