Genome Sequencing and Analysis of Wild Soybean (Glycine soja Sieb. and Zucc.).

The genome of soybean (Glycine max) has recently been sequenced and is one of six crop species to have been sequenced. We sequenced the genome of G. soja var. IT182932, which is the undomesticated ancestor of G. max. The nucleotide sequence of the G. soja genome, which contains 2.5 Mb of substituted bases and 406 kb of small inserted/deleted bases relative to G. max, is ~0.31% different from that of G. max. These data suggest that the G. soja/G. max complex is at least 0.25 million years ago (MYA), before the recent event of domestication, approximately 6,000-9,000 years ago. We collected 104 G. max and G. soja samples that were distributed from China, Korea to Japan for population genetic approach. To understand relationship between G. max and G. soja and soybean domestication history, 17 single-copy nuclear genes were selected and sequenced. G. soja from both China and Korea showed higher variations than other samples, which was supported by phylogenetic analysis. Chloroplast genome of G. soja (var. IT182932) was sequenced and chloroplast sequence-specific primers were designed based on two chloroplast genome sequences of G. max (PI 437654) and G. soja (IT182932). Seven different haplotypes were identified among our soybean samples. Haplotypes were generally grouped by either G. max or G. soja, but some G. soja samples had the genotypes similar to G. max. These nucleotide variations in nuclear and chloroplast sequences provided valuable information on the geographical divergence process of soybean and its wild relatives and soybean domestication history.