Single Nucleotide Polymorphisms In G.soja, G.gracilis And G.max

SNPs are the most abundant source of DNA polymorphisms in various organisms. To study SNPs frequency, haplotype diversity and linkage disequilibrium (LD) structure in G. soja, G. gracilis and G. max systematically is significant for understanding the genetic diversity of soybean and investigating the process and mechanism of soybean domestication on molecular level.DNA fragments of 15 loci in 11.011 kbp, were sequenced in the 110 accessions including 40 accessions of G. soja, 20 accessions of G. gracilis and 50 accessions of G. max. Of the 96 SNPs we found, transitions accounted for 52 (54%) and transversions for 44 (46%), and 14 SNPs were in coding regions, of which, synonymous mutations accounted for 12(76%).93, 62 and 41 SNPs were found respectively in the three populations and the SNPs frequency (θ) was 1.974, 1.587 and 0.831 SNPs/kbp respectively. 108, 58 and 35 haplotypes were detected in the three populations and haplotype heterozygosity (Hs) was 0.571. 0.479 and 0.348 respectively. The distribution of SNPs and haplotypes were compared among the three populations, which implyed that large amount of SNPs and haplotypes lost during soybean domestication. The lost SNPs and haplotypes were mainly rare kind while some common kinds also lost.The genetic distance was also compared among the three populations, which between G. max and G. soja is the longest, and which between G. gracilis and G. soja is longer than that between G. gracilis and G. max in some sort.The analysis of linkage disequilibrium (LD) suggested that as the physical distance increases, the LD strength (r2) of G. max decreases gentliest, and that of G. soja severeliest. It can be concluded that during the domestication of soybean, genetic variation lost gradually and genetic diversity became smaller. Such change of genetic structure is related mostly to genetic shift and shows the existence of obvious bottleneck effectThe SNPs, haplotype heterozygosity and the distribution of LD in above loci were analyzed in 30 additional accessions of G. max in ShanXi, which indicated that the G. max in ShanXi covers almost all the genetic diversity of G. max. ShanXi is therefore assumed to be the origin and the variation center of G. max.