Impacts Of Domestication And Breeding On Single Nucleotide Polymorphisms In Soybean

140Functional gene fragments were chosen in62soybeans, which are composed with wild, landraces and improved cultivars with geographical representative for studying of the genetic structure and the rule of its change during domestication and breeding on DNA sequence level, and identifying candidate genes which impacted by artificial selection during domestication and breeding. The result can give the basis for further identify genes which are related with a agronomic and economic traits, and discover the molecular mechanism of soybean origin and evolution. The main results are as follows:1、381SNP and38indels are identified in62012bp DNA sequence. Relative to the landrace, genetic diversity of wild lost37%(θ value) and24%(πvalue) Relative to the improved cultivar, genetic diversity of the landrace lost12%(0value) and17%(π value). These genetic diversity reduction are significant in statistics. The rare SNP lost significantly during domestication, but not in breeding process. Discover the nucleotide diversity in different region of soybean genome. The result shows that genetic diversity of noncoding region are higher than coding region in three soybean population, and the genetic diversity is reduce both in coding region and noncoding region. In noncoding region, the genetic diversity reduces both in UTR and intron. In coding region, the frequency of synonymous is higher than the frequency of nonsynonumous, and both the frequency of synonymous and nonsynonumous reduce during domestication and breeding.3、The haplotype diversity in wild, landrace, and improved cultivars are0.45,0.35and0.29. Wild soybean lost22%haplotype diversity during domestication and landrace lost17%haplotype diversity during breeding. These haplotype diversity reduction are significant in statistics. We discover that the rare haplotype in wild soybean is much richer than landrace and improved cultivar, and rare haplotype reduce significantly during domestication.4、5genes may be impacted by selective effect with neutral test in140genes during domestication and breeding. Two of these gene are specific transcription regulator. The other are the gene coding asparagine biosynthetic enzyme, the gene coding a glycoside hydrolases from glycoside hydrolase family17and the gene coding an ethylene biosynthetic rate limiting enzyme.5、The locus-by-locus AMOVA revealed that20.12%of whole variation from interpopulation, and79.88%of whole variation from inner population. Both Fst and Gst show that there is obvious differentiation between wild soybean and landrace at the genome level, and little differentiation between landrace and improved cultivars. Calculating gene flow among different soybean population show that there is no reproductive isolation among population, and genes can flow fluently among soybean population.6、Cladogram created by neighbor joining method of62soybean based on SNP and haplotype data respectively. The result all show that G. soja and G. max diverge two sub-population significantly, but landrace and improved cultivar are intermixed in G. max. The two cladograms both show that a wild soybean congregate in landrace of G. max. Based on the geographical information of the wild soybean and the landraces which have closely phylogenetic relationship with the wild soybean, we infer that G. max may originate from Huang-Huai valleys.