Single Nucleotide Polymorphisms Of Fatty Acid Metabolism-Related Genes In Soybean

Soybean is one of the most important sources of phytoprotein and edible fat. The content and component of fatty acid in soybean seeds are important indicators for evaluating the quality of soybean. Therefore, it is of great importance to study the fatty acid metabolism-related genes and its relationships with the content and component of fatty acid in soybean. In this paper,20 species for each of the wild soybeans, improved and breeding cultivars were used to study the single nucleotide polymorphisms of fatty acid metabolism-related genes in them and its changing patterns of genomic sequences during the domestication and breeding process. The results in the present study would play important roles in systematic and theoretical analysis of the fatty acid metabolism-related genes and its relationships with the content and component of soybean fatty acid in soybean, and it would also be of great importance in mapping, cloning and functionally analyzing the key genes related to the content and component of fatty and acid in soybean. The main results are as follows:1. A total of 23501 bp of DNA in 35 gene fragments were successfully sequenced with all the 60 soybean accessions. Totally,224 SNPs were observed. In the three groups of wild soybeans, improved and breeding cultivars, the SNP numbers were 213,121 and 112, respectively, the rare SNP numbers were 90,40 and 28, respectively, theθvalues were 2.01×10-3,1.13×10-3 and 1.08×10-3, respectively, and the n values were 2.16×10-3,1.27×10-3 and 1.25×10-3, respectively. Theses results indicated that it might have been experienced a significant reduction in the numbers and frequencies of SNPs during domestication process, and most of the reduced SNPs were rare SNPs. The effects of breeding process on the genetic diversity of soybean fatty acid metabolism-related genes were very limited.2. In the 23501 bp of sequenced DNA,7899 bp were coding sequences and 15602 bp were noncoding sequences. The total numbers of SNPs for the coding and noncoding sequences were 41 and 183, respectively. In the three groups of wild soybeans, improved and breeding cultivars, theθvalues in the coding sequences were found to be 1.30×10-3,0.93×10-3 and 0.96×10-3, respectively, theπvalues in the coding sequences were observed to be 1.31×10-3, 1.01×10-3 and 0.99×10-3 respectively, while theθvalues in the noncoding sequences were found to be 2.37×10-3,1.23×10-3 and 1.14×10-3, respectively, theπvalues were identified to be 2.58×10-3,1.41×10-3 and 1.41×10-3 respectively. In the coding sequences, the 0 values of the synonymous SNPs for the three soybean groups mentioned above were 0.79×10-3,0.54×10-3 and 0.46×10-3, respectively, theπvalues of the synonymous SNPs for them were 0.80×10-3,0.58×10-3 and 0.51×10-3, respectively; while theθvalues of nonsynonymous SNPs for the three soybean groups were 0.54×10-3 0.39×10-3 and 0.50×10-3, respectively, and theπvalues of nonsynonymous SNPs were 0.51×10-3,0.43×10-3 and 0.41×10-3, respectively. From the above, we considered that the SNP frequencies were higher in the noncoding sequences than in the coding sequences and more obvious reductions of SNP frequencies miht have happened during the domestication process. In addition, in the coding sequences, more distinct reductions were found for the nonsynonymous SNP frequencies than the synonymous SNP frequencies during the domestication process.3. There are 15 key enzyme related genes and 20 noncritical enzyme related genes in the 35 fatty acid metabolism-related genes. In the key enzyme related genes, the 0 values for the wild soybeans, improved and breeding cultivars were 2.07×10-3,1.35×10-3 and 1.29×10-3, respectively, theπvalues for them were 2.13×10-3,1.58×10-3 and 1.58×10-3, respectively. In the noncritical enzyme related genes, theθvalues for the wild soybeans, improved and breeding cultivars were 1.98×10-3,0.97×10-3 and 0.93×10-3, respectively, theπvalues for them were 2.17×10-3,1.05×10-3 and 1×10-3, respectively. This showed that the SNP frequencies in the noncritical enzyme related genes were lower than those in the key enzyme related genes and that more sever SNP frequency reductions should have taken place in the in noncritical enzyme related genes than in the key enzyme related genes during the domestication process.4. A total of 251 haplotypes were identified with the total 224 SNPs. In the three groups of wild soybeans, improved and breeding cultivars, the haplotype nunbers were 197,111 and 104, respectively, the haplotype diversity were 0.57,0.36 and 0.35, respectively, the values of genetic differentiation were 0.1067,0.118 and 0.0285, respectively. The values of Hs and Ht were 0.42 and 0.48, respectively. It was obvious that much higher genetic differentiation was found between the wild and cultivated soybeans than between the improved and breeding cultivars, indicating that greater impacts on fatty acid metabolism-related genes were resulted from the domestication process than the breeding process.5. Based on three kinds of neutrality tests (Tajima's D, Fu and Li's D* and Fu and Li's F*),3 out of the 35 fatty acid metabolism-related genes showed significant deviation form neutral models. These three genes were Glymal0g42470.1, Glyma03g30070.1 and Glymallg07850.1, suggesting that these 3 genes might have been affected by strong selection during the domestication and breeding processes.