Single Nucleotide Polymorphism Of Soybean Mapping Populations Parents

Five pairs of soybean mapping populations parents were chosen for the study of their SNP frequency, characterization and distribution for further effectively developing soybean SNP makers in functional genes and constructing SNP linkage map. The main results were as follows:1. 455 DNA Sequences of soybean functional genes were selected from Genbank database. Firstly, 455 pairs of primers were designed, 300 pairs (65.9%) had good sequence results after PCR amplified and sequence analyzed and 231 pairs had SNPs loci; Then, 155 primers that were bad in first experiment and 69 primers that didn't have SNPs loci were redesigned in different areas of gene fragments, 151 pairs (67.4%) had good sequence results after experimental detection, and 120 pairs had SNPs loci; Finally, 104 primers that were bad in second experiment and didn't have SNP loci were redesigned, 63 pairs (60.6%) had good sequence results and 35 pairs had SNPs loci. In three experiments, achievement ratio of sequencing obviously were higher than research results of predecessor.2. 1 419 SNPs loci were found in total DNA sequence of 219 581 bp; Of the total SNPs, there were 528 and 891 in coding and noncoding region, respectively; Accordingly, nucleotide polymorphism (θvalue) were 0.00143 and 0.00235, which suggested nucleotide diversity of non-coding region were higher than of coding region. This was equal to predecessor's researches. At the same time, calculated SNP frequency was higher than results of Zhu et al. The main reason was related to experimental materials. The 1 419 SNPs loci were composed of 650 transition, 519 transversion and 250 indels, and the proportion of transition and transversion was 1.3:1.3. We found that there had similar polymorphism in G. soja and G. max type of groups of nannong 86-4×PI342618B and nannong 99-10×PI326582B, which was obviously higher than the others; The lowerest group was suinong 14×suinong 20; And the remaining groups were in the middle and had similar polymorphism; According to different polymorphic analyze, we discovered nannong 86-4×PI326582B had most SNPs and polymorphic gene loci in every two materials. SNP and polymorphic loci discovery efficiency would be improved greatly by comparing every two mapping populations parents, which may achieve to 70% of total polymorphic loci; But the efficiency would insignificantly improved when three of five mapping populations parents were combined; the most effective way was to compare five mapping populations parents as a whole.