Evaluation of Genetic Structure Rapeseed (Brassica napus L.) Cultivars with SNP Marker

Understanding the genetic structure of rapeseed cultivars is a prerequisite to assess population structure, haplotype block, phylogenetic pedigree in the target population. In this research, we selected 85 rapeseed (Brassica napus L.) cultivars from various areas. haplotype block, SNP hotspots, and phylogenetic pedigree were analyzed with Single Nucleotide Polymorphisms (SNPs) marker. Population structure is analyzed by using the 5058 SNP marker in the 85 rapeseed cultivars. As K value incremented aside from 1 into 10, ΔK was recognized at K = 2. Hence, the 85 rapeseed cultivars are branched into two subgroups, selected P1 subgroups, also P2 subgroups, including 13 and 72 cultivars respectively. In this research, the haplotype block analysis presented that the SNP markers number in A subgenome is more than the C subgenome, the block numbers on chromosomes A06 and C03 are greater than the other chromosomes and the lowest block number is on chromosome C09. The hotspots of SNP were defined by SNP position, mutation frequency, and the number of SNPs per 100Kbp on the chromosome. The Highest and the lowest numbers of SNP hotspots were found (432) and (134) on chromosome C03 and C09 respectively. The phylogenetic pedigree was constructed; neighbor-joining is built based on genetic similarity and kinship. In this study, 85 rapeseeds are branched into 12 major groups.