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

Abstract: 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.

摘要：解析甘蓝型油菜栽培品种的遗传结构，是评估目标群体的群体结构、单倍型区块（haplotype block）与系统发育谱系的前提条件。本研究从全球各区域选取了85份甘蓝型油菜（Brassica napus L.）栽培品种。采用单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）标记开展单倍型区块、SNP热点区域及系统发育谱系分析。针对该85份油菜栽培品种，研究使用5058个SNP标记进行群体结构分析。当K值从1逐步递增至10时，ΔK在K=2处出现峰值，因此将85份油菜栽培品种划分为两个亚群，分别为P1亚群与P2亚群，二者分别包含13份和72份栽培品种。本研究的单倍型区块分析结果显示，A亚基因组的SNP标记数量多于C亚基因组；A06和C03染色体上的单倍型区块数量多于其他染色体，而C09染色体上的单倍型区块数量最少。SNP热点区域以SNP位点位置、突变频率及每条染色体上每100千碱基对的SNP数量进行定义。C03染色体上的SNP热点区域数量最多（432个），C09染色体上最少（134个）。基于遗传相似性与亲缘关系采用邻接法构建系统发育谱系，本研究中的85份油菜材料被划分为12个主要类群。