Development of cost-effective single nucleotide polymorphism marker assays for genetic diversity analysis in Brassica rapa

文献类型： 外文期刊

第一作者： Su, Tongbing

作者： Su, Tongbing;Li, Peirong;Yang, Jingjing;Sui, Guanglei;Yu, Yangjun;Zhang, Deshuang;Zhao, Xiuyun;Wang, Weihong;Wen, Changlong;Yu, Shuancang;Zhang, Fenglan;Su, Tongbing;Li, Peirong;Yang, Jingjing;Sui, Guanglei;Yu, Yangjun;Zhang, Deshuang;Zhao, Xiuyun;Wang, Weihong;Wen, Changlong;Yu, Shuancang;Zhang, Fenglan;Su, Tongbing;Li, Peirong;Yang, Jingjing;Sui, Guanglei;Yu, Yangjun;Zhang, Deshuang;Zhao, Xiuyun;Wang, Weihong;Wen, Changlong;Yu, Shuancang;Zhang, Fenglan

作者机构：

关键词： Brassica rapa; Chinese cabbage; Genetic diversity; Molecular markers; SNP; KASPar assays

期刊名称：MOLECULAR BREEDING （ 影响因子：2.589； 五年影响因子：2.75 ）

ISSN： 1380-3743

年卷期： 2018 年 38 卷 4 期

页码：

收录情况： SCI

摘要： Competitive allele-specific PCR (KASPar) assay is a user-friendly system that provides flexibility in the numbers of single nucleotide polymorphisms (SNPs) and genotypes. Based on Illumina-GA-IIx genomic data from 10 genotypes with a broad genetic background, 3183 SNPs were selected for KASPar assays development, and 568 were finally converted and selected for Brassica rapa germplasm characterization (17.8%) on the basis of reproducibility, missing data rate, and uniform genetic distribution. High levels of polymorphism of these markers across 231 B. rapa genotypes were verified, illustrating by high polymorphic information content (averaged 0.34), minor allele frequency (0.37), genetic diversity (0.45), and the low observed heterozygosity (0.10). Based on the SNP dataset, structure and principal coordinates analysis, and neighbor-joining phylogenetic methods were used to examine the population structure and gave highly consistent results. The 231 accessions were divided into the four primary subspecies, representing 99 accessions from B. rapa ssp. pekinensis, 85 from B. rapa ssp. chinensis, 30 from B. rapa ssp. rapifera, and 17 from B. rapa ssp. oleifera and were further subdivided into 12 lower-order clusters according to different morphotypes. The genetic variability and pairwise fixation index analysis revealed that the ssp. pekinensis accessions possess the most extensive genetic variation among the four subspecies. The KASPar system is highly useful for validating SNPs and will be valuable for genetics research and breeding applications in B. rapa.

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