Genetic Diversity Analysis of Non-Heading Chinese Cabbage of Resistance to Clubroot Disease Based on SNP Molecular Markers
Liming Miao,
Dandan Xi,
Xiaofeng Li,
Changwei Zhang,
Lu Gao,
Ying Li,
Yuying Zhu,
Hongfang Zhu
Affiliations
Liming Miao
Shanghai Key Laboratory of Horticultural Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Dandan Xi
Shanghai Key Laboratory of Horticultural Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Xiaofeng Li
Shanghai Key Laboratory of Horticultural Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Changwei Zhang
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
Lu Gao
Shanghai Key Laboratory of Horticultural Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Ying Li
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
Yuying Zhu
Shanghai Key Laboratory of Horticultural Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Hongfang Zhu
Shanghai Key Laboratory of Horticultural Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Clubroot disease is a kind of soil-borne disease that seriously infects Brassica species. In this study, we collected 121 varieties of non-heading Chinese cabbages. In order to better understand the genetic variation and to screen suitable clubroot disease-resistant parental material, we re-sequenced them to examine the population genetic structure, population genetic diversity, population differentiation index, and selective sweep based on SNPs. The mapping rate with the reference genome was high, and data quality analysis revealed that the sequencing quality was good. The annotated data indicated that intronic and intergenic areas held the majority of SNPs and indels. Four subgroups of 121 non-heading Chinese cabbages were identified using principal component analysis, phylogenetic tree, and genetic structure analysis. An examination of genetic diversity revealed that while selfing may happen in subgroups C and D, heterozygosity may exist in subgroups A and B. In subgroup B, self-fertilization is not possible. There was a moderate degree of genetic differentiation between subgroups B and C (Fst = 0.0744347). For genes in certain sweep regions, we also ran GO enrichment and KEGG enrichment analysis. Two disease resistance-related genes, BraA01g042910.3.5C and BraA06g019360.3.5C, were examined. These findings will serve as a theoretical foundation for developing novel, clubroot disease-resistant types of non-heading Chinese cabbages.
