Genome re-sequencing, SNP analysis, and genetic mapping of the parental lines of a commercial F(1) hybrid cultivar of Chinese cabbage

The genome-wide characterization of single nucleotide polymorphism (SNP) between cultivars or between inbred lines contributes to the creation of genetic markers that are important for plant breeding. Functional markers derived from polymorphisms within genes that affect phenotypic variation are especially valuable in plant breeding. Here, we report on the genome re-sequencing and analysis of the two parental inbred lines of the commercial F(1) hybrid Chinese cabbage cultivar “W77”. Through the genome-wide identification and classification of the SNPs and indels present in each parental line, we identified about 1,500 putative non-functional genes in each parent. We designed cleaved amplified polymorphic sequence (CAPS) markers using specific mutations found at Eco RI restriction sites in the parental lines and confirmed their Mendelian segregation by constructing a linkage map using 96 F(2) plants derived from the F(1) hybrid cultivar, “W77”. Our results and data will be a useful genomic resource for future studies of gene function and metagenomic studies in Chinese cabbage.