Development of a high-throughput SNP marker set by transcriptome sequencing to accelerate genetic background selection in Brassica rapa

Among the molecular markers used today, single nucleotide polymorphisms (SNP) are the most common type used in genetic diversity analysis due to their abundance. To develop a high-throughput SNP marker set to accelerate genetic background selection in Brassica rapa breeding, we sequenced the transcriptomes of 20 Chinese cabbage accessions representing diversity in traits such as head type, maturity, inner leaf color, and disease resistance. We identified 13,976 SSRs and 380,198 SNPs by aligning their contigs. We chose 189 SNPs that covered the entire B. rapa genome through a filtering process based on criteria such as depth, level of polymorphism, segregation ratio, lack of adjacent SNPs, copy number, and PIC value. To validate the SNP marker set, we genotyped 23 Chinese cabbage accessions and constructed a phylogenetic tree. The results showed that the SNP genotyping data could distinguish the Chinese cabbage accessions according to their phenotypic variations. The 23 accessions were classified into two groups that were characterized by phenotypic traits, especially head type and maturity. In conclusion, the selected SNP marker set is a reliable breeding tool for distribution analysis or selection of different Chinese cabbage accessions and may be applicable for rapid genetic background selection of Chinese cabbages for breeding.