Development of SNP markers based on transcriptome sequences and their application in germplasm identification in radish (Raphanus sativus L.)

Single nucleotide polymorphism (SNP) is the most frequent form of DNA variation in the genome. The cleaved amplified polymorphic sequence (CAPS) and derived CAPS (dCAPS) are co-dominant and cost-effective markers for SNP genotyping. Recently, the large-scale transcriptome sequencing has greatly facilitated SNP detection, and the applications of CAPS/dCAPS markers have been successfully carried out in various plant species. However, SNP detection via transcriptome sequencing and development of CAPS/dCAPS markers remain limited in radish. In this study, 56,089 SNPs were detected in the radish transcriptome, and 4941 high-confidence SNPs were further filtered out and analyzed, which could alter the recognition sites of 222 restriction enzymes. The available frequency of different enzymes varied a great deal, and ten enzymes were selected for marker development. A total of 262 pairs of CAPS and 15 pairs of dCAPS primers were synthesized, among which 148 and six could generate polymorphic bands after enzyme digestion, respectively. Furthermore, the polymorphism information content (PIC) values of 154 SNP markers ranged from 0.0739 to 0.3750. In addition, 24 radish genotypes were gradually distinguished by six CAPS markers with the manual cultivar identification diagram (MCID) approach, indicating the feasibility of CAPS/dCAPS markers in genetic diversity analysis and germplasm identification. These newly developed SNP markers could enrich the types and numbers of functional markers, and could be valuable in facilitating gene tagging, genetic mapping, comparative genomic studies and marker-assisted selection (MAS) of important horticultural traits in radish.