Development of genomic SSR markers and genetic diversity analysis in cultivated radish (Raphanus sativus L.)

Radish (Raphanus sativus L.) is a major vegetable cultivated worldwide. As a member of the family Brassicaceae, this species has diverse morphological characteristics in root. Radish cultivars have been classified based on morphological traits, including root shape and color. Despite its economic importance in Asia, genomic research in radish is less well developed relative to Brassica rapa, a close relative of radish. In this study, we developed genomic simple sequence repeat (SSR) markers using a SSR-enriched library and investigated genetic diversity in a collection of 144 radish cultivars. A total of 237 primer pairs for SSRs were designed and 184 (77.6%) primer pairs produced PCR amplicons. Of these, we selected 27 SSR markers (14.7%) based on polymorphism in a subset of 11 cultivars and then used to assess genetic relationships in the germplasm panel. For these markers, the number of alleles per marker ranged from 2 to 18 with an average of 7.77 alleles and the polymorphism information content (PIC) values ranged from 0.491 to 0.906. The estimates of pairwise F ₛₜ revealed significant genetic differentiation between the five market classes of 135 radish cultivars (74 big, 15 small, 29 young, 12 Altari, and 5 processing). Clustering analysis using NTSYS-pc and STRUCTURE software also found that the 74 big radishes were divided into 5–7 clusters. In addition, all 27 SSR markers were able to differentiate 64 big radish cultivars based on the UPGMA dendrogram and each of the 23 markers independently identified 1 to 17 big radish cultivars. These results suggest that cultivated radishes have different patterns of genetic variation and breeding practices should be a driving force for the genetic differentiation between and within market classes. The SSR markers developed in this study will be a useful resource for genetic study and protection of plant breeder’s intellectual property right through cultivar identification.