Development of a Core Set of SSR Markers for Cultivar Identification and Seed Purity Tests in Oriental Melon (Cucumis melo L. var. makuwa)

Abstract

Oriental melon (Cucumis melo L. var. makuwa), also called ‘Korean melon’ or ‘Chamoe’, is widely grown in East Asia, including Korea, Japan, and China. We used 521 simple sequence repeats (SSRs) to develop a core set of SSR markers as an effective tool for cultivar identification and seed purity tests in oriental melon. The polymorphism test using a subset of seven cultivars identified 20 expressed sequence tag SSR (EST-SSR) and 23 genomic SSR markers that showed high levels of polymorphism and simple segregation patterns. These SSR markers were used for DNA fingerprinting in additional 46 commercial cultivars. The average number of alleles per marker was 2.95 and 4.61 for the EST-SSR and genomic SSR markers in the 53 cultivars, respectively. For polymorphic information content (PIC), we found 0.411 to 0.816 with an average of 0.536 for the EST-SSR markers and 0.453 to 0.862 with an average of 0.568 for the genomic SSR markers. The unweighted pair group mean algorithm (UPGMA) dendrograms with the three sets of SSR markers (20 EST-SSR, 23 genomic SSR, and all 43 SSR markers) revealed that the 53 cultivars were separated into 4 to 5 major clusters. Furthermore, the set of all SSR markers was more effective at identifying the 53 cultivars relative to the other two marker sets. Therefore, the 43 SSR markers as a core set will be a valuable tool for several applications, including cultivar identification and seed purity tests in oriental melon.