DNA profiling of commercial pumpkin cultivars using simple sequence repeat polymorphisms

Abstract

Pumpkin (Cucurbita spp.) is a major vegetable crop grown worldwide. Three species, C. pepo, C. moschata, and C. maxima, are economically important cultivated pumpkins. To develop a core set of markers for DNA profiling and cultivar identification, we used a total of 300 SSRs consisting of 158 CMTp and 142 CMTm that were previously identified in C. pepo and C. moshata, respectively. Polymorphisms in these primers were tested using a subset of 22 cultivars selected from a collection of 160 commercial cultivars. A total of 12 CMTp and 28 CMTm markers were selected based on polymorphism and number of alleles, and these 40 markers were used to genotype all 160 cultivars. Of these, 29 markers (5 CMTp and 24 CMTm) accurately detected a total of 215 alleles with an average of 7.41 alleles per marker in our collection of pumpkin cultivars. Their PIC values ranged from 0.327 to 0.894 with an average of 0.674. Analysis of genetic similarity using the 29 SSR markers revealed that the 160 cultivars were divided into five major clusters representing C. maxima×C. moshata hybrids (cluster I), C. moshata (cluster II), C. maxima (cluster III), C. pepo (cluster IV), and C. ficifolia (cluster V). In clusters I-IV, the cultivars were further separated into 2-3 sub-clusters. In addition, we found that 29 SSR markers were able to differentiate all 160 cultivars. Results from our study will facilitate genetic study and protection of breeders’ intellectual property rights in pumpkins.