Genetic diversity of Cucurbita rootstock germplasm as assessed using simple sequence repeat markers

• Genetic diversity of Cucurbita rootstock germplasm was assessed using SSR.
• Forty-one SSR loci yielded 94 polymorphic alleles.
• Interspecific hybrids of C. maxima × C. moschata were the predominant combinations.
• Rootstock germplasm of C. moschata exhibited abundant genetic diversity.
• Six SSR markers were classified as informative markers for cultivar identification.

Grafting is becoming more popular in cucurbit crop production for soil-borne disease control. The correct choice of rootstock can have a vital role in the success of grafting. An improved understanding of the genetic diversity and potential of rootstock germplasm can be expected to contribute to more efficient breeding for improved rootstocks. Cucurbita spp. (squash and pumpkins) are major sources of rootstocks for grafting cucumbers, melons, and watermelons. The genetic diversity and relatedness of 25 commercial Cucurbita rootstock cultivars and 10 inbred lines were assessed using 80 simple sequence repeat (SSR) markers in this study. Forty-one SSR loci yielded 94 polymorphic alleles, with an average of 2.29 alleles per locus. The polymorphism information content values ranged from 0.16 to 0.60, with an average of 0.36. Cluster analysis and principal coordinate analysis showed that the majority of commercial Cucurbita rootstocks are interspecific hybrids, C. maxima × C. moschata, and these hybrids are closely related. By contrast, the C. moschata inbreds exhibit considerably greater genetic diversity, suggesting that they could be useful for rootstock improvement.