Objective Genetic diversity and relationship of the major grape varieties cultivated in Sichuan were analyzed to facilitate the resource organization and utilization.

Methods Seventy-seven grape germplasms were targeted for the genetic diversity and structure study by using SCoT markers.

Results A total of 68 bands, of which 65 were polymorphic, were amplified by the 10 selected SCoT primers with an average of 6.8 bands per primer. The genetic similarity coefficient of the germplasms was 0.59-0.97. At the coefficient of 0.626, the cultivars were classified into two categories of Pop1 that contained 34 germplasms mostly European and American hybrids and Pop2 that consisted of 43 germplasms largely Eurasian varieties.

Conclusion The SCoT molecular markers could preliminarily identify the germplasms for further genetic studies on the resource in Sichuan, parent selection for hybrids, and molecular marker-assisted breeding of grape.