An efficient strategy for developing genotype identification markers based on simple sequence repeats in grapevine

Microsatellites are valuable resources for breeding and genetic studies of crop species. The development of simple sequence repeat (SSR) markers, which are applied across closely related cultivars, has been slow, labor-intensive, and expensive, with a low success rate. In this study, we demonstrate an efficient strategy for developing cross-species, amplifiable polymorphic SSR markers from grapevine (Vitis vinifera) based on sequence comparison and in silico polymerase chain reaction amplification of the genome sequences of grape cultivars. A total of 21 primer sets targeting unique SSR loci were screened from polymorphism and heterozygosity analyses of 13 grape cultivars and four wild species. The number of alleles varied from 3 to 12, with a mean of 7.52 alleles per locus. The lowest and highest observed heterozygosity values were 0.24 and 0.82, respectively, with an average of 0.54. Polymorphic information content values for the primer sets ranged from 0.32 to 0.86, with an average of 0.70. We successfully identified genetic relationships among 17 grape genotypes using the unweighted pair group method with arithmetic average and principal coordinates analysis of the SSR markers. The results suggest that the strategy developed in this study is applicable to high-throughput cross-amplifiable SSR marker development for the identification of genotype, genetic study, and examination of genetic diversity in grapevines.