Grapevine Phenological Quantitative Trait SSR Genotyping Using High-Throughput HRM-PCR Analysis

Discrimination among grapevine varieties based on quantitative traits,such as flowering, veraison and ripening dates is crucial for variety selection inthe context of climate change and in breeding programs. These traits are undercomplex genetic control for which 6 linked SSR loci (VVS2, VVIn16, VMC7G3,VrZAG29, VMC5G7, and VVIB23) have been identified. Using these markers inHRM-PCR analysis, we assessed genetic diversity among a large collection of192 grapevine varieties. The grapevine germplasm used encompasses the majorityof Greek vineyard with 181 varieties, 3 prominent foreign varieties and 11 varieties of Palestinian origin. The SSR markers used were highly polymorphic, displaying unique melting curves for unusually higher number of samples thangenerally observed in SSR analysis. This prompted us to examine sequence composition for selected samples and found that variation present as SNPs in theflanking sequences of SSR motifs was responsible for the observed polymorphism. Hence, HRM-PCR proved to be a tool of higher analytical power to distinguish genotypes surpassing the discrimination power of conventional gel-basedSSR analysis. The study provides a better understanding of genetic variation ofSSR marker loci associated to phenological traits in grapevine varieties, signifying an analytical methodology that may be of higher discrimination power indetection of polymorphism for utilization in breeding programs.