HRM Efficiency and Limitations for High-Throughput SSR Genotyping: A Case Study Using Grapevine Flavor-Linked Markers

Abstract

High resolution melting is a simple, efficient and cost-effective analysis, compared to alternative approaches used for SSR genotyping. However, it has not been evaluated yet, for its efficiency in high-throughput SSR genotyping, when large sample collections are to be analyzed. In such an approach, we tested its application to discriminate flavor-linked SSR markers, in a large collection of 211 grapevine varieties. Flavored and non-flavored varieties shared common alleles for the three markers VVMD27, VVC6 and VMC7G3, tested in this study. This is indicative of the redundant nature of the marker-linked QTLs along with other genetic determinants for expression of the flavor character in grapevine. The results showed that the three markers were highly polymorphic, detecting also SNPs in the sequences flanking SSR motifs. Such a high level of polymorphism was detected using the semi-automatic approach of HRM. Consequently, HRM proved to be powerful for distinguishing SSR genotypes, although repeated reference samples were needed for correct grouping, presenting a possible limitation of the method.