Abstract: Sweet cherries can be grafted on a wide range of rootstocks belonging to genus Prunus. Identification of sweet cherry rootstocks using morphological traits is almost impossible particularly during the dormant season, yet it is very important for the grower to know exactly the rootstock as this has a major influence on cultivar performance and agricultural practices. However, DNA based molecular analysis carried out on actively growing shoot tips, leaves or dormant buds provides a good opportunity to reliably distinguish rootstocks. Herein, we have integrated High Resolution Melting (HRM) analysis, coupled with five SSR markers in order to facilitate the identification of the most popular sweet cherry rootstocks in Greece. The five SSR loci used were highly informative and generated a unique melting curve profile of microsatellites for each of the six rootstocks tested. In particular, one marker, BPPCT002, with six HRM profiles was sufficient to discriminate all sweet cherry rootstocks studied, highlighting its potential use for rootstock identification. Hence, this assay provided a flexible, cost-effective and closed-tube microsatellite genotyping method well suited to sweet cherry rootstock identification.
Abstract:
Single nucleotide polymorphisms (SNPs) provide an important tool for cultivar identification in studies of genetic diversity, but until now, the time-consuming and costly nature of DNA sequencing has limited the identification of new markers. Herein, we describe the application of high-resolution melting (HRM), a recent enhancement to traditional DNA melting analysis, for the characterization of polymerase chain reaction products and the identification of nine gene-based SNPs for distinguishing the main Greek sweet cherry cultivars. The expected heterozygosity value of nine SNPs averaged at 0.518. The combined power of discrimination for the SNP markers was 0.999969. The ability of HRM to accurately discern nucleotide changes in a DNA sequence makes it a cost- and time-effective alternative to traditional sequencing for the detection of gene-based SNPs.
