Genotype confidence percentage of SSR HRM profiles as a measure of genetic similarity in Rosmarinus officinalis

Abstract

Rosemary (Rosmarinus officinalis L.) is a highly allogamous plant with few genomic resources available. Among these, a discrete set of nuclear and cytoplasmic microsatellite markers is counted. High resolution melting (HRM) is a closed-tube technique widely used for sequence polymorphism detection. Until now, HRM data analysis in plants has been conducted reporting melting profiles to known allelic assets. Even for preliminary studies on general genetic diversity, laborious workflows have been proposed for HRM genotyping of microsatellite's indels as well as of SNPs. Genotype confidence percentage (GCP) of HRM curves is the most commonly used statistical transformation of Euclidean distance between HRM curves to determine whether two curves are identical or not. In the present study we tested an analysis workflow that implies the use of GCPs of HRM profiles as a direct measure of the genetic similarities on SSR loci, bypassing therefore genotyping. The comparison between capillary electrophoresis and HRM-GCPs data demonstrates the efficiency of this new technique in detecting genetic differences between rosemary populations. This method can be used for determining overall genomic similarity in phylogenetic and ecological studies. It is cost and time effective, suitable to complete automation and can be used in other allogamous plants as well.