HRM analysis of chloroplast and mitochondrial DNA revealed additional genetic variability in Prunus

- Molecular characterization of 22 genotypes belonging to 10 Prunus species.
- Analysis of predicted and newly discovered SNPs and SSRs chloroplastic and mitochondrial markers.
- Higher discrimination power using HRM.
- The analysis of nine loci allowed to identify two indels, 37 SNPs and three repeat motif variation.
- Data represent the first overview of cytoplasmic markers using HRM.

The genus Prunus taxonomy has been widely studied using different molecular markers. Among the several markers used for studying the genetic variability on Prunus, extranuclear DNA analysis is a useful tool for population and evolutionary biology studies. High resolution melting (HRM), considered a powerful method to easily detect genetic differences among sequences, was used to analyse a group of 22 genotypes belonging to 10 Prunus species using twelve newly designed chloroplastic single nucleotide variants (SNVs), ten chloroplastic SSRs, and seven universal mitochondrial markers already available in literature. The analysis allowed the investigation of the predicted and newly discovered SNVs and the detection of more alleles because of the variability found in the sequences flanking cpSSR repeat motifs. Overall, five newly discovered chloroplastic markers, four cpSSRs, and three mitochondrial markers, referring to nine loci, allowed the identification of two indels, 37 SNVs, and three repeat motif variation. The results allowed the unambiguous separation of Prunus genotypes at the species as well as at the cultivar level, confirming the discrimination power of the HRM derived markers and previous results on the phylogenetic relationships within the Prunus genus. The developed panel of SNVs and SSR cytoplasmic markers can be employed to identify different varieties and hybrids using the HRM approach without the requirement of the post-PCR procedures required in traditional molecular markers analysis.