Combination of high resolution melting (HRM) analysis and SSR molecular markers speeds up plum genotyping: case study genotyping the Greek plum GeneBank collection

Abstract

In a germplasm bank collection the conservation and characterization of genetic resources is a prerequisite in order to use the material in breeding projects aiming the creation of new cultivars. In the present study, 54 Prunus salicina domestica and Prunus domestica genotypes (including seven Greek cultivars), maintained in the ex situ National Genebank Collection of Greece, were classified using microsatellite (simple sequence repeat, SSR) markers on high resolution melting (HRM) analysis. The SSR primer pairs were chosen from the published literature as originally designed on Prunus species. This combined approach was used to genotype all plum accessions of the collection highlighting the benefits of either method (HRM and SSRs) for cultivar identification. Dendrograms for P. domestica and P. salicina and a combined one with all the genotypes assayed were produced. A total of 15 from the 19 P. domestica accessions analysed, including all the Greek accessions but 'Avgati Skopelou', were grouped into the same clade in the combined dendrogram, whereas the remaining four were dispersed into the P. salinica clades. Bayesian structure analysis confirmed that 'Avgati Skopelou' differs from the rest of the Greek plum cultivars since it was not grouped into the same cluster. The combination of HRM and SSRs, provided a considerably faster, cost-effective, closed-tube microsatellite genotyping method for molecular characterization of plum cultivars.

Identifying Pollen Donors and Success Rate of Individual Pollinizers in European Plum (Prunus domestica L.) Using Microsatellite Markers

“…A relatively high number of alleles, detected among a small set of genotypes, is a consequence of the hexaploid nature of plum as well as the fact that the analyzed cultivars have a very diverse pedigree. High values for the mean number of alleles per locus in plum is reported by numerous studies [19][20][21][22][23][24][25][26]. In the mentioned studies, this value ranged from 18.7 to 29 alleles.…”

“…Microsatellites or SSRs (simple sequence repeats) have previously been used for diversity studies of plum germplasm in France [19], Germany [20], Croatia [21], Sweden [22], Greece [23], Hungary [24], Spain [25], and Romania [26]. This marker system can also efficiently be used for parentage analyses in plum.…”

Simple Sequence Repeat Markers Reveal Hungarian Plum (Prunus domestica L.) Germplasm as a Valuable Gene Resource

“…All genotypes were clearly distinguished with the seven SSRs used in this study, indicating that microsatellite analysis is an appropriate tool for the identification and fingerprinting of plum cultivars. Merkouropoulos et al (2017) also used a total of seven microsatellite markers that were enough to discriminate 54 plum cultivars.…”

Genetic assessment of the pomological classification of plum Prunus domestica L. accessions sampled across Europe

“…Several SSR-based studies have focused on the comparison of local plum germplasm to sets of international reference cultivars (Horvath et al 2011;Halapija Kazija et al 2014;Sehic et al 2015;Merkouropoulos et al 2016;Makovics-Zsohár et al 2017;Urestarrazu et al 2018). Not surprisingly, a major division was found between local germplasm belonging mainly to subsp.…”