Genetic diversity and phylogenetic relationships among citrus germplasm in the Western Caucasus assessed with SSR and organelle DNA markers

Characterization of genetic diversity in germplasm collections is fundamental for an efficient management and utilization. The citrus germplasm in the Western Caucasus represent one of the most northerly citrus collections. The collection contains numerous cultivars specifically selected for frost-tolerance, which are valuable as genetic resources for citrus breeding programs worldwide. Currently, the field citrus collection consists of more than 200 accessions, but their taxonomic assignment, genetic structure and diversity has not been clarified. In our study, 130 different citrus accessions including 24 species or interspecific hybrids maintained and bred at the Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences (FRC SSC RAS) were genetically investigated using 13 biparental (ncSSR) and 13 uniparental (orgDNA) markers. After STRUCTURE analysis, the single accessions were allocated to eight genetic clusters and their relationships were elucidated. This phylogenetic relationship was also confirmed by principal coordinates analysis (PCoA) and by dissimilarity analysis using DARwin. We identified twenty accessions as misclassified and reassigned them to the correct species. For the remaining 110 accessions the taxonomical assignment could be confirmed. A high genetic diversity was observed on basis of the nuclear ncSSR markers, while the detection of 19 different haplotypes allowed the distinct differentiation of the accessions within our collection. Our study showed that the combination of ncSSR and orgDNA was an efficient tool to estimate the genetic diversity, genetic structure and phylogeny in the FRC SSC RAS citrus germplasm collection. The results obtained are valuable for future management of the collection and the usage of individual accessions as genetic resource for citrus cultivar and rootstock breeding, especially in colder regions.