Genetic diversity, structure and parentage analysis within several European apple germplasm collections assessed by microsatellite markers

Cultivated apple (Malus × domestica) is the most important fruit crop of the temperate regions worldwide. The accurate phenotypic and genetic characterization of apple genetic resources is essential for enlarging the genetic bases of breeding populations. Here we investigated the genetic diversity and structure of almost 2,700 European dessert apple accessions (old cultivars) originating from 12 germplasm collections located in 9 European countries, Russia, and Kyrgyzstan using 16 common SSR markers. Funding derived from both national and European (FruitBreedomics) projects. Priority was given to accessions chosen to be both diverse and representative of regional/national landraces. Genotyping made the identification and clarification of many redundancies, among accessions with different names but identical SSR profiles, possible both within and between collections. A total of 1,750 unique diploid genotypes (unique SSR profiles) were retained for further analyses. The average allelic diversity was very high (Na ~23), as were the observed and expected heterozygosities (0.81-0.83). The genetic structure of these accessions was studied by Factorial Component Analysis (FCA) and Structure software. A slight differentiation according to the geographic origin of the accessions (when known) was found (Fst = 0.021 +/-0.003), when subdividing the accessions into 3 large regions (West, South, North-East). Three groups (K=3) were also identified by Structure, but did not fully coincide with the pre-defined geographic regions. Parentage analyses made it possible to infer parents of several old cultivars. Overall, the genetic diversity was very high, but with a weak structure confirming large gene flow across Europe.