Genetic diversity study of modern Russian apple (Malus x domestica Borkh.) cultivars by the SSR loci analysis

SSRs are one of the most suitable DNA-markers for assessment of genetic diversity of plant genetic resources. Microsatellites were used for development of saturated genetic maps of apple (Malus × domestica Borkh.) as well as for wide range of genetic diversity studies. Our study was aimed on the investigation of the genetic relationship within subcollection of modern Russian apple cultivars. Polymorphism of 12 microsatellite loci was estimated for 31 apple cultivars from the SKZNIISiV collection of genetic resources. These cultivars have been bred in North Caucasian Regional Research Institute of Horticulture and Viticulture (SKZNIISiV) and All-Russian Research Institute of Fruit Crop Breeding (VNIISPK). SSR-markers CH01f03b, CH01h01, CH01h10, CH02c06, CH02d08, CH04e05, CH05f06, CH01f02, CH02c11, Hi02c07, CH02c09 and CH03d07, which are recommended by Fruitbreedomics, the European consortium, were used in the study. According to the data of SSR-analysis from 5 to 10 alleles per locus were detected, with an average value of 7.75 alleles per locus. A total of 93 alleles were detected for all 12 loci. All apple cultivars showed individual, distinct SSR-profiles. Comparison with the data on the genetic diversity of the world apple tree gene pool suggests that the SSR-loci polymorphism in studied set of the apple cultivars is relatively high. Expected (He) and observed (Ho) heterozygosity varied within the ranges of 0.548-0.897 and 0.602-0.827 for Ho and He, respectively. The average values of these indexes are Ho = 0.786 and He = 0.755. PIC value ranged from 0.571 to 0.806, and 9 loci showed PIC value higher than 0.712. Results of UPGMA-analysis are consistent with the level of genetic heterogeneity of the studied cultivar set. Five clusters were determined. Distribution of cultivars into clusters in most cases is consistent with their genealogy. For example, Svezhest’ cultivar, formed a distinct cluster № 1, as well as cultivars Imrus and Zimnee utro which formed cluster № 5 are originated from the cultivars, which are not presented as the parental forms of any studied cultivars. Cultivars of VNIISPK breeding such as Solnishko, Stroevskoe, Yubilei Moskvy, Afrodita and Start, which formed distinct cluster № 3 have one common parental cultivar. The structure of dendrite obtained when performing clustering on the results of SSR-analysis may be due to large number of unique alleles studied in genotypes that in turn is due to the high genetic diversity within the studied set of cultivars. At the same time, the fact of incorporation of cultivars with the same genealogy in the same clusters confirms the high significant genetic similarity within groups of such varieties. Results of the study allows to assess the level of the genetic diversity within the set of modern apple cultivars as well as can be used for confirmation of genealogy of apple cultivars and hybrids in the case of disputes, as well as for identification of varieties