Microsatellite inferred genetic diversity and structure of Western Balkan grapevines (Vitis vinifera L.)

A collection of 196 grapevine samples from five countries of the Western Balkan region, representing local and traditional cultivars, was genotyped with 22 SSR markers. Identity analysis revealed 125 unique genotypes, which were further used for diversity assessment. The average number of alleles per locus detected was 11 ± 3.53, ranging from 6 to 21. The low cumulative probability of identical genotypes (2.96 × 10−20) shown in this study implies an even distribution of alleles within the analyzed set of grapevines and a sufficient number of loci. On the basis of the discriminatory power of each SSR, a set of five markers (VVMD5, VVMD7, VVMD28, VChr3a, and VChr8b) was determined as sufficient for high-throughput discrimination of the target cultivars. The maximum discriminating power was evidenced for loci VVMD28 and Vchr8b (0.96, 0.94, respectively). A core collection covering the entire genetic diversity resulted in a set of 60 genotypes representing approximately 50 % of the samples from each country. Structure clustering of Balkan and West European cultivars resulted in four well distinct groups identified according to the classification of Negrul (1946). The lowest level of admixed genotypes was assigned for grapevines from Bosnia and Herzegovina (61 %) and the highest for Serbian (87 %) grapevines. In terms of grape use, the wine cultivars were divided into three groups and the fourth group was intermixed, with half wine and half table grapes. The highest Nei’s genetic distance (0.22) was discovered between Slovenian and Macedonian cultivars, while the lowest (0.09) was between Slovenian and Serbian cultivars. Macedonian cultivars were genetically most distant from the others (0.17). A similar pattern of differentiation among populations is seen with distance-based clustering. Analysis of molecular variance revealed only 1 % of genetic variation among groups of different origin, while the variation among individuals within geographical groups and within individuals explained 13 and 86 % of the total variation, respectively.