Genetic Diversity of Armenian Grapevine (Vitis vinifera L.) Germplasm: Molecular Characterization and Parentage Analysis

Simple Summary The knowledge of genetic diversity and relatedness among grapevine varieties is important for recognizing gene pools. One of the major goals of the present large-scale study was to evaluate the level and relationships of existing genetic diversity across Armenia, aiming to identify genotypes that could provide genetic insights into the Armenian grapevine germplasm structure. A combination of nuclear microsatellite markers and ampelography proved useful to determine the identity of collected samples recovered from old vineyards and home gardens. Synonyms, homonyms, alternative spellings, and misnomers were clarified. First-degree genetic relationships between autochthonous varieties were partly uncovered. Missing parents might still exist in old vineyards but were not sampled yet or might have disappeared over time. The continuation of prospections to fill that gap is planned. The high number of new bred varieties included in the study reflects the enormous breeding activity in Armenia. The high number of alleles, high level of observed and effective heterozygosity, and presence of female APT3-allele 366, which is absent in western European cultivars, illustrate the huge diversity of the Armenian germplasm. Presumably, these findings are related to recurrent introgression of Vitis sylvestris into the cultivated compartment during domestication events. So far, the present study is the first most representative and comprehensive analysis of Armenian grape germplasm. Armenia is an important country of origin of cultivated Vitis vinifera subsp. vinifera and wild Vitis vinifera subsp. sylvestris and has played a key role in the long history of grape cultivation in the Southern Caucasus. The existence of immense grapevine biodiversity in a small territory is strongly linked with unique relief and diverse climate conditions assembled with millennium-lasting cultural and historical context. In the present in-depth study using 25 nSSR markers, 492 samples collected in old vineyards, home gardens, and private collections were genotyped. For verification of cultivar identity, the symbiotic approach combining genotypic and phenotypic characterization for each genotype was carried out. The study provided 221 unique varieties, including 5 mutants, from which 66 were widely grown, neglected or minor autochthonous grapevine varieties, 49 turned out to be new bred cultivars created within the national breeding programs mainly during Soviet Era and 34 were non-Armenian varieties with different countries of origin. No references and corresponding genetic profiles existed for 67 genotypes. Parentage analysis was performed inferring 62 trios with 53 out of them having not been previously reported and 185 half-kinships. Instability of grapevine cultivars was detected, showing allelic variants, with three and in rare cases four alleles at one loci. Obtained results have great importance and revealed that Armenia conserved an extensive grape genetic diversity despite geographical isolation and low material exchange. This gene pool richness represents a huge reservoir of under-explored genetic diversity.