Single nucleotide polymorphism (SNP) analysis reveals ancestry and genetic diversity of cultivated and wild grapevines in Croatia

Background Croatia is a geographically small country, but it has a remarkable genetic diversity of cultivated and wild grapevines. Local germplasm has been characterised by microsatellite markers, but a detailed analysis based on single nucleotide polymorphisms (SNPs) is still lacking. Here we characterize the genetic diversity of 149 accessions from three germplasm repositories and four natural sites using 516,101 SNPs to identify complete parent-offspring trios and their relations with spontaneous populations, offering a proof-of-concept for the use of reduced-representation genome sequencing in population genetics and genome-wide association studies. Results Principal component analysis revealed a clear discontinuity between cultivated ( V. vinifera ) and spontaneous grapevines, supporting the notion that the latter represent local populations of the wild progenitor ( V. sylvestris ). ADMIXTURE identified three ancestry components. Two vinifera components are alternatively predominant in cultivars grown either in northern Adriatic Croatia and Continental Croatia or in Dalmatia (i.e. central and southern Adriatic Croatia). A sylvestris component, which is predominant in accessions from natural sites, is a minor ancestry component in cultivated accessions. TREEMIX provided evidence of a unidirectional gene flow from the vineyards to natural sites, suggesting that the introduced domesticated germplasm has colonized local wild populations stronger than vice versa . Identity-by-descent analysis indicated an extensive kinship network, including 14 complete parent-offspring trios and involving only cultivated accessions, and 6 full-sibling relationships, and invalidated a presumed pedigree of the most intriguing ones, the one of ‘Plavac Mali’. Despite this strong population structure, significant association was found between 143 SNPs and berry skin colour and between 2 SNPs and leaf hairiness, across two known QTL regions. Conclusions The genetic separation between Croatian cultivars and sylvestris excluded the hypothesis that cultivars originated from independent events of local domestication. On the other hand, the evidence of a crop-to-wild gene flow, especially in but not limited to the Modro jezero population, signals the need for an urgent adoption of conservation strategies that preserve the genetic integrity of wild relatives. The SNP panel enables enhanced parentage assignment for grapevine cultivars historically grown in Croatia.