Patterns of SNP distribution provide a molecular basis for high genetic diversity and genetic differentiation in Vitis species

Grape (Vitis L.) is one of the most economically valuable fruit crops in the world. The molecular basis for high genetic diversity and genetic differentiation thus conferring broad adaptability in the Vitis genus remains elusive. Genetic patterns in Vitis were comprehensively characterized by re-sequencing of 6862 nuclear SNPs in this study. Nucleotide diversity (π = 0.0073), genetic differentiation (pairwise differences, 0.24) and SNP variation in Vitis species were relatively high compared to most woody plant species. Molecular variance among accessions within species (FIS = 0.369) and among 30 species (FST = 0.511) suggested strong population structure in Vitis (P 95 %) of minor SNPs to engender high differentiation among species thus high genetic diversity in the whole genus. This confers potentially broad adaptability thus a broad base for natural selection in this genus. Species from three geographical regions were discerned into independent quadrants in the principle coordinate analysis (PCoA) plot and their clustered patterns suggested that their molecular identities represented geographical origins of Vitis species. Species extinction will be an irreversible loss for breeding and genetic conservation. Species with low diversity, low heterozygosity, and high agronomical value should be given priority for conservation. Survey of species-specific SNPs will facilitate germplasm conservation and grape breeding programs. This study greatly adds to our knowledge of genetic patterns and molecular bases for ecological habits of Vitis species and provides valuable information for germplasm conservation and utilization, and grape breeding.