Discovery and characterization of SNPs in Vitis vinifera and genetic assessment of some grapevine cultivars

Single nucleotide polymorphisms (SNPs) are among the current generation of molecular markers. SNPs occur at high frequencies in both plant and animal genomes and can provide broader genome coverage and reliable estimates of genetic relevance. In this study, 144 sequences, amplified by 9 pairs of primers from 16 cultivars of Vitis vinifera, were cloned. The sequence alignment of the 9 group sequences derived from 16 sample cultivars yielded 154 SNPs in a combined length of 3443 bp genomic sequences. SNPs were discovered with an average frequency of one SNP per 23 bp. The distribution of the SNPs comprised of 70% transitions, 20% transversions, 8% InDels and 2% others. A phylogenetic tree constructed from these data showed that all the 16 cultivars were separated well and grouped differently in the entire dendrogram derived from the SNP data, therefore confirming that single nucleotide polymorphisms could be an efficient and powerful method for grapevine cultivar identification and genetic diversity analysis in grapevine.