SNP detection and genotyping in Vitis

Single Nucleotide Polymorphisms (SNPs) are a highly abundant class of DNA polymorphisms in plant and animal genomes. SNPs can occur anywhere in the genome, and can contribute directly to a phenotype or can be associated with a phenotype as a result of linkage disequilibrium, making them highly useful tools for studying the genetics of complex phenotypic traits. An understanding of the patterns of SNP diversity and frequency within the Vitis genome will aid the utilization of SNPs for molecular breeding and genomics research in grape. Our objectives were to estimate the SNP genotype and haplotype frequency within Vitis vinifera as well as several additional North American Vitis species. The DNA sequence diversity of 16 loci derived from expressed sequence tags and full-length cDNA sequences was measured. Each locus Was sequenced from 10 individuals representing Vitis vinifera and 4 additional North American Vitis species. The data indicated that Vitis vinifera has one SNP approximately every 34 bp. The haplotype frequency was approximately 15/kb. Additional loci and genotypes are now being sequenced and the identified SNPs are being tested on a larger pool of un-sequenced genotypes. Many high-throughput assays exist for the large-scale genotyping of SNPs. The testing of SNP genotyping assays and the utility of these assays for grape breeding and genomics research will be discussed.