Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Proceedings
Publication Acceptance Date: 10/6/2003
Publication Date: 1/11/2004
Citation: OWENS, C.L., BALDO, A.M. MINING THE EST DATABASE AND GENOMIC SEQUENCES FOR SNP DISCOVERY IN VITIS. PLANT AND ANIMAL GENOME ABSTRACTS. 2004.
Technical Abstract: Single nucleotide polymorphisms (SNPs) are a highly abundant class of DNA polymorphisms in plant and animal genomes. As molecular markers, SNPs can be used to saturate the linkage map with markers in gene rich regions. Notably, SNPs can be tied directly to functional polymorphisms, and can be associated via linkage disequilibrium to both simply and complexly inherited traits. Levels of heterozygosity are high within both wild and cultivated Vitis germplasm and initial estimates suggested that SNP frequency averaged 1 SNP per 45 base pairs of coding sequence. A larger scale study to discover and validate SNPs across the V. vinifera genome was conducted by two methods: direct sequencing and alignment of the genomic regions corresponding to full length cDNAs, and by mining the over 130,000 Vitis ESTs. The majority of publicly available Vitis ESTs were derived from only two cultivars, 'Chardonnay' and 'Cabernet Sauvignon'. However, the high level of eterozygosity between these cultivars has resulted in a high frequency of putative SNPs. Validation of these EST derived SNPs as well as initial construction of an EST based transcript map will be discussed.