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United States Department of Agriculture

Agricultural Research Service

Title: Discovery of Csnp Between Vitis Shuttleworthii and Vitis Vinifera 'cabernet Sauvignon' Ests, Prediction of Subsesquent Amino Acids and Protein Function Changes

item Huang, Hong - FLORIDA A&M UNIV.
item Bradley, F. - FLORIDA A&M UNIV.
item Ren, Z. - FLORIDA A&M UNIV.
item Hunter, Wayne
item Dang, Phat
item Liang, J. - FLORIDA A&M UNIV.

Submitted to: American Society of Enology and Viticulture Annual Meeting Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: May 17, 2005
Publication Date: July 12, 2005
Citation: Huang, H., Bradley, F., Ren, Z., Hunter, W.B., Dang, P.M., Liang, J. 2005. Discovery of CSNP between Vitis shuttleworthii and Vitis vinifera 'Cabernet Sauvignon' ESTs, prediction of subsesquent amino acids and protein function changes [abstract]. American Society of Enology and Viticulture Annual Meeting Abstracts.

Technical Abstract: Single nucleotide polymorphisms (SNPs) are the most common type of alleles found within and between varieties of a crop species. These polymorphisms could be used as genetic makers for genotyping, variety identification, phylogenetic tree construction, and gene mapping. In this research, SNPs were isolated between ESTs of V. shuttleworthii, a highly disease-resistant grape species which originated in the southeastern United States, and V. vinifera, a predominant grape grown world-wide but highly susceptible to most diseases found in the southeastern U.S. A set of 9,831 EST sequences generated from PD infected leaves of ‘Cabernet Sauvignon’ (retrieved from the NCBI database) and 10,704 ESTs from V. shuttleworthii were used for the SNP analysis. Contigs were assembled among the 20,535 combined ESTs, from which 1,614 SNP sites were identified in 148 contigs. The SNP frequency was estimated in an average of 1 SNP per 83 bp among the SNP-contigs. When blasted against the NCBI non-redundant protein database, 87 out of the 148 contigs were positively matched with proteins related to disease resistance. The high percentage of the SNP-contigs correlated to disease resistance found between V. shuttleworthii and V. vinifera warranted further investigation of the single nucleotide substitutions and amino acid changes among disease-resistant related proteins. The amino acid analysis showed that about half of the single nucleotide substitutions resulted in amino acid changes. Alterations in 3D protein structure were also found among the putative proteins with ‘amino acid mutations’. Identification and analysis of the cSNPs by comparison of V. shuttleworthii and V. vinifera ESTs is a viable alternative approach to isolate genes associated with disease resistance in grapes.

Last Modified: 4/20/2015
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