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United States Department of Agriculture

Agricultural Research Service

Title: Genome Structure and Functional Annotation by Massive Est Analysis of Vitis Shuttleworthii Grape and Comparative Genomics Analysis with Vitis Vinifera Ests

item Lu, Jiang - FLORIDA A&M UNIV.
item Huang, Hong - FLORIDA A&M UNIV.
item Ren, Z. - FLORIDA A&M UNIV.
item Bradley, F. - FLORIDA A&M UNIV.
item Hunter, Wayne

Submitted to: American Society of Enology and Viticulture Annual Meeting Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: May 20, 2005
Publication Date: July 12, 2005
Citation: Lu, J., Huang, H., Ren, Z., Bradley, F., Hunter, W.B., Dang, P.M. 2005. Genome structure and functional annotation by massive EST analysis of Vitis shuttleworthii grape and comparative genomics analysis with Vitis vinifera ESTs [abstract]. American Society of Enology and Viticulture Annual Meeting Abstracts.

Technical Abstract: A functional genomic project with emphasis on identifying and isolating disease resistant genes and genetic markers was jointly initiated at the Center for Viticulture, Florida A&M University and the USDA-ARS Horticultural Laboratory at Fort Pierce, Florida. Vitis shuttleworthii, one of the most disease and pest resistant grape species originated from the southeast United States, was chosen for the EST sequencing. The project is gearing towards to: 1) identify and isolate genes for disease resistance from V. shuttleworthii grapes; 2) conduct comparative genomics analysis between V. shuttleworthii and V. vinifera grapes and other Vitis species; 3) develop SSR and SNP markers for gene mapping and genotyping. Among the 25,000 ESTs sequenced from a single cDNA library derived from mixed tissues, about 78% of the first 2,000 ESTs were unigenes. When the number of ESTs reached 10,000, about 30% of the ESTs yielded additional new genes, and about 25% of them were new additions as the ESTs increased to 15,000. The percentage of new genes derived from the ESTs decreased as the number of EST increased. When compared to the V. vinifera ESTs and unigenes, about 18% of the V. shuttlwworthii ESTs/unigenes did not find homologies to the 160,000 ESTs and unigenes of V. vinifera. High frequency of SNPs were detected between the V. shuttlwworthii and the V. vinifera genomes. Functional analysis revealed that high percentage of the SNPs found between V. shuttleworthii and V. vinifera are correlated to disease resistance. About 3% of the ESTs contained SSRs, and 14% of which are related to disease resistance.

Last Modified: 4/21/2015
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