Submitted to: Trade Journal Publication
Publication Type: Trade Journal
Publication Acceptance Date: 9/12/2006
Publication Date: 1/19/2007
Citation: Lu, J. 2007., Hunter, W.B. 2007. Moving towards disease resistance in grapes. Wine East. January-February 2007. pp 10-15, 52, 53. Interpretive Summary:
Technical Abstract: We produced the North American Native Grape Genome database to host grape research data for the U.S. viticulture industry. Within this database we have produced and identified hundreds of genetic markers (~800) which are being screened to expedite the selection of new grape varieties with increased disease and pest resistance. The need and development for disease and insect resistant grape varieties has become more intense with the spread of the glassy-winged sharpshooter, GWSS, (Homalodisca vitripennis) into southern California. The GWSS has a wider host range, prefers to feed in cultivated vineyards, and tree crops, and can disperse long distances up to five miles at a time. The changing dynamics of the epidemiology of Pierce’s disease, has thus focused on the management of the insect vector more intensely. As new grape varieties are being produced, grape breeders can now also include grape characteristics that may reduce the feeding and/or preference of leafhoppers such that Pierce’s disease becomes less of an economic problem. Discussed are the successful approaches being used to develop new grape varieties which includes: 1. Traditional breeding: hybridization and seedling selection: parental selections, seed production, selection for desired traits among the seedlings. 2. Induced mutations and selection. 3. Clonal selection. 4. Molecular breeding: using molecular methods to speed up the process of traditional plant breeding. These methods result in the movement of desirable grape genes from one grape variety into another, and reduces the amount of time and costs normally associated with traditional plant breeding, seed production, and variety selection. We have produced and sequenced nearly 25,000 expressed sequence tags, EST’s, which are small genetic sequences of the genes being expressed inside the growing grapevines (V. shuttleworthii, and Noble). These sequences were analyzed in silico using computers, to identify the proteins that are produced. The protein sequences are then compared to the GenBank database (http://www.ncbi.nlm.nih.gov/. By isolating these sequences from the plants, we have identified over 800 sequences for use as genetic markers, and have identified specific genes associated with disease resistance, fruit quality, drought tolerance, insect resistance and more. Over 25,906 cDNA clones were sequenced, resulting in ~19,200 high-quality ESTs. After sequence assembly the cDNAs resulted in 12,440 total sequences, including both contiguous sequences and singlets. The putative protein transcript of each assembled sequence was annotated based on the biochemical function of matching gene sequences using BLASTX, TBLASTX, and BLASTN analyses, GenBank, nr ESTdb. The subsequent unigene set produced ~6,000 sequences which had significant identities with homologous genes in the GenBank’s database. The remaining ~4000 of the cDNA’s showed ‘no significant homology’ in either the non-redundant protein or nucleic acid databases, demonstrating that de novo EST sequencing projects still provide new information to the scientific community. The grape gene expression data set advances current research efforts, and provide the focus for the identification of genes and physiological processes of North American grapes. The genomic information and database is also being used as a teaching tool in one of the first Bioinformatics programs at an 1890’s University aimed at increasing minority participation in the fields of Bioinformatics and Genomics.