Progress 10/01/12 to 09/30/13
Outputs
Progress Report Objectives (from AD-416): To conduct genetic association analysis in grape for variation in amino acid composition of ripening berries using a population genomics approach in a large collection of V. vinifera genotypes. Approach (from AD-416): The funding proposal comprises a large multi-faceted project to answer several questions related to grape and yeast genomics. A central question of the proposal is to more closely examine changes in vine and berry amino acid composition and the effect on the resultant fruit/wine quality. The portion of the work to be conducted by C. Owens is to conduct a genetic association analysis for amino acid composition in a sub-set of the U.S. national grape germplasm collection. This work will also take advantage of recent advances in SNP genotyping technologies developed by ARS scientists. Additional funding will expand the scope of the in-house work I perform pursuant to Objective 1 of the CRIS project plan and contribute to the genetic dissection of important traits of grape, enabling the more rapid and efficient development of improved grape varieties. Objective 1 of the CRIS Project Plan is to �Determine some of the key genetic factors controlling environmental adaptation and fruit quality differences among cultivated grapes and between cultivated and wild grapes�. To help determine the genetic basis for variation in the accumulation of nitrogenous compounds, specifically amino acids in developing berries, fruit tissue was collected for 374 accessions from the USDA clonal germplasm repository in Davis, CA. These accessions were selected based on several criteria: equal representation of both table and wine grape gene pools, full representation of the world�s growing regions, and maximization of genetic diversity based on molecular marker-derived diversity values. Two pools of molecular markers were utilized to genotype the diverse panel of 374 accesssions of Vitis vinifera: 1) approximately 6000 SNPs developed from the Vitis9K SNP chip and 2) a large number of randomly generated SNP markers developed through a restriction-enzyme anchored whole genome sequencing approach that provide in excess of 200K additional SNPS randomly distributed throughout the genome. Amino acid concentration was measured by the University of British Columbia. Genome-wide association mapping was conducted using the structured association module of the EMMA software package to test for genetic associations of each individual aromatic compound. Results indicated substantial variation in amino acid concentration and content as well as variation in individual terpenoid compounds. Genetic association testing was largely unsuccessful due to limitations in marker density. Results from this project are currently being drafted for publication.
Impacts
(N/A)
Publications
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Progress 10/01/11 to 09/30/12
Outputs
Progress Report Objectives (from AD-416): To conduct genetic association analysis in grape for variation in amino acid composition of ripening berries using a population genomics approach in a large collection of V. vinifera genotypes. Approach (from AD-416): The funding proposal comprises a large multi-faceted project to answer several questions related to grape and yeast genomics. A central question of the proposal is to more closely examine changes in vine and berry amino acid composition and the effect on the resultant fruit/wine quality. The portion of the work to be conducted by C. Owens is to conduct a genetic association analysis for amino acid composition in a sub-set of the U.S. national grape germplasm collection. This work will also take advantage of recent advances in SNP genotyping technologies developed by ARS scientists. Additional funding will expand the scope of the in-house work I perform pursuant to Objective 1 of the CRIS project plan and contribute to the genetic dissection of important traits of grape, enabling the more rapid and efficient development of improved grape varieties. Objective 1 of the CRIS Project Plan is to �Determine some of the key genetic factors controlling environmental adaptation and fruit quality differences among cultivated grapes and between cultivated and wild grapes�. To help determine the genetic basis for variation in the accumulation of nitrogenous compounds, specifically amino acids in developing berries, fruit tissue was collected for 374 accessions from the USDA clonal germplasm repository in Davis, CA. These accessions were selected based on several criteria: equal representation of both table and wine grape gene pools, full representation of the world�s growing regions, and maximization of genetic diversity based on molecular maker-derived diversity values. Two pools of molecular markers were utilized to genotype the diverse panel of 374 accesssions of Vitis vinifera: 1) approximately 6000 SNPs developed from the Vitis9K SNP chip and 2) a large number of randomly generated SNP markers developed through a restriction-enzyme anchored whole genome sequencing approach (GBS) that provide in excess of 200K additional SNPS randomly distributed throughout the genome. Amino acid concentration were measured by the University of British Columbia. Genome-wide association mapping was conducted using the structured association module of the EMMA software package to test for genetic associations of each individual aromatic compound. Data analysis is continuing.
Impacts
(N/A)
Publications
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