Project Number: 1910-21220-004-25
Project Type: Trust

Start Date: May 01, 2010
End Date: Dec 31, 2012

Objective:
Adapt a genotyping strategy to obtain 50,000 markers per seedling and apply this strategy for discovering markers associated with powdery mildew resistance and other important traits. Develop a pipeline for applying molecular markers in public grape breeding programs at no cost to the breeder.

Approach:
DNA will be provided by USDA-ARS from 400 individuals of the Vitis aestivalis mapping population. Whole genome amplification (WGA) will be completed. To select a restriction enzyme for preferential sequencing of gene-rich regions, an in silico digestion of the V. vinifera ‘Pinot noir’ genome sequence will be completed. Then the chosen restriction enzyme will be used to apply established restriction sequencing protocols for pooled, barcoded samples. A computational pipeline modified from the one used in the USDA-ARS maize hapmap project will be used to assign SNPs to individual seedlings and filter out low quality SNPs. For the new SNP markers developed during this project, a redundant, locus-based assay will be developed and applied using SNPlex or a similar 24-48 multiplex technology. Additional publicly available markers can be immediately applied for marker assisted breeding. DNA will be provided by USDA-ARS for up to 1000 progeny and by Cornell for up to 1000 progeny. After WGA, the following existing markers will be screened for segregation and then across the entire population when appropriate: Run1, Rpv1, V. cinerea, V. romanetii, Ren1, and Regent.