Project Number: 1265-31000-098-06
Project Type: Reimbursable

Start Date: Jan 01, 2007
End Date: Dec 31, 2009

Objective:
Design and fabricate whole-genome and custom fine-tiling comparative genomic hybridization (CGH) arrays for copy number variation (CNV) detection in cattle. Evaluate copy number polymorphisms (CNP) in normal cattle breeds. Integrate the CNP data with the single-nucleodite polymorphisms (SNP) data to accelerate genetic improvement through comprehensive prediction of genetic merit. Identify CNV as well as candidate genes associated with early embryonic loss for further study.

Approach:
Use of version 3 bovine genome assembly sequence information to design oligonucleodite CGH arrays for whole-genome screening and fine-tiling analysis. Assess CNP in normal cattle breeds (tentatively n=135 individuals from the bovine HapMap project - 9 breeds, 15 individuals each breed) using array CGH and confirm selected events using FISH and/or Q-PCR. Screen CNV associated with early embryonic loss in cattle (tentatively n=30 individuals), pinpoint their breakpoints by fine-tiling analysis, confirm selected events using FISH and/or Q-PCR and genotype ~50,000 single-nucleotide polymorphisms (SNP). All CNV results will be stored in a database with the bovine HapMap data housed locally and relevant data will be served through a public web interface.