2007 Annual Report 1a.Objectives (from AD-416) 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. 1b.Approach (from AD-416) 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. 3.Progress Report This report documents research conducted under a reimbursable agreement between ARS and NRI under a USDA-CSREES-NRI grant. Additional details of the research can be found in the report for the parent project 1265-31000-090-00D, "Development of Bioinformatics Tools for Livestock." The objectives are. 1)Design and fabricate whole-genome and custom fine-tiling comparative genomic hybridization (CGH) arrays for copy number variation (CNV) detection in cattle. . 2)Evaluate copy number polymorphisms (CNP) in normal cattle breeds. . 3)Identify CNV as well as candidate genes associated with early embryonic loss for further study. Oligonucleotide CGH arrays were designed and fabricated to cover all chromosomes with an average interval of 6 kb using the version 3 of bovine genome assembly. In the initial screening, three Holstein bulls were selected to represent major branches of the Holstein breed with some maternal linkages between branches. Dual-label hybridizations were performed using either Hereford L1 Dominette 01449 or L1 Domino 99375 as reference. Our data, for the first time, demonstrated that significant amounts of CNV exist in cattle; many CNV are common both across diverse cattle breeds and among individuals within a breed; and array CGH is an effective way to detect these bovine CNV. Selected CNVs were further successfully confirmed by independent methods using Q-PCR. The final objective is to integrate the CNP data with the single-nucleotide polymorphisms (SNP) data to accelerate genetic improvement through comprehensive prediction of genetic merit. Monitoring activities associated with this project included annual updates presented to CSREES-NRI, NPS in adjunction with Plant and Animal Genome (PAG) Conferences, and submission to CSREES-NRI of an annual progress report. This research continues to support two objectives of its related in-house project to develop biological resources and computational tools to enhance characterization of the bovine genome sequence (objective #1) and to characterize conserved genome elements and identify functional genetic variation (objective #3).