1a. Objectives (from AD-416)
The objective of this cooperative research project is to design tools to process and annotate livestock genome sequences, including gene expression data, single nucleotide polymorphisms for breed specific Haplotype map development and also support the on-going genomic selection, genome-wide association analysis and QTL fine mapping projects.
1b. Approach (from AD-416)
Software will be developed or adapted for use in annotating whole genome sequence data being generated as part of international collaborations that include ARS, including gene prediction, use of comparative mapping information, and identifying novel genetic markers (polymorphisms) and positional candidate genes. Emphasis should be given to problems specific to post-analysis of the bovine genome sequencing project, as BFGL is leading those efforts and development of tools with wide utility for the community is a priority. Tools will be developed or adopted to quickly identify positional candidate genes from QTL map position integration with signatures of selection, gene expression and breed specific polymorphism information. Methods for comparison of genetic variation in coding genes between sub-species of cattle need to be investigated.
3. Progress Report
To date, 48 million bovine SNPs were classified according to location in relation to genes annotated in the bovine genome assembly using the UMD3.1 genome build. Each SNP was categorized as either intronic, 5' UTR, 3' UTR, 5' upstream, 3' downstream, splice site, or coding. For SNPs in coding sequence the peptide change produced (if any) was determined. The results were validated by comparing the classifications of the subset of the SNPs already submitted to dbSNP with the classifications produced by dbSNP's annotation software. Analysis of breed-specific allele frequencies is being undertaken to identify SNPs associated with breed specific traits. Monitoring activities associated with this project included regular email correspondence, face-to-face meetings, workshop in conjunction with an international meeting, and conference calls. This research supported two objectives of its related in-house project: 1) to develop biological resources and computational tools to enhance characterization of the bovine genome sequence (obj. #1).