Objective:
Objective 1: Develop biological resources and computational tools to enhance characterization of the bovine genome sequence. Objective 2: Use genotypic data and resulting bovine haplotype map to enhance genetic improvement in dairy cattle through development and implementation of whole genome selection and enhanced parentage verification approaches. Objective 3: Characterize conserved genome elements and identify functional genetic variation.

Approach:
Completion of our objectives is expected, in the short term, to result in development and implementation of genome-wide selection. Ultimately the longer term objective of QTN discovery to better understand livestock biology will require a combination of quantitative genetics, LD-MAS, genome annotation, and gene expression analyses, all of which are components of this proposal and areas of expertise in our group. Efforts to characterize genome activity and structure conservation and variation are an extension of our current research program in QTL mapping and bioinformatics. This proposal completely leverages the resources derived from the Bovine Genome and HapMap projects, for which the authors of this proposal have played prominent roles. As more of the genetic variation for a specific trait is explained, a better understanding of pleiotropic and epistatic gene action will be needed. This knowledge will be developed through characterizing changes at a very fine level combined with studies of animals with known genotype associated with phenotypes resulting from selection programs. Tools used in this characterization are likely to include, but not be limited to, gene expression patterns, protein expression or structural changes, or regulatory changes.