Project Number: 1265-31000-098-05
Project Type: Reimbursable

Start Date: Jan 01, 2006
End Date: Dec 31, 2008

Objective:
The first objective is to generate genotypic data on 10,000 SNP for 1200 Holstein bulls. This data will serve as a resource for the remaining components. The second objective is to infer haplotypes for genotyped bulls, create a Holstein-specific HapMap, and provide genotypic data to the bovine HapMap project. The final objective is to develop statistical methods and infrastructure to implement genomic selection and to combine the genetic merit prediction using genomic data with results from the national genetic evaluation system.

Approach:
The SNP genotyping will be conducted using the most-cost-effective platform available at the time. Data from the HapMap consortium will be used to identify the optimal set of SNP to genotype. For objective two, algorithms used to infer haplotypes can generally be divided into two groups, those that are based on pedigree information and those assuming unrelated individuals. We expect to evaluate algorithms or software packages representing each of these groups of algoithms. Further, we intend to identify haplotype blocks specific to the Holstein breed. By determining the haplotypes at any given region in the population, we can identify which SNP will be redundant and which can be used to represent the haplotype in further studies. The latter SNP are often referred to as haplotype tag SNP. The programs htSNPer and HapBlock will each be tested using these data. The final objective will be accomplished using the genomic selection procedure described by Meuwissen et al. (2001). Given haplotype data genetic merit is modeled as a function of haplotype effects. Several alternative strategies will be investigated to determine the best approach to model these data.