Bovine HapMap

Abstract

The primary goal of this project is to validate and characterize sufficient bovine SNP loci that we can develop tools for the livestock genomics research community for high-resolution linkage and linkage disequilibrium (LD) mapping. The rationale that underlies this research is that we will not be able to elucidate the identities of QTL until we are able to efficiently map their locations at very high resolution and this can only be accomplished using high-throughput SNP genotyping platforms.

Consequently, we developed a program of fundamental research that is both vital and germane in view of the 2 million putative SNPs expected from the assembly of the bovine genome sequence. Illumina BeadStations at the Universities of Missouri and Alberta will be used to characterize roughly 50,000 evenly-spaced putative SNPs within the genera Bos, Bison, Bubulus and Ovis using multigeneration families. (see below) Our efforts will identify numerous validated SNPs with minor allele frequency >0.2 in all breeds of cattle for use in platform-independent, massively-multiplexed typing assays representing a bovine whole genome (WG) linkage map at an average resolution of <500-kb. This project will provide the necessary reagents for the cost-effective and rapid application of WG scans by linkage or LD in cattle and (at lower resolution) in sheep. We shall generate chromosome-length haplotypes, identify tagSNPs and will determine the distribution of LD within cattle. SNP multiplexes will also be designed for individual chromosome linkage and LD analysis.

Finally, Project resources including a subset of DNA samples and all quality-processed genotypes will be made publicly available through deposit in public databases and through the Co-PD's websites to ensure the sustainability of all reagents generated in this Project.

The major difference between the International HapMap consortium project and the Missouri/Alberta project lies in the populations and pedigree structure of the animals being used. The International Consortium will genotype 18 breeds with 20-50 individuals per breed arranged in parent-offspring trios. The Missouri/Alberta project is based on three generation pedigrees (grandsire-sire- 4 sons) so that phase can be determined. We have also increased the number of animals and pedigree depth for the two most economically important breeds in the U.S. Additionally, we have included animals from different genera as well as ancient DNA specimens.

Fourteen-generation Angus pedigree (N=200)

Seven-generation Holstein pedigree (N=200)

8 three-generation Hereford families (N=48)

8 three-generation Limousin families (N=48)

8 three-generation Brahman families (N=48)

8 three-generation Nelore families (N=48)

8 three-generation N'Dama families (N=48)

8 three-generation Hanwoo families (N=48)

8 three-generation Water Buffalo families (N=48)

1 three-generation Bison family (N=17)

2 three-generation Rambouillet sheep families (N=15)

5 ancient auroch (12-60K years old)

5 ancient bison (12-60K years old)