Bovine HapMap

An Overview of the Bovine HapMap Project

The International Bovine HapMap Consortium is made up of members of the bovine research community from around the world as well as researchers at the Baylor College of Medicine Human Genome Sequencing Center who are sequencing the bovine genome.

Abstract presented at ISAG 2006, Porto Seguro, Brazil August 20-25, 2006

The International Bovine HapMap Consortium

Contacting author's email: curtvt@anri.barc.usda.gov

The International Bovine Hapmap Project was initiated in 2004 as a component of the whole genome sequencing effort. The objectives of the project are to: (1) discover single nucleotide polymorphisms (SNP); (2) validate at least 20,000 SNP by genotyping a panel representing diverse Bos taurus and Bos indicus breeds; (3) to use the genotypic data to infer common haplotypes; (4) to estimate linkage disequilibrium; and (5) examine diversity among breeds. As part of the first objective, nearly 350,000 shotgun sequences were generated from six cows representing Angus, Brahman, Holstein, Jersey, Limousin, and Norwegian Red breeds. These sequences were then aligned to the draft genome sequence from the Hereford cow L1 Dominette 01449, resulting in a total of 118,000 putative SNP. Additional putative SNP were identified from EST data and from comparison of BAC end sequences derived from Holstein animals. The second objective is in progress and will genotype breed panels with 20-50 individuals per breed. Each breed panel includes sets of trios to assist SNP validation and haplotype determination. Due to reduced costs, a total of 28,000 genome-wide SNP will be characterized. Initial results from approximately 10,000 SNP indicated that the existing coverage was insufficient to accurately examine local linkage disequilibrium. Consequently, an additional effort to discover and genotype high-density SNP was initiated. SNP discovery for this effort will use low-coverage BAC sequencing from the RPCI-42 library (derived from a Holstein bull) for selected regions on three chromosomes and a total of 4,500 SNP will be genotyped. The remaining objectives will proceed once genotypic data generation and the third whole genome sequence assembly are completed. Strategies for accomplishing these objectives will be discussed. Combined, the project will genotype approximately 33,000 SNP on 474 animals of 18 breeds, providing a resource for selection of SNP to support immediate application in high-density marker-assisted selection projects, QTL fine mapping efforts, and gene discovery research.

Links:

Bovine Genome Resources: http://www.ncbi.nlm.nih.gov/genome//guide/cow/

Bovine Genome Sequencing Project: http://www.hgsc.bcm.tmc.edu/projects/bovine/