A primary assembly of a Bovine Haplotype Block Map based on a 15,036-Single-Nucleotide Polymorphism Panel genotyped in Holstein–Friesian Cattle

Khatkar, Mehar S., Zenger, Kyall R., Hobbs, Matthew, Hawken, Rachel J., Cavanagh, Julie A.L., Barris, Wes, McClintock, Alexander E., McClintock, Sara, Thomson, Peter C., Tier, Bruce, Nicholas, Frank W., and Raadsma, Herman W. (2007) A primary assembly of a Bovine Haplotype Block Map based on a 15,036-Single-Nucleotide Polymorphism Panel genotyped in Holstein–Friesian Cattle. Genetics, 176. pp. 763-772.

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Abstract

Analysis of data on 1000 Holstein–Friesian bulls genotyped for 15,036 single-nucleotide polymorphisms (SNPs) has enabled genomewide identification of haplotype blocks and tag SNPs. A final subset of 9195 SNPs in Hardy–Weinberg equilibrium and mapped on autosomes on the bovine sequence assembly (release Btau 3.1) was used in this study. The average intermarker spacing was 251.8 kb. The average minor allele frequency (MAF) was 0.29 (0.05–0.5). Following recent precedents in human HapMap studies, a haplotype block was defined where 95% of combinations of SNPs within a region are in very high linkage disequilibrium. A total of 727 haplotype blocks consisting of $3 SNPs were identified. The average block length was 69.7 6 7.7 kb, which is 5–10 times larger than in humans. These blocks comprised a total of 2964 SNPs and covered 50,638 kb of the sequence map, which constitutes 2.18% of the length of all autosomes. A set of tag SNPs, which will be useful for further fine-mapping studies, has been identified. Overall, the results suggest that as many as 75,000–100,000 tag SNPs would be needed to track all important haplotype blocks in the bovine genome. This would require 250,000 SNPs in the discovery phase.

Item ID: 9742
Item Type: Article (Refereed Research - C1)
Keywords: animal genomics; dairy cattle; haplotype map; SNP loci
ISSN: 1943-2631
Date Deposited: 30 Mar 2010 02:05
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060408 Genomics @ 100%
SEO Codes: 83 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 8303 Livestock Raising > 830302 Dairy Cattle @ 60%
97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 40%
Citation Count from Web of Science Web of Science 41
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