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Originally published as Genetics Published Articles Ahead of Print on April 15, 2007.
Genetics, Vol. 176, 763-772, June 2007, Copyright © 2007
doi:10.1534/genetics.106.069369
A Primary Assembly of a Bovine Haplotype Block Map Based on a 15,036-Single-Nucleotide Polymorphism Panel Genotyped in Holstein–Friesian Cattle
Mehar S. Khatkar*,
,1,
Kyall R. Zenger*,,
Matthew Hobbs*,,
Rachel J. Hawken,
,
Julie A. L. Cavanagh*,,
Wes Barris,,
Alexander E. McClintock*,,
Sara McClintock,
,
Peter C. Thomson*,,
Bruce Tier,
Frank W. Nicholas*, and
Herman W. Raadsma*,
* Centre for Advanced Technologies in Animal Genetics and Reproduction (ReproGen), University of Sydney, Camden NSW 2570, Australia, CSIRO Livestock Industries, St. Lucia QLD 4067, Australia, Animal Genetics and Breeding Unit, University of New England, Armidale NSW 2351, Australia and CRC for Innovative Dairy Products, Melbourne, Vic 3000, Australia
1 Corresponding author: Centre for Advanced Technologies in Animal Genetics and Reproduction (ReproGen), University of Sydney, PMB 3, Camden NSW 2570, Australia.
E-mail: mehark{at}camden.usyd.edu.au
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 ± 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.
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