A primary assembly of a bovine haplotype block map based on a 15,036-single-nucleotide polymorphism panel genotyped in holstein-friesian cattle

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 > or =3 SNPs were identified. The average block length was 69.7 +/- 7.7 kb, which is approximately 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 approximately 250,000 SNPs in the discovery phase.

Figure 1.—

(a) The distribution of SNP spacing [the distance in base pairs (kilobases) from one SNP marker to the next SNP marker]. (b) Frequency distribution of size of haplotype blocks consisting of more than two SNPs.

Figure 1.—

(a) The distribution of SNP spacing [the distance in base pairs (kilobases) from one SNP marker to the next SNP marker]. (b) Frequency distribution of size of haplotype blocks consisting of more than two SNPs.

Figure 2.—

Haplotype block map of a portion of BTA6 (89.5–111.76 Mb) in the form of a heat map of confidence bounds of D′. This map was prepared by Haploview software. Dark shading indicates strong LD, light shading is uninformative, and open areas suggest strong evidence of historical recombination. The haplotype block maps of all autosomes are presented in supplemental Figure S1 at http://www.genetics.org/supplemental/.

Figure 3.—

Haplotype blocks comprising three or more SNPs plotted to actual scale in red. Gray ticks indicate the positions of the SNPs analyzed.