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Title: High-resolution haplotype block structure in the cattle genome

item VILLA-ANGULO, RAFAEL - George Mason University
item MATUKUMALLI, LAKSHMI - George Mason University
item GILL, CLARE - Texas A&M University
item CHOI, JUNGWOO - Texas A&M University
item Van Tassell, Curtis - Curt
item GREFENSTETTE, JOHN - George Mason University

Submitted to: Journal of Animal Breeding and Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/24/2009
Publication Date: 4/24/2009
Citation: Villa-Angulo, R., Matukumalli, L.K., Gill, C.A., Choi, J., Van Tassell, C.P., Grefenstette, J.J. 2009. High-resolution haplotype block structure in the cattle genome. Journal of Animal Breeding and Genetics. 24(10):19.

Interpretive Summary: For the purposes of implementation of genome selection and estimation of effective population sizes it is critical to have accurate estimates of both short range and long range linkage disequilibrium (LD) in cattle. Prior studies using microsatellite markers provided estimates of only long range LD. In this study we sequenced selected regions from Chr 6,14 and 25 genome and identified SNPs. These SNPs were genotyped for the Bovine HapMap population to estimate short range LD. This first study on short range LD in cattle produced unexpected results that short range LD in cattle is similar to that of humans. These results have high significance in fine mapping of traits and also provided a glimpse into the past and current effective population sizes in various cattle breeds for the purposes of maintaining diversity.

Technical Abstract: The Bovine HapMap Consortium has generated assay panels to genotype ~30,000 single nucleotide polymorphisms (SNPs) from 501 animals sampled from 19 worldwide taurine and indicine breeds, plus two outgroup species (Anoa and Water Buffalo). Within the larger set of SNPs we targeted 101 high density regions spanning up to 7.6 Mb with an average density of approximately one SNP per 4 kb, and characterized the linkage disequilibrium (LD) and haplotype block structure within individual breeds and groups of breeds in relation to their geographic origin and use. From the 101 targeted high-density regions on bovine chromosomes 6, 14, and 25, between 57 and 95% of the SNPs were informative in the individual breeds. The regions of high LD extend up to ~100 kb and the size of haplotype blocks ranges between 30 bases and 75 kb (10.3 kb average). On the scale from 1–100 kb the extent of LD and haplotype block structure in cattle has high similarity to humans. The estimation of effective population sizes over the previous 10,000 generations conforms to two main events in cattle history: the initiation of cattle domestication (~12,000 years ago), and the intensification of population isolation and current population bottleneck that breeds have experienced worldwide within the last ~700 years. Haplotype block density correlation, block boundary discordances, and haplotype sharing analyses were consistent in revealing unexpected similarities between some beef and dairy breeds, making them non-differentiable. Clustering techniques permitted grouping of breeds into different clades given their similarities and dissimilarities in genetic structure. This work presents the first high-resolution analysis of haplotype block structure in worldwide cattle samples. Several novel results were obtained. First, cattle and human share a high similarity in LD and haplotype block structure on the scale of 1–100 kb. Second, unexpected similarities in haplotype block structure between dairy and beef breeds make them non-differentiable. Finally, our findings suggest that ~30,000 uniformly distributed SNPs would be necessary to construct a complete genome LD map in Bos taurus breeds, and ~580,000 SNPs would be necessary to characterize the haplotype block structure across the complete cattle genome.