Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds.

Authors: GIBBS, RICHARD A - BAYLOR COLLEGE OF MED; Van Tassell, Curtis - Curt; WEINSTOCK, GEORGE - BAYLOR COLLEGE OF MED; Green, Ronald; HAMERNIK, DEBORA - CSREES; Kappes, Steven - Steve; Liu, Ge - George; MATUKUMALLI, LAKSHMI - GEORGE MASON UNIVERSITY; MATUKUMALLI, ARUNA - 1265-90-00; Sonstegard, Tad; Silva, Marcos

Submitted to: Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/15/2009
Publication Date: 4/24/2009
Citation: Gibbs, R., Van Tassell, C.P., Weinstock, G.M., Green, R.D., Hamernik, D.L., Kappes, S.M., Liu, G., Matukumalli, L.K., Matukumalli, A., Sonstegard, T.S., Silva, M.V. 2009. Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds. Science. 24:528-532.

Interpretive Summary: The cow genome was sequenced to enhance the rate of gains in production and health based traits as well as provides an understanding of the genetic basis of selection. As part of the genome sequencing effort several random single nucleotide polymorphisms (SNPs) distributed throughout the genome were identified ( ~150,000) between major cattle breeds. A significant fraction of these SNPs ( ~35,000) were used to develop high throughput genotyping assays and analyze a sample of diverse cattle populations (501) from across the globe. The genotype data was then analyzed by the international bovine hapmap consortium. The results from these analyses showed that, despite the historic bottlenecks associated with breed formation and the ongoing intense quantitative genetic-based selection of contemporary breeds, ample variation exists to enable the use of high-density genotyping techniques to explore and genetically alter important production, adaptation, and fitness traits.

Technical Abstract: A deep draft sequence assembly derived from shotgun reads from a single Hereford female and comparative sampling sequences from cows representing six additional bovine breeds has enabled the development of genetic probes to interrogate single nucleotide polymorphisms for population and breed analyses. The major analyses performed include (i) the proportion of shared alleles within and across different breeds, (ii) extent of linkage disequilibrium, (iii) identification of signatures of selection, (iv) development of a unified marker set for paternity testing and (v) accurate estimation of inbreeding coefficients. The extent of within-breed and between-breed variability shows that, despite the historic bottlenecks associated with breed formation and the ongoing intense quantitative genetic-based selection of contemporary breeds, ample variation exists to enable the use of high-density genotyping techniques to explore and genetically alter important production, adaptation, and fitness traits.