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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping

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Author(s):
Porto-Neto, Laercio R. [1, 2] ; Sonstegard, Tad S. [3] ; Liu, George E. [3] ; Bickhart, Derek M. [3] ; Da Silva, Marcos V. B. [4] ; Machado, Marco A. [4] ; Utsunomiya, Yuri T. [5] ; Garcia, Jose F. [5] ; Gondro, Cedric [2] ; Van Tassell, Curtis P. [3]
Total Authors: 10
Affiliation:
[1] Univ Queensland, Sch Vet Sci, Anim Genet Lab, Gatton, Qld 4343 - Australia
[2] Univ New England, Sch Environm & Rural Sci, Armidale, NSW 2351 - Australia
[3] ARS, USDA, Bovine Funct Genom Lab, Beltsville, MD 20705 - USA
[4] Embrapa Dairy Cattle, Bioinformat & Anim Genom Lab, Juiz De Fora, MG - Brazil
[5] Univ Estadual Paulista, UNESP, Aracatuba, SP - Brazil
Total Affiliations: 5
Document type: Journal article
Source: BMC Genomics; v. 14, DEC 13 2013.
Web of Science Citations: 55
Abstract

Background: Natural selection has molded evolution across all taxa. At an arguable date of around 330,000 years ago there were already at least two different types of cattle that became ancestors of nearly all modern cattle, the Bos taurus taurus more adapted to temperate climates and the tropically adapted Bos taurus indicus. After domestication, human selection exponentially intensified these differences. To better understand the genetic differences between these subspecies and detect genomic regions potentially under divergent selection, animals from the International Bovine HapMap Experiment were genotyped for over 770,000 SNP across the genome and compared using smoothed F-ST. The taurine sample was represented by ten breeds and the contrasting zebu cohort by three breeds. Results: Each cattle group evidenced similar numbers of polymorphic markers well distributed across the genome. Principal components analyses and unsupervised clustering confirmed the well-characterized main division of domestic cattle. The top 1% smoothed F-ST, potentially associated to positive selection, contained 48 genomic regions across 17 chromosomes. Nearly half of the top F-ST signals (n = 22) were previously detected using a lower density SNP assay. Amongst the strongest signals were the BTA7:similar to 50 Mb and BTA14:similar to 25 Mb; both regions harboring candidate genes and different patterns of linkage disequilibrium that potentially represent intrinsic differences between cattle types. The bottom 1% of the smoothed F-ST values, potentially associated to balancing selection, included 24 regions across 13 chromosomes. These regions often overlap with copy number variants, including the highly variable region at BTA23:similar to 24 Mb that harbors a large number of MHC genes. Under these regions, 318 unique Ensembl genes are annotated with a significant overrepresentation of immune related pathways. Conclusions: Genomic regions that are potentially linked to purifying or balancing selection processes in domestic cattle were identified. These regions are of particular interest to understand the natural and human selective pressures to which these subspecies were exposed to and how the genetic background of these populations evolved in response to environmental challenges and human manipulation. (AU)

FAPESP's process: 10/52030-2 - Genome wide association study for reproductive traits in zebu bulls (Bos indicus) using high-density SNP chip
Grantee:José Fernando Garcia
Support type: Regular Research Grants