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

Porto-Neto, Laercio R, Sonstegard, Tad S, Liu, George E, Bickhart, Derek M, Da Silva, Marcos VB, Machado, Marco A, Utsunomiya, Yuri T, Garcia, Jose F, Gondro, Cedric and Van Tassell, Curtis P (2013) Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping. BMC Genomics, 14 1: 876.1-876.12. doi:10.1186/1471-2164-14-876

Author Porto-Neto, Laercio R
Sonstegard, Tad S
Liu, George E
Bickhart, Derek M
Da Silva, Marcos VB
Machado, Marco A
Utsunomiya, Yuri T
Garcia, Jose F
Gondro, Cedric
Van Tassell, Curtis P
Title Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2013-12
Year available 2013
Sub-type Article (original research)
DOI 10.1186/1471-2164-14-876
Open Access Status DOI
Volume 14
Issue 1
Start page 876.1
End page 876.12
Total pages 12
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2014
Language eng
Formatted 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 FST. 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 FST, potentially associated to positive selection, contained 48 genomic regions across 17 chromosomes. Nearly half of the top FST signals (n = 22) were previously detected using a lower density SNP assay. Amongst the strongest signals were the BTA7:~50 Mb and BTA14:~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 FST 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:~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.
Keyword Bos
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
School of Veterinary Science Publications
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