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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS

Location: Animal Genomics and Improvement Laboratory

Title: High overlap of CNVs and selection signatures revealed by varLD analyses of taurine and zebu cattle

Authors
item Perez O'Brien, Ana Maria -
item Meszaros, Gabor -
item Utsunomiya, Yuri Tani -
item Garcia, Jose Fernando -
item Van Tassell, Curtis
item Sonstegard, Tad
item Solkner, Johan -

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: March 15, 2013
Publication Date: August 26, 2013
Citation: Perez O'Brien, A., Meszaros, G., Utsunomiya, Y., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Solkner, J. 2013. High overlap of CNVs and selection signatures revealed by varLD analyses of taurine and zebu cattle. Book of Abstracts of the 64th Annual Meeting of the European Association for Animal Production, Nantes, France 2013 pp.604.

Technical Abstract: Selection Signatures (SS) assessed through analysis of genomic data are being widely studied to discover population specific regions selected via artificial or natural selection. Different methodologies have been proposed for these analyses, each having specific limitations as to the age of the selection process aimed to discover and the genomic parameters behind the methods used, being able to assess population, breed or species-wise SS. On a different side of the work on genomic characterization of the genome, interest has re-emerged on the identification of Copy Number Variants (CNVs) and other types of variations, showing that a considerable amount of the variation in the genome can be explained by this type of genomic variants. We identified putative regions of divergent selection between Indicine and Taurine cattle, of Dairy and Beef type, through the varLD methodology, analyzing differential regional Linkage Disequilibrium (LD) variation across populations, compared to population specific background LD levels. Subsequently, the identified regions were compared to recently reported CNVs, to find possible candidate regions where the selection process has been acting on advantageous CNVs. Four cattle breeds, Angus, Brown Swiss, Nellore and Gyr (30 to 100 individuals per breed) were included in the analyses, genotyped with the Illumina Bovine HD Beadchip. Our results show a large overlap of regions discovered through the SS analyses and reported CNVs. Of the 164 varLD regions covering 0.35% of the autosomal genome, 30 (18.3%) overlapped with CNV regions reported in another study, covering 2.1% of the genome. Additionally, some of the regions found in common, have been previously identified by other types of studies (GWAS, SS) as having productive or adaptive importance in different bovine breeds.

Last Modified: 10/25/2014
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