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Detection of selective sweeps in cattle using genome-wide SNP data
Holly R Ramey1, Jared E Decker, Stephanie D McKay
1Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.
BMC Genomics
|June 14, 2013
Summary
Human selection during cattle domestication created genomic selective sweeps. This study identified these sweeps in cattle breeds, revealing selection for traits like coat color and behavior.
Area of Science:
- Genomics
- Animal Genetics
- Evolutionary Biology
Background:
- Cattle domestication and breeding have significantly altered genome variation.
- Selective sweeps, regions of reduced genetic diversity, result from strong selection.
- Identifying these sweeps in cattle is crucial for understanding breed development.
Purpose of the Study:
- To identify and characterize genomic regions in cattle that have undergone selective sweeps.
- To investigate the impact of domestication and breed formation on bovine genome variation.
Main Methods:
- Utilized BovineSNP50 data to identify 28 putative sweep regions across 14 cattle breeds.
- Employed Affymetrix BOS 1 assay data for validation and identification of additional sweep regions.
- Confirmed findings using an ultra-high-density assay.
Main Results:
- Identified 28 putative selective sweep regions using BovineSNP50 data and 85 regions using Affymetrix BOS 1 data.
- Validated 5 regions identified with BovineSNP50 using the higher-density assay.
- Observed no shared sweep regions between indicine and taurine breeds, indicating divergent selection histories.
Conclusions:
- The common SNP bias in the BovineSNP50 assay favored recent sweeps over ancient domestication events.
- Limited SNP density impacted false discovery rates, but ultra-high-density assays confirmed shared sweeps.
- Divergent selection histories and adaptations explain the lack of shared sweeps between indicine and taurine cattle.
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