Classic Selective Sweeps Revealed by Massive Sequencing in Cattle
Open accessAbstract
Human driven selection during domestication and subsequent breed formation has likely left detectable signatures within the genome of modern cattle. The elucidation of these signatures of selection is of interest from the perspective of evolutionary biology, and for identifying domestication-related genes that ultimately may help to further genetically improve this economically important animal. To this end, we employed a panel of more than 15 million autosomal SNPs identified from re-sequencing of 43 Fleckvieh animals. We mainly applied two somewhat complementary statistics, the integrated Haplotype Homozygosity Score (iHS) reflecting primarily ongoing selection, and the Composite of Likelihood Ratio (CLR) having the most power to detect completed selection after fixation of the advantageous allele. We find 106 candidate selection regions, many of which are harboring genes related to phenotypes relevant in domestication, such as coat coloring pattern, neurobehavioral functioning and sensory perception including KIT, MITF, MC1R, NRG4, Erbb4, TMEM132D and TAS2R16, among others. To further investigate the relationship between genes with signatures of selection and genes identified in QTL mapping studies, we use a sample of 3062 animals to perform four genome-wide association analyses using appearance traits, body size and somatic cell count. We show that regions associated with coat coloring significantly (P<0.0001) overlap with the candidate selection regions, suggesting that the selection signals we identify are associated with traits known to be affected by selection during domestication. Results also provide further evidence regarding the complexity of the genetics underlying coat coloring in cattle. This study illustrates the potential of population genetic approaches for identifying genomic regions affecting domestication-related phenotypes and further helps to identify specific regions targeted by selection during speciation, domestication and breed formation of cattle. We also show that Linkage Disequilibrium (LD) decays in cattle at a much faster rate than previously thought.
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GRIK3 has been targeted in modern human evolution and in multiple domestication events, including in dogs, sheep, yaks, and across multiple cattle breeds.
“This gene has been targeted in modern human evolution and in multiple domestication events, including in dogs, sheep, yaks, and across multiple cattle breeds [16, 19, 20].”
From Gene expression profiles underlying aggressive behavior in the prefrontal cortex of cattle (2021) · cites this paper as [20]
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Genomic insights into ruminant evolution: from past to future prospects
Wang, B., Chen, L., & Wang, W. (2019) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2019.061 · Cited by 25 · see citing works
Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals
Hou, Y., Qi, F., Bai, X., Ren, T., Shen, X., Chu, Q., Zhang, X., & Lu, X. (2020) · BMC Genomics · doi:10.1186/s12864-020-6613-1 · Cited by 25 · see citing works
- Authors
- Qanbari, S., Pausch, H., Jansen, S., Somel, M., Strom, T. M., Fries, R., Nielsen, R., & Simianer, H.
- Affiliations
- University of Göttingen (DE)
- Technical University of Munich (DE)
- University of California, Berkeley (US)
- Helmholtz Munich (DE)
- Corresponding author
- Qanbari, Saber
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-02-27
- Volume
- 10
- Issue
- 2
- Pages
- e1004148
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC3937232
- OpenAlex
- W2047669864
- Semantic Scholar
- b97615af7d0e16d1c4ecfdba9de4183b17efa05b
- Cited by
- 233
- References
- 79
- Citations by year
- 2026: 8 · 2025: 12 · 2024: 12 · 2023: 13 · 2022: 16 · 2021: 26 · 2020: 24 · 2019: 20 · 2018: 20 · 2017: 17 · 2016: 23 · 2015: 32 · 2014: 10
- FWCI
- 17.90
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Figshare (submittedVersion, cc-by)
- GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, cc-by)
- OpenMETU (Middle East Technical University) (submittedVersion, cc-by-nc-nd)
- Site cant be reached (submittedVersion, cc-by)
- GRO (submittedVersion, cc-by)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
- ETH Zürich Research Collection (cc-by)
- Funders
- Deutsche Forschungsgemeinschaft
- Bundesministerium für Bildung und Forschung (FKZ 0315528, 0315528)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- cattle domestication, selective sweeps, Simmental cattle, coat color inheritance, KIT, MITF, MC1R, ErbB4, TAS2R16, linkage disequilibrium decay, genome-wide association study, body size, somatic cell count, breed formation
- MeSH terms
- Animals, Animals, Domestic, Breeding, Cattle, Genetics, Population, Haplotypes, Humans, Selection, Genetic, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Genome-Wide Association Study
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