ArticlePloS one2013
Detecting loci under recent positive selection in dairy and beef cattle by combining different genome-wide scan methods.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers, 1 of them a synthesis that pooled it.
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Who cites it
57 citing papers in PubMed, 1 synthesis or guideline pooled it, 112 citations in OpenAlex.
- A Meta-Assembly of Selection Signatures in Cattle.PloS one · 2016Pooled it
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- Bovine Genome Database: new curated collection of selective sweeps in bovine populations across the world.Nucleic acids research · 2026Article
- Genetic Diversity, Admixture, and Selection Signatures in a Rarámuri Criollo Cattle Population Introduced to the Southwestern United States.International journal of molecular sciences · 2025Article
- Dynamic Outlier Slicing Allows Broader Exploration of Adaptive Divergence: A Comparison of Individual Genome and Pool-Seq Data Linked to Humic Adaptation in Perch.Molecular ecology · 2025Article
- Genome-wide scan for signatures of selection in Hanwoo and Angus cattle using whole-genome sequence data.PloS one · 2025Article
- Genomic Signatures of Domestication in European Seabass (Ecology and evolution · 2024Article
- Ancestral alleles defined for 70 million cattle variants using a population-based likelihood ratio test.Genetics, selection, evolution : GSE · 2024Article
- Signatures of selection in Angus and Hanwoo beef cattle using imputed whole genome sequence data.Frontiers in genetics · 2024Article
- A genomic analysis of the University of Nebraska Replicated Recurrent Selection program.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Whole Genome Resequencing Reveals Selection Signals Related to Wool Color in Sheep.Animals : an open access journal from MDPI · 2023Article
- Power of neutrality tests for detecting natural selection.G3 (Bethesda, Md.) · 2023Article
- Whole-Genome Resequencing Reveals Selection Signal Related to Sheep Wool Fineness.Animals : an open access journal from MDPI · 2023Article
- Analysis of dog breed diversity using a composite selection index.Scientific reports · 2023Article
- Assessing genetic diversity and defining signatures of positive selection on the genome of dromedary camels from the southeast of the Arabian Peninsula.Frontiers in veterinary science · 2023Article
- Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure.Scientific reports · 2022Article
- Favored single nucleotide variants identified using whole genome Re-sequencing of Austrian and Chinese cattle breeds.Frontiers in genetics · 2022Article
- Genome analyses revealed genetic admixture and selection signatures in Bos indicus.Scientific reports · 2021Article
- Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle.PLoS genetics · 2021Article
- Investigation of ancestral alleles in the Bovinae subfamily.BMC genomics · 2021Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As the methodologies available for the detection of positive selection from genomic data vary in terms of assumptions and execution, weak correlations are expected among them. However, if there is any given signal that is consistently supported across different methodologies, it is strong evidence that the locus has been under past selection. In this paper, a straightforward frequentist approach based on the Stouffer Method to combine P-values across different tests for evidence of recent positive selection in common variations, as well as strategies for extracting biological information from the detected signals, were described and applied to high density single nucleotide polymorphism (SNP) data generated from dairy and beef cattle (taurine and indicine). The ancestral Bovinae allele state of over 440,000 SNP is also reported. Using this combination of methods, highly significant (P<3.17×10(-7)) population-specific sweeps pointing out to candidate genes and pathways that may be involved in beef and dairy production were identified. The most significant signal was found in the Cornichon homolog 3 gene (CNIH3) in Brown Swiss (P = 3.82×10(-12)), and may be involved in the regulation of pre-ovulatory luteinizing hormone surge. Other putative pathways under selection are the glucolysis/gluconeogenesis, transcription machinery and chemokine/cytokine activity in Angus; calpain-calpastatin system and ribosome biogenesis in Brown Swiss; and gangliosides deposition in milk fat globules in Gyr. The composite method, combined with the strategies applied to retrieve functional information, may be a useful tool for surveying genome-wide selective sweeps and providing insights in to the source of selection.
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