title: Detecting loci under recent positive selection in dairy and beef cattle by combining different genome-wide scan methods.
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.
authors.affiliation: Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP-Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil.
authors.forename: Yuri Tani
authors.initials: YT
authors.lastname: Utsunomiya
authors.forename: Ana Maria
authors.initials: AM
authors.lastname: Pérez O'Brien
authors.forename: Tad Stewart
authors.initials: TS
authors.lastname: Sonstegard
authors.forename: Curtis Paul
authors.initials: CP
authors.lastname: Van Tassell
authors.forename: Adriana Santana
authors.initials: AS
authors.lastname: do Carmo
authors.forename: Gábor
authors.initials: G
authors.lastname: Mészáros
authors.forename: Johann
authors.initials: J
authors.lastname: Sölkner
authors.forename: José Fernando
authors.initials: JF
authors.lastname: Garcia
mesh_terms: D000818:Animals; D002417:Cattle; D055106:Genome-Wide Association Study; D008962:Models, Theoretical; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics; D012641:Selection, Genetic / Q000235:genetics*