Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods

dc.contributorUniversidade Estadual Paulista (UNESP)
dc.creatorUtsunomiya, Yuri Tani
dc.creatorPérez O'Brien, Ana Maria
dc.creatorSonstegard, Tad Stewart
dc.creatorVan Tassell, Curtis Paul
dc.creatordo Carmo, Adriana Santana
dc.creatorMészáros, Gábor
dc.creatorSölkner, Johann
dc.creatorGarcia, José Fernando
dc.date2014-05-27T11:29:30Z
dc.date2016-10-25T18:48:31Z
dc.date2014-05-27T11:29:30Z
dc.date2016-10-25T18:48:31Z
dc.date2013-05-16
dc.date.accessioned2017-04-06T02:23:58Z
dc.date.available2017-04-06T02:23:58Z
dc.identifierPLoS ONE, v. 8, n. 5, 2013.
dc.identifier1932-6203
dc.identifierhttp://hdl.handle.net/11449/75408
dc.identifierhttp://acervodigital.unesp.br/handle/11449/75408
dc.identifier10.1371/journal.pone.0064280
dc.identifierWOS:000319081900077
dc.identifier2-s2.0-84877834696.pdf
dc.identifier2-s2.0-84877834696
dc.identifierhttp://dx.doi.org/10.1371/journal.pone.0064280
dc.identifier.urihttp://repositorioslatinoamericanos.uchile.cl/handle/2250/896152
dc.descriptionAs 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.
dc.languageeng
dc.relationPLOS ONE
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectcalpain
dc.subjectcalpastatin
dc.subjectganglioside
dc.subjectallele
dc.subjectbeef cattle
dc.subjectbiogenesis
dc.subjectbiological activity
dc.subjectCNIH3 gene
dc.subjectcontrolled study
dc.subjectdairy cattle
dc.subjectdairy product
dc.subjectdata analysis
dc.subjectDNA footprinting
dc.subjectgene
dc.subjectgene frequency
dc.subjectgene identification
dc.subjectgene locus
dc.subjectgenetic association
dc.subjectgenetic database
dc.subjectgenetic selection
dc.subjectgenetic transcription
dc.subjectgenetic variability
dc.subjectgluconeogenesis
dc.subjectglycolysis
dc.subjecthaplotype
dc.subjectheterozygosity
dc.subjecthomozygosity
dc.subjectluteinizing hormone release
dc.subjectmeat
dc.subjectnonhuman
dc.subjectpopulation genetics
dc.subjectribosome
dc.subjectsignal detection
dc.subjectsingle nucleotide polymorphism
dc.titleDetecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods
dc.typeOtro


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