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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Author(s):
Utsunomiya, Yuri Tani [1] ; O'Brien, Ana Maria Perez [2] ; Sonstegard, Tad Stewart [3] ; Van Tassell, Curtis Paul [3] ; do Carmo, Adriana Santana [1] ; Meszaros, Gabor [2] ; Soelkner, Johann [2] ; Garcia, Jose Fernando [4]
Total Authors: 8
Affiliation:
[1] UNESP Univ Estadual Paulista, Fac Ciencias Agr & Vet, Dept Med Vet Prevent & Reprod Anim, Sao Paulo - Brazil
[2] BOKU Univ Nat Resources & Life Sci, Div Livestock Sci, Dept Sustainable Agr Syst, Vienna - Austria
[3] ARS, Bovine Funct Genom Lab, USDA, Beltsville, MD - USA
[4] UNESP Univ Estadual Paulista, Fac Med Vet Aracatuba, Dept Apoio Saude & Prod Anim, Sao Paulo - Brazil
Total Affiliations: 4
Document type: Journal article
Source: PLoS One; v. 8, n. 5 MAY 16 2013.
Web of Science Citations: 52
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 x 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 x 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. (AU)

FAPESP's process: 11/16643-2 - Genome-Wide Association Study for detection of chromosomal regions related to scrotal circumference in Nellore cattle
Grantee:Yuri Tani Utsunomiya
Support type: Scholarships in Brazil - Master
FAPESP's process: 10/52030-2 - Genome wide association study for reproductive traits in zebu bulls (Bos indicus) using high-density SNP chip
Grantee:José Fernando Garcia
Support type: Regular Research Grants