Detecting loci under recent positive selection in dairy and beef cattle by combining different genome-wide scan methods

PLoS One. 2013 May 16;8(5):e64280. doi: 10.1371/journal.pone.0064280. Print 2013.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Cattle
  • Genome-Wide Association Study
  • Models, Theoretical*
  • Polymorphism, Single Nucleotide / genetics
  • Quantitative Trait Loci / genetics
  • Selection, Genetic / genetics*

Grant support

This research received support from the European Science Foundation and the Advances in Farm Animal Genomic Resources project (process n°3726), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (processes 560922/2010-8 and 483590/2010-0), Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) (processes 2011/16643-2 and 2010/52030-2) and USDA Agricultural Research Service (project 1265-31000-098D). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.