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. 2016 Jul 13;11(7):e0158165.
doi: 10.1371/journal.pone.0158165. eCollection 2016.

Pleiotropic Genes Affecting Carcass Traits in Bos indicus (Nellore) Cattle Are Modulators of Growth

Anirene G T Pereira  1   2 , Yuri T Utsunomiya  3   2 , Marco Milanesi  4   2 , Rafaela B P Torrecilha  3   2 , Adriana S Carmo  3   2 , Haroldo H R Neves  5 , Roberto Carvalheiro  6 , Paolo Ajmone-Marsan  7 , Tad S Sonstegard  8 , Johann Sölkner  9 , Carmen J Contreras-Castillo  1 , José F Garcia  3   4   2
Affiliations

Pleiotropic Genes Affecting Carcass Traits in Bos indicus (Nellore) Cattle Are Modulators of Growth

Anirene G T Pereira et al. PLoS One. .

Abstract

Two complementary methods, namely Multi-Trait Meta-Analysis and Versatile Gene-Based Test for Genome-wide Association Studies (VEGAS), were used to identify putative pleiotropic genes affecting carcass traits in Bos indicus (Nellore) cattle. The genotypic data comprised over 777,000 single-nucleotide polymorphism markers scored in 995 bulls, and the phenotypic data included deregressed breeding values (dEBV) for weight measurements at birth, weaning and yearling, as well visual scores taken at weaning and yearling for carcass finishing precocity, conformation and muscling. Both analyses pointed to the pleomorphic adenoma gene 1 (PLAG1) as a major pleiotropic gene. VEGAS analysis revealed 224 additional candidates. From these, 57 participated, together with PLAG1, in a network involved in the modulation of the function and expression of IGF1 (insulin like growth factor 1), IGF2 (insulin like growth factor 2), GH1 (growth hormone 1), IGF1R (insulin like growth factor 1 receptor) and GHR (growth hormone receptor), suggesting that those pleiotropic genes operate as satellite regulators of the growth pathway.

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Conflict of interest statement

Competing Interests: HHRN is employed by Gensys Consultores Associados and TSS is employed by Recombinetics, Inc. This does not alter the authors' adherence to PLOS ONE policies on sharing data and materials. Mention of trade name proprietary product or specified equipment in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the authors or their respective institutions.

Figures

Fig 1
Fig 1. Genome-wide Multi-Trait Meta-Analysis for loci affecting carcass traits in Bos indicus (Nellore) cattle.
The dashed horizontal line represents the significance threshold (p < 9.20 x 10−5). Results are shown before (A) and after (B) the removal of the effect of marker rs136543212 (probe ID BovineHD1400007373).
Fig 2
Fig 2. Association plot of chromosome 14 region.
LD (r2) with the top scoring marker rs136543212 (probe ID BovineHD1400007373) is represented according to the indicated color scale. The dashed horizontal line represents the significance threshold (p < 9.20 x 10−5). The chromosome-wise plot (A) and the regional plot around PLAG1 (B) reveal that the association is driven by a single large LD block.
Fig 3
Fig 3. Network of candidate pleiotropic genes for carcass traits in Bos indicus (Nellore) cattle.
The network was built from known protein-protein interactions (edges) between gene products (nodes). The size of the node is proportional to the number of traits the gene is associated with. In A, the network is portrayed according to the list of genes obtained from the VEGAS analyses. In B, after the inclusion of five essential genes (in blue) form the growth pathway, the network presented itself as a satellite, and four more genes (in red) could be incorporated, including the major pleotropic gene PLAG1.
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