Deregressed estimated breeding values (dEBV) and genome-wide SNP effects correlations (inside brackets) for weight and carcass traits in <i>Bos indicus</i> (Nellore) bulls.

<p>Deregressed estimated breeding values (dEBV) and genome-wide SNP effects correlations (inside brackets) for weight and carcass traits in <i>Bos indicus</i> (Nellore) bulls.</p

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

<div><p>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 <i>Bos indicus</i> (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 (<i>PLAG1</i>) as a major pleiotropic gene. VEGAS analysis revealed 224 additional candidates. From these, 57 participated, together with <i>PLAG1</i>, in a network involved in the modulation of the function and expression of <i>IGF1</i> (insulin like growth factor 1), <i>IGF2</i> (insulin like growth factor 2), <i>GH1</i> (growth hormone 1), <i>IGF1R</i> (insulin like growth factor 1 receptor) and <i>GHR</i> (growth hormone receptor), suggesting that those pleiotropic genes operate as satellite regulators of the growth pathway.</p></div

Network of candidate pleiotropic genes for carcass traits in <i>Bos indicus</i> (Nellore) cattle.

<p>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 <i>PLAG1</i>.</p

Genome-wide Multi-Trait Meta-Analysis for loci affecting carcass traits in <i>Bos indicus</i> (Nellore) cattle.

<p>The dashed horizontal line represents the significance threshold (<i>p</i> < 9.20 x 10⁻⁵). Results are shown before (A) and after (B) the removal of the effect of marker rs136543212 (probe ID BovineHD1400007373).</p