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.
Highlights
Carcass yield plays a major economic role in beef cattle, as the carcass retail price is essentially determined by its weight
On average (Table 1), deregressed breeding values (dEBV) were moderately correlated across traits (r = 0.442), and strikingly similar results were found for t-values across traits (r = 0.423)
Besides pleomorphic adenoma gene 1 (PLAG1), we found a series of growth-related genes, including growth differentiation factors 2 (GDF2) [41], (GDF10) [42] and (GDF11) [43], growth arrest-specific 2 like 3 (GAS2L3) [44], fibroblast growth factor 22 (FGF22) [45], PH domain and leucine rich repeat protein phosphatase 1 (PHLPP1) [46], signal transducer and activator of transcription 2 (STAT2) [47], SMAD family member 4 (SMAD4) [48], and insulin-like growth factor binding protein 5 (IGFBP5) [49]
Summary
Carcass yield plays a major economic role in beef cattle, as the carcass retail price is essentially determined by its weight. As differences in carcass yield between steers are partially heritable, selection and breeding are determinant operations in the beef cattle sector [1]. Pleiotropic Genes Affecting Carcass Traits in Bos indicus in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section
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