Genomic regions and metabolic pathways associated with carcass yield in Nellore cattle using the single step procedure

The objective of this study was to identify genomic regions and metabolic pathways associated to carcass yield in Nellore polled cattle population. The analyzed data set was provided by the Guapor? Agropecuaria S/A and the Embrapa. The slaughters were carried out in commercial slaughterhouses. The mean yield carcass was 55.3 ? 2.44 % (n = 436). The animals were genotyped using the Bovine HD Beadchip 777k and the Chip GGP-Indicus-77k. The animals genotyped with the Chip GGP-Indicus-77k were imputed to Bovine HD Beadchip 777k using the FImpute software. The markers with minor allele frequency (MAF) and call rate higher than 5% and 95%, respectively, were considered, as well as samples with a call rate higher than 93%. After quality control of markers, there were available 590,915 SNPs for 609 animals. The SNP markers effects and their variances were estimated using the single-step genome wide association method (ssGWAS). The (co)variance components were estimated by Bayesian inference using the gibbs2f90 software. The model included the random additive animal effect, the fixed effects of slaughter, sex and the animal age at slaughter as covariable (linear and quadratic effect). A total of 7 genomic regions were identified that explained more than 1.0% of additive genetic variance for carcass yield. For identification and positioning the SNPs in the bovine genome was realized research on the database available at NCBI and Ensembl websites. In the window located in BTA16 at position 71 Mb, the PPP1R12B gene was found. This gene is responsible for the activation of myosin phosphatase and actin cytoskeleton regulation. The PRKAB1 gene, found in BTA17 at position 58 Mb, is responsible for the activation of myosin indirectly, remodeling the actin cytoskeleton and has a growth factor related to the AMP-activated protein kinase (AMPK). Ten other genes linked to growth factor were found, such as DUSP19, TSPAN13, AGR2, PCSK1, TOPORS, PRG4, PTPN14, PTPN7, CIT and ACAD10 that have activities of tyrosine or serine/threonine kinases. These results would support to elucidate the pathways associated with carcass yield in Nellore polled cattle, suggesting hypertrophy and oxidative capacity can occur simultaneously in skeletal muscle.