Mecanismos de regulação gênica relacionados a eficiência alimentar em bovinos da raça Nelore

Abstract

Brazil is one of the main beef producers and exporters, with herds predominantly composed of Nellore Zebu animals (Bos indicus). In this scenario, genomics can contribute to the identification of potential biomarkers of agricultural interest features. In previous studies, COL1A1, CTGF, CYP2B6, EGR1 and PRUNE2 were differentially expressed genes (DEGs) between groups of animals contrasting for the residual feed intake phenotype in liver tissue. The objective of this work was to select single nucleotide polymorphisms (SNPs) that potentially affect regulatory regions in the genes mentioned and associate them with different phenotypic measures of feed efficiency (FE). For this, using imputed genotypes of 398 Nellore steers, SNPs were selected in a window from 2 Kb upstream to the transcription start site to the end of the 3' UTR reduced of the DEGs. In the functional annotation, performed with the VEP software, variants in intronic regions, synonyms and those that are not possible regulatory splicing were not considered. For the selected SNPs, the linkage disequilibrium was analyzed by PLINK and Haploview software, and the in silico prediction of transcription factor binding sites (TFBSs) and microRNAs (miRNAs) binding sites was made using the LASAGNA and RNAhybrid software, respectively. A linear regression model was applied to associate SNPs with the phenotypic measures of FE, and significant SNPs were compared to regions of quantitative trait loci (QTLs) of phenotypes of livestock interest from studies in the same experimental population and from the Cattle QTL database. After functional annotation, two SNPs were selected in the upstream region of the CTGF gene; three referring to COL1A1, one in a splicing region and two in the upstream; 15 for the CYP2B6 gene, among them, one missense variant, four in 5 'UTR and three in 3' UTR, upstream and downstream; five for the EGR1 gene, one of these in the 3’ UTR region and four in the upstream region; and 33 SNPs referring to the PRUNE2 gene, three in the upstream region and six in the downstream region, and 24 missense variants. Among these, the SNPs for the five DEGs have the potential to influence TFBSs and have also been integrated into QTL regions of bovine phenotypes. SNPs of the CYP2B6 and EGR1 genes have the potential to influence the binding of several bovine miRNAs. Finally, two SNPs located in the CTGF gene were associated with the phenotypic measure of gross feed efficiency, one SNP in the COL1A1 gene was associated with the measures of average daily gain and feed conversion, and 19 SNPs in the PRUNE2 were associated with residual feed intake, respectively. The SNPs identified increase the knowledge about the possible role regulation of genes involved with phenotypic features of FE.