Identification of gene expression regulatory polymorphisms in muscle tissue and their association with carcass traits in cattle

• Grant number: 19/18385-2
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: December 01, 2019
• End date: February 28, 2023
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Luiz Lehmann Coutinho
• Grantee: Bárbara Silva Vignato
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil

Abstract

The primary objective of the meat industry has been the production of animals with a high yield of cuts and an adequate proportion of carcass fat. Thus, research that aimed to understand the molecular mechanisms involved in the regulation of traits associated with muscle and fat deposition in the carcass, such as ribeye area (REA) and backfat thickness (BFT), have been highlighted. The present study aims to identify gene expression regulatory polymorphisms (eQTL - expression trait loci) associated with REA and BFT in the skeletal muscle of Nellore cattle. For this, RNA-Seq data from Longissimus dorsi muscle of 200 animals will be used. The GATK will be used to identify SNPs in RNA-Seq data with the haplotype option. A genomic association study will be performed to associate the identified markers with the phenotype. EMMAX will be employed to eQTL identification, based on SNP and gene expression data. For each SNP in the dataset, the association with gene expression will be estimated by adjusting the genomic relationship matrix to explain population structure. Will be considered cis- and trans-eQTLs. The functional annotation of the genes within the eQTL regions will be performed using Biomart/Ensembl. DAVID and WebGestalt will be employed in the enrichment analysis to discover Gene Ontology terms and metabolic pathways in which these genes are involved. These results will allow us to understand gene expression mechanisms involved in the regulation of economic relevant carcass traits, increasing its accuracy in animal selection programs and, contributing to scientific research progress in the area.