Genome-Wide Association Analysis Reveals Novel Loci Related with Visual Score Traits in Nellore Cattle Raised in Pasture–Based Systems

SIMPLE SUMMARY: Genome-wide association studies attempt to understand the genetic structure through the expression of genes that influence a given productive trait. This work studied the associations between single nucleotide polymorphism with visual score traits in beef cattle, identifying genomic regions and candidate genes with greater effects for body conformation, precocity, and muscularity. Several novel genomic regions that had not been previously identified in the literature were revealed. Our results will contribute to a better understanding of the molecular mechanism involved in Zebu cattle growth, serving as a base reference in adjacent research related to the application of molecular markers in the detection of new genomic regions related to traits of economic interest in beef cattle. ABSTRACT: Body conformation traits assessed based on visual scores are widely used in Zebu cattle breeding programs. The aim of this study was to identify genomic regions and biological pathways associated with body conformation (CONF), finishing precocity (PREC), and muscling (MUSC) in Nellore cattle. The measurements based on visual scores were collected in 20,807 animals raised in pasture-based systems in Brazil. In addition, 2775 animals were genotyped using a 35 K SNP chip, which contained 31,737 single nucleotide polymorphisms after quality control. Single-step GWAS was performed using the BLUPF90 software while candidate genes were identified based on the Ensembl Genes 69. PANTHER and REVIGO platforms were used to identify key biological pathways and STRING to create gene networks. Novel candidate genes were revealed associated with CONF, including ALDH9A1, RXRG, RAB2A, and CYP7A1, involved in lipid metabolism. The genes associated with PREC were ELOVL5, PID1, DNER, TRIP12, and PLCB4, which are related to the synthesis of long-chain fatty acids, lipid metabolism, and muscle differentiation. For MUSC, the most important genes associated with muscle development were SEMA6A, TIAM2, UNC5A, and UIMC1. The polymorphisms identified in this study can be incorporated in commercial genotyping panels to improve the accuracy of genomic evaluations for visual scores in beef cattle.