Weight Gain and Tenderness in Nelore Cattle: Genetic Association and a Potential Pleiotropic Role of Transcription Factors and Genes

The inclusion of meat quality traits in breeding programs is a promising strategy to improve beef by selecting animals based on both growth and meat quality. This study aimed to estimate genetic parameters for average daily gain (ADG) and Warner-Bratzler shear force (WBSF), as well as to perform genome-wide association studies (GWAS) to identify genomic regions and transcription factor (TF) binding sites associated with both traits in Nelore cattle. Genetic parameters were estimated using a bi-trait Bayesian model, and GWAS identified key SNPs explaining over 1% of variance in genomic estimated breeding values. Candidate genes near these SNPs were annotated, TF binding sites predicted, and gene-TF networks constructed. Genetic estimates indicated moderate heritability for ADG, low heritability for WBSF, and a small negative genetic correlation between traits. Genomic regions contained 116 and 151 candidate genes for ADG and WBSF, respectively, with 35 shared between traits. Functional analyses highlighted <i>MYBPC1</i> and <i>PENK</i> for WBSF, and <i>GHRS</i> and <i>NPY</i> for ADG. TF analysis identified 25 TFs, with 3 key ones highlighted. Gene-TF networks revealed candidates including <i>CAPN1</i> and <i>LTBP3</i> for WBSF, and <i>CARM1</i> and <i>GH1</i> for ADG. Shared candidate genes identified in the combined network provide valuable insights into the genetic architecture of growth and tenderness in Nelore cattle.