PSIV-28 Unveiling the genomic architecture of novel profitability phenotypes in Nelore cattle.

Abstract The development of new traits can increase productivity and sustainability in beef production systems, particularly during the finishing phase, which faces challenges such as nutritional costs, price fluctuations, and genetic variability. Profit margins in feedlots are often narrow, requiring economies of scale for sustainable returns. This study proposes genome-wide association studies (GWAS) for two new traits: accumulated feedlot profitability (AFP) and profit per kilogram of live weight gain (PFT). GWAS provides important insights into the genetic architecture of complex and polygenic traits, especially those that are difficult, expensive, and time-consuming to measure. In this context, this study aimed to estimate (co)variance components and genetic parameters and to conduct a genome-wide association study (GWAS) to identify genomic regions associated with profitability traits in Nelore beef cattle. The dataset included 3,614 phenotypic records of AFP and PFT from animals born between 2020 and 2022, participating in the Nelore Brazilian breeding program from the National Association of Breeders and Researchers (ANCP). From this total, 2,127 animals were genotyped with the Clarifide® Nelore 3.0 SNP panel. After quality control, 2,127 genotyped animals and 35,658 SNPs remained in the dataset for analysis. The variance components were estimated using the restricted maximum likelihood method, using software BLUPF90+ through a single-trait model. The weighted single-step approach for genome-wide association (WssGWAS) methodology was used to identify genomic regions associated with AFP and PFT. A single-trait animal model was applied to predict genetic values, and SNP effect solutions were obtained from these values. Genomic windows of 10–SNP sliding windows that explained more than 0.5% of the additive genetic variance of each trait were selected to investigate potential candidate genes. The heritability estimates were moderate to low, with values of 0.24 for AFP and 0.05 for PFT, respectively. These results suggest additive genetic variability, and AFP and PFT should respond to selection. A total of 83 genes within 21 windows and 268 genes within 52 windows associated with the AFP and PFT were identified, respectively. Several genes related to fertility, feed efficiency, carcass traits, muscle and adipose tissue development and metabolism, and lipid and carbohydrate metabolism were identified, along with genes associated with animal behavior. Furthermore, 22 gene ontology terms associated with biological processes and cellular components were found and enrichment analysis revealed functional pathways (p-value ≤ 0.05), such as glucose homeostasis (GO:0042593), lipid homeostasis (GO:0055088), proteolysis (GO:0006508), PI3K-Akt signaling pathway (bta04151), calcium signaling (bta04020) and metabolic pathways (bta01100). The identification of these potential candidate genes and pathways provides us with a better understanding of the regulatory mechanisms (physiological and genetic) responsible for the expression of AFP and PFT in Nellore animals.