Genome-wide association study of novel feedlot profitability-related traits in Nelore cattle

Abstract

This study aimed to conduct a genome-wide association study to identify genomic regions associated with profitability traits in Nelore beef cattle. The dataset included 3614 phenotypic records of accumulated feedlot profitability (AFP) and profit per 15 kg of liveweight gain (PFT) from animals born between 2020 and 2022, participating in the Nelore Brazilian breeding program from the National Association of Breeders and Researchers. From this total, 2127 animals were genotyped with the Clarifide® Nelore 3.0 SNP panel. After quality control, 2127 genotyped animals and 35 658 SNPs remained in the dataset for analysis. The weighted single-step approach for genome-wide association 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 >0.5% of the additive genetic variance of each trait were selected to investigate potential candidate genes. 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. The results revealed that identifying genomic regions and their respective candidate genes contributes substantially to a better understanding of the genetic mechanisms regarding these novel profitability-related phenotypes in Nelore beef cattle.