Genome-wide association study for feed efficiency indicator traits in Nellore cattle considering genotype-by-environment interactions

Joao B. Silva Neto^1,2*Luiz Brito¹Lucio F. M. Mota²Claudio U. Magnabosco³Fernando Baldi²

• ¹Purdue University, West Lafayette, United States
• ²Faculty of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal, São Paulo, Brazil
• ³Embrapa Arroz e Feijão, Santo Antônio de Goiás, Goiás, Brazil

Feed efficiency is a key factor in animal production sustainability, directly affecting production costs, environmental efficiency, and farmer profitability. The inclusion of feeding efficiency traits in cattle breeding programs has occurred later than other species due to longer life cycles and the high costs associated with measuring feed intake. However, genomic selection has facilitated the inclusion of difficult-to-measure traits in selection schemes. Thus, the primary objective of this study was to conduct a genome-wide association study (GWAS) based on single-step genomic reaction norm models to identify genomic regions associated with dry matter intake (DMI) and residual feed intake (RFI) in Nellore cattle, considering genotype-environment interactions (G×E). Phenotypic data from 23,170 animals (young bulls and heifers) were recorded during 301 feed efficiency trials. Ten and eleven genomic windows explaining more than 1% of the total direct additive genetic variance were identified for the intercept and slope of RFI, respectively, while 12 and 17 genomic windows were identified for DMI. Multiple protein-coding genes (RFI: 66 for intercept and 47 for slope; DMI: 107 for intercept and 109 for slope) located within these regions were associated with critical biological functions, including insulin, leptin, glucose, protein, and lipid metabolism, energy balance, heat stress response, feeding behavior, digestion process, and nutrient absorption. The large functional variability in genes highlights the plasticity of the genetic network in response to environmental variation. While some genes remained central in both average and more challenging environments, others emerged as crucial in modulating genetic responses to environmental fluctuations, underscoring the role of G×E in regulating these traits. The SNPs located in the relevant genomic regions showed differences in the magnitude and direction of effects across the environmental gradient levels, further reinforcing the presence of G×E interactions. As a result, the genomic estimated breeding values for the animals also varied between extreme environmental gradients for DMI and RFI. These results highlight the adaptability of genetic networks to environmental changes and are essential for refining strategies to improve feed efficiency in Nellore cattle.