Genome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle

Understanding genotype-by-environment interactions (GxE) is crucial to understand environmental adaptation in mammals and improve the sustainability of agricultural production. Here, we present an extensive study investigating the interaction of genome-wide SNP markers with a vast assortment of environmental variables and searching for SNPs controlling phenotypic variance (vQTL) using a large beef cattle dataset. We showed that GxE contribute 10.1%, 3.8%, and 2.8% of the phenotypic variance of birth weight, weaning weight, and yearling weight, respectively. GxE genome-wide association analysis (GWAA) detected a large number of GxE loci affecting growth traits, which the traditional GWAA did not detect, showing that functional loci may have non-additive genetic effects regardless of differences in genotypic means. Further, variance-heterogeneity GWAA detected loci enriched with GxE effects without requiring prior knowledge of the interacting environmental factors. Functional annotation and pathway analysis of GxE genes revealed biological mechanisms by which cattle respond to changes in their environment, such as neurotransmitter activity, hypoxia-induced processes, keratinization, hormone, thermogenic and immune pathways. We unraveled the relevance and complexity of the genetic basis of GxE underlying growth traits, providing new insights into how different environmental conditions interact with specific genes influencing adaptation and productivity in beef cattle and potentially across mammals.

Automated summary

Understanding genotype-by-environment interactions is crucial for environmental adaptation and sustainability in mammals. This study explored the impact of GxE on growth traits in beef cattle, identifying functional loci with non-additive genetic effects and revealing biological mechanisms of environmental response through functional annotation and pathway analysis of GxE genes. The complexity of genetic basis underlying GxE provides new insights into how specific genes interact with different environmental conditions to influence adaptation and productivity.