GxE

Genotype-by-environment interaction and genomic basis of adaptation to altitude in local cattle breeds

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Abstract

Understanding the adaptation of local cattle breeds to harsh and variable environments is important for developing sustainable production systems. This study investigated genotype-by-environment interactions (GxE) related to altitude in two local dual-purpose breeds, Aosta Black Pied-and-Chestnut (ABPC) and Aosta Red Pied (ARP), to assess the genetic sensitivity of milk traits to environmental gradients and identify the genomic and biological bases of resilience altitude based. The two populations are native to the Italian West-Alpine arc, with herds typically located in mountain areas.The dataset comprised about 1.5 million test-day records from ~93,000 cows, including ~12,000 genotyped animals with ~80k imputed SNPs, from herds located between 314 and 2,005 meters. Random regression models (RRMs) with a random intercept and first- and second-order polynomials of altitude were implemented for five traits: milk yield (ABPC 11.1 kg; ARP 14.8 kg), fat (3.41%; 3.46%) and protein (3.40%; 3.28%) content, fat (0.38 kg; 0.51 kg) and protein (0.37 kg; 0.48 kg). Variance components were estimated using GIBBSF90+. Single-step GWAS were then performed on the estimated intercept and slope effects using non-overlapping windows of 25 adjacent SNPs, selecting the top 0.5% based on proportion of variance explained. Genes were annotated using the R package GALLO based on ARS-UCD2.0.Genetic correlations between low and high altitudes were generally positive (ABPC: 0.79 ± 0.09; ARP: 0.95 ± 0.03). However, 22% of environmental pairs across altitude quantiles in ABPC and 4% in ARP showed correlations below 0.8, suggesting mild breed-specific GxE effects. Across traits, additive variances associated with the first- and second-order polynomials represented 14.5 ± 9.1% of total additive variance in ABPC and 9.4 ± 6.3% in ARP, confirming limited but consistent genetic variability in environmental sensitivity.The analyses of selected windows identified several core genes responsive to altitude and shared between both breeds. These genes primarily regulate metabolic resilience (AFM, ALB), vascular adaptation (ANKRD17), oxidative and inflammatory stress (PAFAH2, AFP, EXTL1), and nutrient transport (SLC30A2, COX18). Functional enrichment highlighted pathways for lipid metabolism, oxidative stress, and vascular homeostasis, supporting their roles in the adaptation to high altitudes. The overlap between genes influencing environmental sensitivity (first- and second-order polynomials) and mean productivity (intercept) was greater in ARP (over 50%) than in ABPC, suggesting a tighter coupling between production and adaptability in the more selected breed. In contrast, ABPC displayed a relatively higher genetic plasticity and a more distinct GxE pattern, maybe reflecting the issue that milk yield is not the primary interest for ABPC farmers.In conclusion, GxE interactions related to altitude in local Aosta breeds are modest but biologically coherent, suggesting the presence of adaptive mechanisms to altitude integrating metabolism, vascular function, and stress resilience.

Keywords: 2026

How to Cite:

Rulli, E., Mancin, E., López-Carbonell, D., Gomez Proto, G., Oian, A., Varona, L., Mantovani, R. & Sartori, C., (2026) “Genotype-by-environment interaction and genomic basis of adaptation to altitude in local cattle breeds”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285407. doi: https://doi.org/10.31274/wcgalp.23688

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