Sheep & Goats

Genome-wide association study for general resilience indicators in dairy sheep

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Abstract

Resilience, the ability to withstand or rapidly recover from disturbances, is a trait of interest in livestock due to its association with reduced handling and veterinary costs and improved longevity. Understanding the genetic basis of resilience could facilitate the selection of animals better adapted to challenges. Accordingly, this study aimed to identify genetic markers linked to general resilience in dairy sheep. Daily milk yield records from 1,448 Spanish Assaf ewes from two flocks were included. Resilience indicators were estimated after fitting individual lactation curves up to 210 days in milk (DIM) using a 5th-percentile cubic spline with knots at 36, 68, 100, 132, and 165 DIM. Three resilience indicators (RIs) were calculated from the deviations between observed and estimated yield: the natural logarithm of the variance (LnVar), the lag-1 autocorrelation coefficient (rauto), and the skewness (Skew). A genome-wide association study (GWAS) was conducted for the three RIs using 1,499 animals and 40,783 SNPs after quality control (individual call rate > 0.90, genotypic call rate > 0.95, minor allelic frequency > 0.05, and Hardy-Weinberg equilibrium deviations > 1×10⁻⁵) followed by QCF90 software. Variance components were estimated using Gibbsf90 with genomic and pedigree data, fitting flock-year-lambing season, number of lambs born alive, and lambing age as fixed effects. The GWAS was performed using the single-step GBLUP (ssGBLUP) approach with the same model, and the variance explained by genomic regions was estimated using 1 Mb non-overlapping SNP windows. Heritability estimates were 0.28 ± 0.06 for LnVar, 0.09 ± 0.04 for rauto, and 0.05 ± 0.07 for Skew (± standard deviations). Additive genetic variances (σ2a) were 0.102, 0.001, and 0.021 respectively. Genomic windows explaining >1% of σ²a were further examined, following common empirical thresholds. For LnVar, 30 windows were identified, accounting for 48.69% of σ2a. The window explaining the largest σ2a proportion (2.95%) was on chromosome 2 with 18 SNPs. For rauto, 19 windows were found, explaining 47.22% of σ2a, with the top-explaining window (8.08% of σ2a) on chromosome 1 (17 SNPs). For Skew, no genomic windows were identified due to the very small σ2a relative to the residual variance. A total of 11 candidate genes were extracted from the genomic windows explaining the highest proportion of variance for LnVar and rauto using the R package GALLO (8 for LnVar and 3 for rauto; GRIN3A and DPH5 were the closest genes to each trait top-variance window, respectively). For the 11 candidates, a preliminary functional annotation analysis with ToppGene identified terms associated with synaptic and lipid-mediated signaling, energy metabolism, and ubiquitin-mediated protein modification. These findings provide an initial insight into the genetic basis of general resilience in dairy sheep, suggesting relevant biological mechanisms underlying this complex trait.

Keywords: 2026

How to Cite:

Arranz, J., Arribas Gonzalo, R., de Faria, A., Fonseca, P., Gutiérrez-Gil, B., Pelayo, R. & Suárez-Vega, A., (2026) “Genome-wide association study for general resilience indicators in dairy sheep”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286405. doi: https://doi.org/10.31274/wcgalp.23987

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