Genetic gain & Inbreeding

Genomic and pedigree inbreeding estimates and their impact on sheep production traits

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Abstract

The increasing availability of genomic information enables the estimation of genomic inbreeding coefficients and assessment of their impact on phenotypic performance. This study estimates pedigree and genomic inbreeding coefficients and assesses whether inbreeding depression exists. Pedigree and genomic data were obtained from the Irish national sheep database on 43,531 purebred animals representing five breeds (Belclare = 7,215, Charollais = 9,849, Suffolk = 7,187, Texel = 16,036, Vendeen = 3,244), with ≥3 complete generation equivalents. Genotypes originated from three medium density SNP panels and were imputed to the common density (47,182 SNPs). Pedigree-based inbreeding coefficients, including classical (FPed) and Ballou's ancestral (FBal) were estimated. Genomic-based inbreeding coefficients were calculated based on total runs of homozygosity (ROH; FROH) as well as short (FROH_1-8Mb) and long (FROH >8Mb) ROH. The effect of inbreeding on lambing and weight traits was estimated using linear models which included trait-specific fixed effects and the inbreeding coefficient of interest; direct and maternal genetic effects were included as random effects. Across breeds, pedigree-based classical inbreeding (FPed) was low, ranging from 0.01 (SD 0.02; Charollais) to 0.04 (SD 0.02; Belclare); higher ancient inbreeding (FBal) was estimated for Suffolk and Belclare. Compared to pedigree metrics, greater within and across-breed variation in genomic inbreeding coefficients were observed; FROH ranged from 0.06 (SD 0.02; Charollais) to 0.13 (SD 0.04; Suffolk). Belclare, Suffolk and Texel breeds had lower ancient genomic relative to ancient pedigree inbreeding coefficients. Ancient genomic inbreeding (FROH_1-8Mb) contributed more to FROH than recent inbreeding (FROH >8Mb). Moderate correlations (0.27 to 0.70) were observed among pedigree and genomic metrics, although the intercept of the regression of all genomic inbreeding coefficients on pedigree coefficients were greater than zero, suggesting pedigree-based inbreeding underestimated genome homozygosity. With the exception of lamb mortality and vigour, evidence of inbreeding depression was observed for all traits (PPed impacted lambing and lamb weight traits, with estimates of inbreeding depression ranging from 0.09% to 0.61% of the phenotypic mean. Increasing FPed by 1% reduced lambing ease score (-0.01) and weaning weight (-0.06 kg). Genomic estimates (FROH) for lambing ease score and weight traits were significant and, on average, slightly lower than FPed estimates (PROH_1-8Mb); relative to FPed a 1% increase was associated with a doubling of the reduction in lambing ease score and weaning weight. Recent genomic inbreeding (FROH >8Mb) reduced all weight traits to a greater extent than FROH. Results from this study show moderate correlations between pedigree and genomic inbreeding coefficients, with inbreeding depression reducing lambing and lamb weight performance. Future breeding strategies should utilise genomic data to reduce inbreeding levels, thereby increasing animal performance.

Keywords: 2026

How to Cite:

McHugh, N., Pabiou, T., Purfield, D. & Rahman, M., (2026) “Genomic and pedigree inbreeding estimates and their impact on sheep production traits”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286966. doi: https://doi.org/10.31274/wcgalp.24182

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