Sheep & Goats

Genome-Wide Association Analysis of Ewe Mature Weight Across Five Sheep Breeds

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Abstract

Ewe mature weight is a key performance indicator of both economic and environmental efficiency of sheep production systems. Although greater mature weight has been positively associated with reproductive performance, this relationship plateaus whereby heavier ewes incur greater feed requirements without necessarily delivering proportional gains in output. Therefore, given the central role of ewe mature weight in determining flock efficiency, understanding the underlying trait genetic architecture is essential for improving selection strategies. The objective of this study was to perform a genome-wide association study (GWAS) to identify genomic regions associated with ewe mature weight within and across five sheep breeds. Genotype data and predicted transmitting abilities (PTAs) were obtained from the Sheep Ireland database. Only purebred animals from the five most populous breeds were retained; Belclare (7,474), Charollais (10,084), Suffolk (7,878), Texel (16,867) and Vendeen (3,350). PTAs were deregressed using the secant method. Genotypes for all 45,623 animals were imputed to high-density using FImpute 2.2. All genotyped animals had a call rate ≥ 90% and only autosomal SNPs, a call rate ≥ 90% and minor allele frequency >0.001 were retained, resulting in 565,945 SNPs for analysis. Within-breed GWAS were performed using an animal mixed linear model in GCTA where all SNP, scored as 0, 1, or 2, were included individually as a fixed effect covariate in the model. A weighted Z-score meta-analysis across all breeds was completed using METAL. To detect suggestive quantitative trait locus (QTL), a genome-wide suggestive significance threshold of P ≤ 1 à— 10−5, in line with reporting standards of the NHGRI GWAS Catalog, was applied. Significant SNPs within a 1 Mb window and in strong linkage disequilibrium (r² ≥ 0.7) were grouped into a single QTL. Several QTL associated with ewe-mature weight were detected within each breed, although the number and significance of these varied among breeds; Belclare (n=4), Charollais (n=3), Suffolk (n=3), Texel (n=5), Vendeen (n=3) and across breed meta-analysis (n=5). Notably, the strongest QTL associations were identified on chromosome 9 and 11 within each breed. The QTL on chromosome 9, spanning from 19.92 to 20.36 Mb, encompassed the ZFAT gene, which is implicated in adipocyte maintenance and differentiation. The strongest association within this QTL was rs1091929706 with a p-value of 2.87x10-10 in the Charollais breed and remained the strongest SNP association in the meta-analysis (p=3.54x10-12). The QTL on chromosome 11, spanning from 27.72 to 28.66 Mb, contained several candidate genes, including MYH10, which has been previously associated with weight-related traits in cattle. Overall, ewe mature weight was influenced by many small effect polymorphisms, however, the identification of across-breed QTL suggests that a proportion of the genomic variance attributable to ewe mature weight is conserved and can be potentially exploited to improve system efficiency.

Keywords: 2026

How to Cite:

Purfield, D., Carthy, T., Pabiou, T. & McHugh, N., (2026) “Genome-Wide Association Analysis of Ewe Mature Weight Across Five Sheep Breeds”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2287290. doi: https://doi.org/10.31274/wcgalp.24257

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