Authors
Ferran Llobet-Cabau, Antonio Reverter, Maria Ballester, Josep M Folch
Published in
Journal of animal science. Nov 12, 2026. Epub Nov 12, 2026.
Abstract
Fatty acid (FA) metabolism depends on tissue dynamics, with liver having a key role. We examine the ability of cis-acting variants affecting gene expression (cis-eQTLs) to capture additive genetic variance for a total of 68 traits (8 carcass traits and the content of 20 FAs in adipose tissue, liver and muscle) in a population of 332 Duroc pigs with genotypes for 37,700 autosomal SNPs. A total of 1,601 hepatic cis-eQTLs tagged by 1,312 cis-SNPs were used to build a cis-Genomic Relationship Matrix (cis-GRM) and compare it to the GRM built with a set of 36,388 remaining SNPs (rem-GRM). We examined the power of the cis-GRM at capturing heritability (h2) based on four genomic-based models: M1 with a GRM (tot-GRM) built with the totality of 37,700 SNPs; M2 with the cis-GRM only; M3 with the rem-GRM only; and M4 with both the cis-GRM and the rem-GRM. Compared to the h2 estimated from M1 (hM12), the equivalent from M2 (hM22) was best for adipose tissue with a non-zero estimate of hM22in 19 out of 20 FAs and averaging 96.27% of hM12. In muscle tissue, hM22 was > 0 in 4 FAs and averaging 111.84% of hM12. In contrast, the estimated hM22 for FA content in liver was > 0 in 10 FAs and averaged 61.87% of hM12. Finally, for carcass traits hM22 was > 0 for all 8 traits and averaged 76.32% of hM12. The exceptional performance of M2 at capturing genetic variation for FA in adipose tissue was attributed to the numerical stability of FA content in adipose tissue compared to liver or muscle. To determine the significance of the performance of M2, we ran 10,000 random permutation tests of a poor-performer trait, carcass weight (CWT) (hM22 = 49.25% of hM12); and a good-performer trait, dihomo-γ-linolenic acid (C20:3(n-6)) in adipose tissue (hM22 = 109.96% of hM12). The empirical p-values were 98.85%, and 0.10% for CWT and C20:3(n-6) respectively, indicating that a random set of 1,312 SNP could perform as good or better than M2 for CWT almost always, while almost never could rival M2 for C20:3(n-6). Hence, C20:3(n-6) content is affected by the pleiotropic activity of all cis-eQTL and the major-effect cis-eQTL of FADS1. Our results reflect the life-long activity of cis-eQTL genes and demonstrate that, under a sound biological context, a low-density SNP panel derived from cis-eQTL can be used to capture a significant amount of additive genetic variance for FA composition in adipose tissue.
PMID:
43016360
Bibliographic data and abstract were imported from PubMed on 12 Nov 2026.
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