GWAS & Selection signatures

Non-additive GWAS identifies a recessive region on pig chromosome 1 associated with backfat and mortality

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Abstract

Recessive lethal alleles are gene variants that cause death or severe physiological dysfunction when present in a homozygous state. Heterozygous individuals typically appear healthy, allowing these alleles to persist and even spread in breeding populations, particularly when they are linked to favorable traits. This increases the risk of producing homozygous offspring with reduced viability or performance. The objective of this study was to perform both additive and non-additive genome-wide association analyses (GWAS) for backfat thickness in Duroc pigs, aiming to identify recessive regions that could indicate the presence of deleterious alleles and better capture non-additive genetic effects. By integrating phenotypic data from 60,000 Duroc pigs and a high-density SNP panel (660K), we identified a leading SNP associated with backfat thickness and evaluated its effects on mortality. Our results revealed a highly significant recessive peak for backfat on chromosome 1 (p=1.74e-134), where the homozygote allele frequency was 2%, indicating a rare variant with a strong effect in homozygous form. The top SNP from the GWAS is an intronic variant in the argininosuccinate synthase 1 (ASS1) gene, which plays a critical role in normal nitrogen metabolism, growth, and health in pigs. The same variant showed an association with decreased mortality. Together with its favorable effect on backfat, this indicates that the allele has a concordant effect on both production and survival traits.Interestingly, the top SNP is in complete linkage disequilibrium with a previously reported stop-gain mutation in ASS1 in Duroc pigs, identified in another study, which is predicted to abolish protein function. Loss of ASS1 activity would lead to citrullinemina, hyperammonemia, and potentially death in homozygous individuals. However, the effect of this mutation was reported to be restored by a compensatory mutation in the same codon, resulting in an L315Q missense mutation. Further studies are needed to clarify if this is the causal variant underlying our association signal.In conclusion, our study identifies a recessive region in the ASS1 gene associated with increased backfat and suggests additional effects on mortality. These findings highlight the importance of considering both additive and non-additive genetic effects.

Keywords: 2026

How to Cite:

van Son, M., van der Spek, D., Derks, M. & Grindflek, E., (2026) “Non-additive GWAS identifies a recessive region on pig chromosome 1 associated with backfat and mortality”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2284579. doi: https://doi.org/10.31274/wcgalp.23596

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