Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of complex traits in pig.

Xu, Z.; Lin, Q.; Cai, X.; Zhong, Z.; Li, B.; Teng, J.; Zeng, H.; Gao, Y.; Cai, Z.; Wang, X.; Shi, L.; Wang, Y.; Zhang, Z.; Lin, Y.; Liu, S.; Yin, H.; Bai, Z.; Wei, C.; Zhou, J.; Zhang, W.; Zhang, X.; Shi, S.; Wu, J.; Diao, S.; Liu, Y.; Pan, X.; Feng, X.; Liu, R.; Su, Z.; Chang, C.; Zhu, Q.; Wu, Y.; The PigGTEx Consortium,; Zhou, Z.; Bai, L.; Li, K.; Wang, Q.; Pan, Y.; Peng, X.; Mei, S.; Mo, D.; Liu, X.; Zhang, H.; Yuan, X.; Liu, G. E.; Su, G.; Sahana, G.; Lund, M.; Ma, L.; Xiang, R.; Shen, X.; Li, P.; Huang, R.; Ballester, M.; Crespo-Piazuelo, D.; Amills, M.; Clop,

doi:10.1101/2023.10.09.561393

Home/Archive/bioRxiv

bioRxiv · 10.1101/2023.10.09.561393

Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of complex traits in pig.

View original source ↗Export metadata ↓

Abstract

Understanding the molecular and cellular mechanisms that underlie complex traits in pigs is crucial for enhancing their genetic improvement program and unleashing their substantial potentials in human biomedicine research. Here, we conducted a meta-GWAS analysis for 232 complex traits with 28.3 million imputed whole-genome sequence variants in 70,328 individuals from 14 pig breeds. We identified a total of 6,878 genomic regions associated with 139 complex traits. By integrating with the Pig Genotype-Tissue Expression (PigGTEx) resource, we systemically explored the biological context and regulatory circuits through which these trait-associated variants act and finally prioritized 16,664 variant-gene-tissue-trait circuits. For instance, rs344053754 regulates the expression of UGT2B31 in the liver by affecting the activity of regulatory elements and ultimately influences litter weight at weaning. Furthermore, we investigated the conservation of genetic and regulatory mechanisms underlying 136 human traits and 232 pig traits. Overall, our multi-breed meta-GWAS in pigs provides invaluable resources and novel insights for understanding the regulatory and evolutionary mechanisms of complex traits in both pigs and humans.

Source connections

Published article ↗

Explore related subjects

genetics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Xu, Z., Lin, Q., Cai, X., Zhong, Z., Li, B., Teng, J., Zeng, H., Gao, Y., Cai, Z., Wang, X., Shi, L., Wang, Y., Zhang, Z., Lin, Y., Liu, S., Yin, H., Bai, Z., Wei, C., Zhou, J., Zhang, W., Zhang, X., Shi, S., Wu, J., Diao, S., Liu, Y., Pan, X., Feng, X., Liu, R., Su, Z., Chang, C., Zhu, Q., Wu, Y., The PigGTEx Consortium,, Zhou, Z., Bai, L., Li, K., Wang, Q., Pan, Y., Peng, X., Mei, S., Mo, D., Liu, X., Zhang, H., Yuan, X., Liu, G. E., Su, G., Sahana, G., Lund, M., Ma, L., Xiang, R., Shen, X., Li, P., Huang, R., Ballester, M., Crespo-Piazuelo, D., Amills, M., Clop,. 2023-10-11. Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of complex traits in pig.. https://doi.org/10.1101/2023.10.09.561393

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

OPA1 controls mitochondrial dysfunction-driven liver fibrosis in MASLD

Progressive hepatic fibrosis is the principal determinant of morbidity and mortality in metabolic dysfunction-associated steatotic liver disease and steatohepatitis (MASLD/MASH). Mitochondrial dysfunction is a hallmark of MASH, and the release of mitochondrial damage-associated molecular patterns (mito-DAMPs) from injured hepatocytes can promote fibrosis. However, how mitochondrial dynamics and quality control shape the fibrotic response in MASLD/MASH remains unclear. Here, through large-scale genomic analyses of mitochondrial genes governing mitophagy, fusion and fission in human MASLD, with a power-equivalent sample size of approximately 700,000 individuals, we identify a strong association between hepatic fibrosis and the mitochondrial fusion factor dynamin-like GTPase optic atrophy 1 (OPA1). OPA1 transcripts and protein abundance in the liver epithelium were progressively dysregulated with advancing fibrosis. In mice, hepatocyte-specific OPA1 loss alone was sufficient to induce hepatic stellate cell activation and fibrosis in zone 3, promoted the release of mito-DAMPs into the circulation and exacerbated fibrosis in experimental MASH. These findings identify OPA1 as a central regulator of the hepatic fibrotic response and connect defective mitochondrial homeostasis to mito-DAMP release, hepatic stellate cell activation and fibrosis in MASLD.

genetics↗

bioRxiv2026

Mechanism-selective deep mutational scanning distinguishes ERCC2 disease phenotypes

Pathogenic ERCC2 variants cause xeroderma pigmentosum (XP), trichothiodystrophy (TTD) or both, yet variant effect scores are usually interpreted only as measures of pathogenicity rather than of which disease mechanism is disrupted. XPD, the ERCC2-encoded TFIIH subunit, functions in both nucleotide excision repair and transcription. Using yeast complementation deep mutational scanning, we measured the effects of nearly all XPD amino acid substitutions. The assay was mechanism-selective: it preferentially reported transcription-associated function, with pronounced intolerance at the p44 interface, whereas many substitutions affecting DNA binding and helicase activity retained near-wild-type fitness. Accordingly, TTD variants had much lower fitness than XP variants. Computational predictors discriminated pathogenic from benign variants similarly across phenotypes, but the DMS distinguished XP from TTD variants better than all 73 predictors tested. Phenotype-specific ACMG/AMP calibration provided evidence in both directions for TTD but mainly pathogenic evidence for XP. Thus, the selectivity of functional assays, often viewed as a limitation, can reveal disease mechanisms and support phenotype-aware variant interpretation.

genetics↗

bioRxiv2026

Temporal control of mitochondrial mutagenesis reveals the fate of mtDNA mutations with age

Mutations in the mitochondrial genome (mtDNA) play a critical role in the aging process and a wide variety of age-related diseases. However, it remains unclear when the mutations that drive physiological decline arise. To answer this question, we generated a new mouse model in which mitochondrial mutagenesis can be confined to a defined window of time. Surprisingly, we found that mutations that arise during the first two months of life are sufficient to drive a wide variety of age-related pathologies, and that the severity of this pathology is broadly regulated by distinct, tissue-specific selective pressures that control the fate of mtDNA mutations with age. Further, we found that selection against deleterious variants can be modulated by manipulation of mitochondrial fusion in vitro and in vivo. These observations raise the possibility that in some tissues, the pace of aging is pre-determined by events that occur early in life and that interventions targeting mitochondrial fusion may be able to slow down or reverse the expansion of these pathogenic variants. These results carry far-reaching implications for strategies aimed at preventing or delaying age-related decline.

genetics↗