Xu Z, Lin Q, Cai X, Zhong Z, Teng J, Li B, Zeng H, Gao Y, Cai Z, Wang X, Shi L, Wang X, 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, Xu Zhong, Peng X, Mei S, Mo D, Liu X, Zhang H, Yuan X, Liu Y, Liu G, Su G, Sahana G, Lund MS, Ma L, Xiang R, Shen X, Li P, Huang R, Ballester M, Piazuelo DC, Amills M, Clop A, Mortensen PK, Fredholm M, Tang G, Li M, Li X, Ding X, Li J, Chen Y, Zhang Q, Zhao Y, Zhao F, Fang L, Zhang Z
(Contact: zhezhang@scau.edu.cn)
Affiliation:
State Key Laboratory of Swine & Poultry Breeding Industry, Natl. Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural Univ., Guangzhou, China
Title:
Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs
Understanding the molecular and cellular mechanisms that underlie complex traits in pigs is crucial for enhancing their genetic improvement via artificial selection and unleashing their suitability as models for human disease and biology. Here, we conducted a comprehensive meta-GWAS analysis for 232 pig complex traits with 28.3 million imputed whole-genome sequence variants in 70,328 individuals from 14 breeds. We identified a total of 6,878 genomic regions significantly 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 and intestines by affecting the activity of enhancer and ultimately influences litter weight at weaning in pigs. Furthermore, we observed certain conservation of genetic and regulatory mechanisms underlying homologous traits between humans and pigs. 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.
