Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs
Xu, Zhiting coord. (South China Agricultural University)
Lin, Qing (South China Agricultural University)
Cai, Xiaodian (South China Agricultural University)
Zhong, Zhanming (South China Agricultural University)
Teng, Jinyan (South China Agricultural University)
Li, Bingjie (Scotland's Rural College)
Zeng, Haonan (South China Agricultural University)
Gao, Yahui (University of Maryland)
Cai, Zexi (Aarhus University)
Wang, Xiaoqing (Chinese Academy of Agricultural Sciences)
Shi, Liangyu (Chinese Academy of Agricultural Sciences)
Wang, Xue (China Agricultural University)
Wang, Yi (China Agricultural University)
Zhang, Zipeng (China Agricultural University)
Lin, Yu (Sichuan Agricultural University)
Liu, Shuliang (Westlake Laboratory of Life Sciences and Biomedicine)
Yin, Hongwei (Agricultural Genomics Institute at Shenzhen)
Bai, Zhonghao (Aarhus University)
Wei, Chen (South China Agricultural University)
Zhou, Jun (South China Agricultural University)
Zhang, Wenjing (South China Agricultural University)
Zhang, Xiaoke (South China Agricultural University)
Shi, Shaolei (South China Agricultural University)
Wu, Jun (South China Agricultural University)
Diao, Shuqi (South China Agricultural University)
Liu, Yuqiang (South China Agricultural University)
Pan, Xiangchun (South China Agricultural University)
Feng, Xueyan (South China Agricultural University)
Liu, Ruiqi (South China Agricultural University)
Su, Zhanqin (South China Agricultural University)
Chang, Chengjie (South China Agricultural University)
Zhu, Qianghui (South China Agricultural University)
Wu, Yuwei (South China Agricultural University)
Zhou, Zhongyin (Kunming Institute of Zoology)
Bai, Lijing (Agricultural Genomics Institute at Shenzhen)
Li, Kui (Agricultural Genomics Institute at Shenzhen)
Wang, Qishan (Zhejiang University)
Pan, Yuchun (Zhejiang University)
Xu, Zhong (Hubei Provincial Academy of Agricultural Sciences)
Peng, Xianwen (Hubei Provincial Academy of Agricultural Sciences)
Mei, Shuqi (Hubei Provincial Academy of Agricultural Sciences)
Mo, Delin (Sun Yat-sen University)
Liu, Xiaohong (Sun Yat-Sen University)
Zhang, Hao (China Agricultural University)
Yuan, Xiaolong (China Agricultural University)
Liu, Yang (Nanjing Agricultural University)
Liu, George E. (Henry A. Wallace Beltsville Agricultural Research Center)
Su, Guosheng (Aarhus University)
Sahana, Goutam (Aarhus University)
Lund, Mogens Sandø (Aarhus University)
Ma, Li (University of Maryland)
Xiang, Ruidong (University of Melbourne)
Shen, Xia (University of Edinburgh)
Li, Pinghua (Nanjing Agricultural University)
Huang, Ruihua (Nanjing Agricultural University)
Ballester Devis, Maria (Department of Animal and Food Science)
Crespo-Piazuelo, Daniel (Institut de Recerca i Tecnologia Agroalimentàries)
Amills i Eras, Marcel (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Clop, Alex (Centre for Research in Agricultural Genomics. Spanish National Research Council (CSIC). Instituto de Química Avanzada de Cataluña (IQAC))
Karlskov-Mortensen, Peter (University of Copenhagen)
Fredholm, Merete (University of Copenhagen)
Tang, Guoqing (Sichuan Agricultural University)
Li, Mingzhou (Sichuan Agricultural University)
Li, Xuewei
Ding, Xiangdong
Li, Jiaqi
Chen, Yaosheng
Zhang, Qin
Zhao, Yunxiang
Zhao, Fuping
Fang, Lingzhao
Zhang, Zhe (South China Agricultural University)

Date:	2025
Description:	17 pàg.
Abstract:	Understanding the molecular and cellular mechanisms underlying complex traits in pigs is crucial for enhancing genetic gain via artificial selection and utilizing pigs as models for human disease and biology. Here, we conducted comprehensive genome-wide association studies (GWAS) followed by a cross-breed meta-analysis for 232 complex traits and a within-breed meta-analysis for 12 traits, using 28. 3 million imputed sequence variants in 70 328 animals across 14 pig breeds. We identified 6878 quantitative trait loci (QTL) for 139 complex traits. Leveraging the Pig Genotype-Tissue Expression resource, we systematically investigated the biological context and regulatory mechanisms behind these trait-QTLs, ultimately prioritizing 14 829 variant-gene-tissue-trait regulatory circuits. For instance, rs344053754 regulates UGT2B31 expression in the liver and intestines, potentially by modulating enhancer activity, ultimately influencing litter weight at weaning in pigs. Furthermore, we observed conservation of certain genetic and regulatory mechanisms underlying complex traits between humans and pigs. Overall, our cross-breed meta-GWAS in pigs provides invaluable resources and novel insights into the genetic regulatory and evolutionary mechanisms of complex traits in mammals.
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	PigGTEx ; Complex traits ; meta-GWAS ; molQTL ; Pig ; SDG 3 - Good Health and Well-being
Published in:	National science review, Vol. 12, Num. 5 (2025) , art. nwaf048, ISSN 2053-714X

DOI: 10.1093/nsr/nwaf048
PMID: 40330097

17 p, 45.5 MB

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