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 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...

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Detalles Bibliográficos
Autores: Xu, Zhiting, Lin, Qing, Cai, Xiaodian, Zhong, Zhanming, Teng, Jinyan|||0000-0002-3046-1452, Li, Bingjie|||0000-0002-8528-1889, Zeng, Haonan, Gao, Yahui, Cai, Zexi|||0000-0002-9579-3415, Wang, Xiaoqing, Shi, Liangyu, Wang, Xue, Wang, Yi, Zhang, Zipeng, Lin, Yu, Liu, Shuliang, Yin, Hongwei|||0000-0002-9373-5166, Bai, Zhonghao, Wei, Chen, Zhou, Jun, Zhang, Wenjing, Zhang, Xiaoke, Shi, Shaolei, Wu, Jun, Diao, Shuqi, Liu, Yuqiang, Pan, Xiangchun, Feng, Xueyan, Liu, Ruiqi, Su, Zhanqin, Chang, Chengjie, Zhu, Qianghui, Wu, Yuwei, Zhou, Zhongyin, Bai, Lijing, Li, Kui, Wang, Qishan|||0000-0002-6475-0009, Pan, Yuchun, Xu, Zhong, Peng, Xianwen, Mei, Shuqi, Mo, Delin, Liu, Xiaohong, Zhang, Hao, Yuan, Xiaolong, Liu, Yang, Liu, George E.|||0000-0003-0192-6705, Su, Guosheng, Sahana, Goutam|||0000-0001-7608-7577, Lund, Mogens Sandø, Ma, Li, Xiang, Ruidong, Shen, Xia|||0000-0003-4390-1979, Li, Pinghua, Huang, Ruihua, Ballester Devis, Maria|||0000-0002-5413-4640, Crespo-Piazuelo, Daniel|||0000-0001-7896-2507, Amills i Eras, Marcel|||0000-0002-8999-0770, Clop, Alex|||0000-0001-9238-2728, Karlskov-Mortensen, Peter|||0000-0002-2491-2763, Fredholm, Merete|||0000-0002-3563-7648, Tang, Guoqing, Li, Mingzhou|||0000-0001-8681-7684, Li, Xuewei, Ding, Xiangdong, Li, Jiaqi, Chen, Yaosheng, Zhang, Qin, Zhao, Yunxiang, Zhao, Fuping, Fang, Lingzhao|||0000-0003-1103-3679, Zhang, Zhe
Tipo de recurso: artículo
Fecha de publicación:2025
País:España
Institución:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:325588
Acceso en línea:https://ddd.uab.cat/record/325588
https://dx.doi.org/urn:doi:10.1093/nsr/nwaf048
Access Level:acceso abierto
Palabra clave:PigGTEx
Complex traits
meta-GWAS
molQTL
Pig
SDG 3 - Good Health and Well-being
Descripción
Sumario: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.

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