Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs

被引：1

作者：

Xu, Zhiting ^{[1
]}

Lin, Qing ^{[1
]}

Cai, Xiaodian ^{[1
]}

Zhong, Zhanming ^{[1
]}

Teng, Jinyan ^{[1
]}

Li, Bingjie ^{[2
]}

Zeng, Haonan ^{[1
]}

Gao, Yahui ^{[1
,3
,4
]}

Cai, Zexi ^{[5
]}

Wang, Xiaoqing ^{[6
]}

Shi, Liangyu ^{[6
]}

Wang, Xue ^{[7
]}

Wang, Yi ^{[7
]}

Zhang, Zipeng ^{[7
]}

Lin, Yu ^{[8
]}

Liu, Shuli ^{[9
]}

Yin, Hongwei ^{[10
]}

Bai, Zhonghao ^{[5
]}

Wei, Chen ^{[1
]}

Zhou, Jun ^{[1
]}

Zhang, Wenjing ^{[1
]}

Zhang, Xiaoke ^{[1
]}

Shi, Shaolei ^{[1
]}

Wu, Jun ^{[1
]}

Diao, Shuqi ^{[1
]}

Liu, Yuqiang ^{[1
]}

Pan, Xiangchun ^{[1
]}

Feng, Xueyan ^{[1
]}

Liu, Ruiqi ^{[1
]}

Su, Zhanqin ^{[1
]}

Chang, Chengjie ^{[1
]}

Zhu, Qianghui ^{[1
]}

Wu, Yuwei ^{[1
]}

Zhou, Zhongyin ^{[11
]}

Bai, Lijing ^{[10
]}

Li, Kui ^{[10
]}

Wang, Qishan ^{[12
]}

Pan, Yuchun ^{[12
]}

Xu, Zhong ^{[13
]}

Peng, Xianwen ^{[13
]}

Mei, Shuqi ^{[13
]}

Mo, Delin ^{[14
]}

Liu, Xiaohong ^{[14
]}

Zhang, Hao ^{[1
]}

Yuan, Xiaolong ^{[1
]}

Liu, Yang ^{[15
]}

Liu, George E. ^{[3
]}

Su, Guosheng ^{[5
]}

Sahana, Goutam ^{[5
]}

Lund, Mogens Sando ^{[5
]}

机构：

[1] South China Agr Univ, State Key Lab Swine & Poultry Breeding Ind, Guangdong Prov Key Lab Agroanim Genom & Mol Breedi, Natl Engn Res Ctr Breeding Swine Ind,Coll Anim Sci, Guangzhou 510642, Peoples R China

[2] Scotlands Rural Coll SRUC, Roslin Inst Bldg, Easter Bush EH25 9RG, Midlothian, Scotland

[3] ARS, Anim Genom & Improvement Lab, Henry A Wallace Beltsville Agr Res Ctr, Beltsville, MD 20705 USA

[4] Univ Maryland, College Pk, MD 20742 USA

[5] Aarhus Univ, Ctr Quantitat Genet & Genom QGG, DK-8000 Aarhus, Denmark

[6] Chinese Acad Agr Sci, Inst Anim Sci, Beijing 100193, Peoples R China

[7] China Agr Univ, Coll Anim Sci & Technol, Beijing 100193, Peoples R China

[8] Sichuan Agr Univ, Coll Anim Sci & Technol, Key Lab Agr Bioinformat, Minist Educ, Chengdu 611130, Peoples R China

[9] Westlake Lab Life Sci & Biomed, Hangzhou 310024, Peoples R China

[10] Chinese Acad Agr Sci, Shenzhen Branch, Guangdong Lab Lingnan Modern Agr, Genome Anal Lab,Minist Agr,Agr Genom Inst Shenzhen, Shenzhen 518120, Peoples R China

[11] Chinese Acad Sci, State Key Lab Genet Resources & Evolut, Kunming Inst Zool, Kunming 650223, Peoples R China

[12] Zhejiang Univ, Coll Anim Sci, Hangzhou 310058, Peoples R China

[13] Hubei Prov Acad Agr Sci, Inst Anim Husb & Vet, Hubei Key Lab Anim Embryo & Mol Breeding, Wuhan 430064, Peoples R China

[14] Sun Yat Sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangzhou 510275, Peoples R China

[15] Nanjing Agr Univ, Coll Anim Sci & Technol, Nanjing 210095, Peoples R China

[16] Univ Melbourne, Fac Vet & Agr Sci, Parkville, Vic 3010, Australia

[17] AgriBio Ctr AgriBiosci, Agr Victoria Res, Bundoora, Vic 3083, Australia

[18] Fudan Univ, Sch Life Sci, State Key Lab Genet Engn, Shanghai 200438, Peoples R China

[19] Fudan Univ, Greater Bay Area Inst Precis Med Guangzhou, Ctr Intelligent Med Res, Guangzhou 510000, Peoples R China

[20] Univ Edinburgh, Usher Inst, Ctr Global Hlth Res, Edinburgh EH16 4UX, Scotland

[21] Nanjing Agr Univ, Inst Swine Sci, Nanjing 210095, Peoples R China

[22] Minist Agr & Rural Areas, Key Lab Nanjing Evaluat & Utilizat Livestock & Pou, Nanjing 210095, Peoples R China

[23] Inst Recerca & Tecnol Agroalimentaries IRTA, Anim Breeding & Genet Programme, Caldes De Montbui 08140, Spain

[24] Campus Univ Autonoma Barcelona, Ctr Res Agr Genom CRAG, CSIC IRTA UAB UB, Bellaterra 08193, Spain

[25] Univ Autonoma Barcelona, Dept Ciencia Anim & Dels Aliments, Bellaterra 08193, Spain

[26] Univ Copenhagen, Dept Vet & Anim Sci, Anim Genet & Breeding, DK-1870 Frederiksberg C, Denmark

[27] Shandong Agr Univ, Coll Anim Sci & Technol, Tai An 271018, Peoples R China

[28] Guangxi Univ, Coll Anim Sci & Technol, Nanning 530004, Peoples R China

来源：

NATIONAL SCIENCE REVIEW | 2025年 / 12卷 / 05期

基金：

澳大利亚研究理事会; 美国食品与农业研究所; 中国国家自然科学基金; 国家重点研发计划; 美国农业部;

关键词：

pig; meta-GWAS; PigGTEx; molQTL; complex traits; REPRODUCTIVE TRAITS; GENOMIC SELECTION; WELLNESS TRAITS; BIRTH-WEIGHT; ASSOCIATION; MODEL; EXPRESSION; DISEASE; RISK; GLUCURONOSYLTRANSFERASE;

D O I：

10.1093/nsr/nwaf048

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：17

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