Xu Zhiting, Lin Qing, Cai Xiaodian, Zhong Zhanming, Teng Jinyan, Li Bingjie, Zeng Haonan, Gao Yahui, Cai Zexi, Wang Xiaoqing, Shi Liangyu, Wang Xue, Wang Yi, Zhang Zipeng, Lin Yu, Liu Shuli, Yin Hongwei, 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, Pan Yuchun, Xu Zhong, Peng Xianwen, Mei Shuqi, Mo Delin, Liu Xiaohong, Zhang Hao, Yuan Xiaolong, Liu Yang, Liu George E, Su Guosheng, Sahana Goutam, Lund Mogens Sandø, Ma Li, Xiang Ruidong, Shen Xia, Li Pinghua, Huang Ruihua, Ballester Maria, Crespo-Piazuelo Daniel, Amills Marcel, Clop Alex, Karlskov-Mortensen Peter, Fredholm Merete, Tang Guoqing, Li Mingzhou, Li Xuewei, Ding Xiangdong, Li Jiaqi, Chen Yaosheng, Zhang Qin, Zhao Yunxiang, Zhao Fuping, Fang Lingzhao, Zhang Zhe
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
Department of Animal and Veterinary Sciences, The Roslin Institute Building, Scotland's Rural College (SRUC), Easter Bush, Midlothian EH25 9RG, UK.
Natl Sci Rev. 2025 Feb 17;12(5):nwaf048. doi: 10.1093/nsr/nwaf048. eCollection 2025 May.
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 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.
了解猪复杂性状背后的分子和细胞机制对于通过人工选择提高遗传增益以及将猪用作人类疾病和生物学模型至关重要。在此，我们进行了全面的全基因组关联研究（GWAS），随后对232个复杂性状进行了杂交品种荟萃分析，对12个性状进行了品种内荟萃分析，使用了来自14个猪品种的70328只动物的2830万个推算序列变异。我们确定了139个复杂性状的6878个数量性状基因座（QTL）。利用猪基因型-组织表达资源，我们系统地研究了这些性状-QTL背后的生物学背景和调控机制，最终确定了14829个变异-基因-组织-性状调控回路。例如，rs344053754可能通过调节增强子活性来调节肝脏和肠道中的表达，最终影响猪的断奶窝重。此外，我们观察到人类和猪之间复杂性状背后的某些遗传和调控机制具有保守性。总体而言，我们在猪中的杂交品种荟萃GWAS为哺乳动物复杂性状的遗传调控和进化机制提供了宝贵的资源和新的见解。
