A multi-tissue atlas of genetic regulatory effects in sheep

作者：Mian Gong, Ziyang Zhuang, Xiangrong Sun, Yuan Xu, Huan-Huan Zhang, Yanan Wang, Dailu Guan, Ran Li, Xiaoning Lu, Zhonghao Bai, Pingjie Feng, Meiwen Song, Min Tian, Jingsheng Lu, Mingshan Wang, Xuemei Lu, Dong‐Dong Wu, Peng Su, Peiyao Liu, Guoqing Zhang, Jianxin Shi, Mingzhu Shan, Yuanyuan Zhang, Meng Zhu, Hao Li, Xijing He, Jianqi Yang, Yize Song, Xinyue Li, Xiaolong Du, Xiaoxu Zhang, Hao Yang, Jinyan Teng, Houcheng Li, Xiaoning Zhu, Huicong Zhang, Qing Lin, Dongjie Zhu, Bingjin Lin, Xinfeng Liu, Jianquan Liu, Weijie Zheng, Wentao Gong, Bailing An, Qi Zhang, Goutam Sahana, Mogens Sandø Lund, Cong Li, Jiazhong Guo, Xihong Wang, Yuwen Liu, Bingru Zhao, Xiaolei Yao, Yanli Zhang, Feng Wang, Wenxin Zheng, Juncheng Huang, Sen Wang, Jiang Di, Hanikezi Tulafu, Zhihong Liu, Shaoyin Fu, Yongbin Liu, Zijun Zhang, Yongju Zhao, Yinghui Lin, Jianning He, Jinshan Zhao, Hengbo Shi, Zhengguang Wang, Bingjie Li, Ruidong Xiang, Amanda J. Chamberlain, Weimin Wang, Qiuyue Liu, Jiyuan Li, Feng‐Hua Lv, Ze Yan, Qi‐En Yang, Guiping Zhao, Lin Jiang, Xianyong Lan, Huaijun Zhou, R.P.M.A. Crooijmans, Ole Madsen, David E. MacHugh, John F. O’Grady, Marcel Amills, Gwenola Tosser-Klopp, Emily L. Clark, Jianlin Han, Mingxing Chu, Weiwei Wu, Yu Jiang, Zhangyuan Pan, Lingzhao Fang · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2025 · DOI：10.1101/2025.11.03.686346 · 被引用次数：4 · 研究领域：Genetic Mapping and Diversity in Plants and Animals、Genetic and phenotypic traits in livestock、Genomics and Rare Diseases

Abstract Characterizing the impact of genomic variants on genome function and ultimately complex traits in livestock is essential for the development of sustainable precision agriculture and comparative genomics. Here, as part of the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we present the pilot phase of the SheepGTEx resource through analyzing 6,761 RNA-sequencing samples of 51 primary tissues in a multi-breed population of sheep. We identify millions of regulatory variants associated with seven types of molecular phenotypes, and fine-map 322,468 primary and 114,017 non-primary effects, revealing a high degree of regulatory allelic heterogeneity. We systematically characterize the pleiotropic effects of these variants on molecular phenotypes, assess their context-specific regulatory patterns across tissues, breeds, sexes, and developmental stages, as well as explore their evolutionary constraints across mammals. Finally, we demonstrate the substantial potential of the SheepGTEx resource ( https://sheepgtex.farmgtex.org ), by providing examples of regulatory mechanisms underpinning 34 complex traits, population divergence between European and Asian breeds, and adaptive evolution in sheep over the past ten millennia.