The enhanced multi-tissue atlas of regulatory effects in cattle

The enhanced multi-tissue atlas of regulatory effects in cattle - Find this author on Google Scholar - Find this author on PubMed - Search for this author on this site - For correspondence: xiaowangzntc{at}163.com xuemeilu{at}mail.kiz.ac.cn yu.jiang{at}nwafu.edu.cn yangzhou{at}mail.hzau.edu.cn wang_yu{at}nwafu.edu.cn bingjie.li{at}sruc.ac.uk pso{at}qgg.au.dk lingzhao.fang{at}qgg.au.dk - Find this author on Google Scholar - Find this author on PubMed - Search for this author on this site - For correspondence: xiaowangzntc{at}163.com xuemeilu{at}mail.kiz.ac.cn yu.jiang{at}nwafu.edu.cn yangzhou{at}mail.hzau.edu.cn wang_yu{at}nwafu.edu.cn bingjie.li{at}sruc.ac.uk pso{at}qgg.au.dk lingzhao.fang{at}qgg.au.dk - Find this author on Google Scholar - Find this author on PubMed - Search for this author on this site - For correspondence: xiaowangzntc{at}163.com xuemeilu{at}mail.kiz.ac.cn yu.jiang{at}nwafu.edu.cn yangzhou{at}mail.hzau.edu.cn wang_yu{at}nwafu.edu.cn bingjie.li{at}sruc.ac.uk pso{at}qgg.au.dk lingzhao.fang{at}qgg.au.dk - Find this author on Google Scholar - Find this author on PubMed - Search for this author on this site - For correspondence: xiaowangzntc{at}163.com xuemeilu{at}mail.kiz.ac.cn yu.jiang{at}nwafu.edu.cn yangzhou{at}mail.hzau.edu.cn wang_yu{at}nwafu.edu.cn bingjie.li{at}sruc.ac.uk pso{at}qgg.au.dk lingzhao.fang{at}qgg.au.dk - Find this author on Google Scholar - Find this author on PubMed - Search for this author on this site - For correspondence: xiaowangzntc{at}163.com xuemeilu{at}mail.kiz.ac.cn yu.jiang{at}nwafu.edu.cn yangzhou{at}mail.hzau.edu.cn wang_yu{at}nwafu.edu.cn bingjie.li{at}sruc.ac.uk pso{at}qgg.au.dk lingzhao.fang{at}qgg.au.dk - Find this author on Google Scholar - Find this author on PubMed - Search for this author on this site - For correspondence: xiaowangzntc{at}163.com xuemeilu{at}mail.kiz.ac.cn yu.jiang{at}nwafu.edu.cn yangzhou{at}mail.hzau.edu.cn wang_yu{at}nwafu.edu.cn bingjie.li{at}sruc.ac.uk pso{at}qgg.au.dk lingzhao.fang{at}qgg.au.dk - Find this author on Google Scholar - Find this author on PubMed - Search for this author on this site - For correspondence: xiaowangzntc{at}163.com xuemeilu{at}mail.kiz.ac.cn yu.jiang{at}nwafu.edu.cn yangzhou{at}mail.hzau.edu.cn wang_yu{at}nwafu.edu.cn bingjie.li{at}sruc.ac.uk pso{at}qgg.au.dk lingzhao.fang{at}qgg.au.dk - Find this author on Google Scholar - Find this author on PubMed - Search for this author on this site - For correspondence: xiaowangzntc{at}163.com xuemeilu{at}mail.kiz.ac.cn yu.jiang{at}nwafu.edu.cn yangzhou{at}mail.hzau.edu.cn wang_yu{at}nwafu.edu.cn bingjie.li{at}sruc.ac.uk pso{at}qgg.au.dk lingzhao.fang{at}qgg.au.dk Abstract Cattle are integral to global food security, yet the molecular architecture of their complex traits remains poorly understood. Here, we present the Cattle Genotype–Tissue Expression (CattleGTEx) Phase 1 resource (https://cattlegtex.farmgtex.org/), a substantial expansion of the pilot study. By leveraging 12,422 RNA-seq profiles across 43 tissues and 82 breeds, we characterized 433,972 primary and 161,428 non-primary regulatory effects spanning seven molecular phenotypes. This high-resolution atlas resolves 75% of GWAS signals for 44 complex traits, significantly addressing the "missing regulation" in livestock. We propose a genetic regulatory model demonstrating how variants across multiple biological layers interact with specific biological contexts to shape phenotypic variation. Furthermore, CattleGTEx elucidates mechanisms underlying adaptive evolution between Bos taurus and Bos indicus, as well as artificial selection in dairy and beef breeds. Finally, by mapping evolutionary constraints on these regulatory effects, we demonstrate the translational value of this resource for prioritizing causal variants in human complex diseases. Together, Phase 1 of CattleGTEx provides a transformative framework for functional genomics, precision breeding, and comparative genetics. Competing Interest Statement The authors have declared no competing interest. Footnotes ↵† Co-first authors Emails for all authors: Houcheng Li: houcheng.li{at}qgg.au.dk; Huicong Zhang: huicongz{at}qgg.au.dk; Di Zhu: zhudi{at}qgg.au.dk; Pengju Zhao: zhaopengj—{at}gmail.com; Zhenyu Wei: weizhenyu{at}nwafu.edu.cn; Jingsheng Lu: lujingsheng{at}mail.kiz.ac.cn; Mian Gong: gongmian2767{at}qgg.au.dk; Qi Zhang: yiguizhang_666{at}163.com; Weijie Zheng: weijiezheng426{at}163.com; Xinfeng Liu: liuxinfeng{at}qgg.au.dk; Dailu Guan: dguan{at}ucdavis.edu; Jinyan Teng: jinyan.teng{at}scau.edu.cn; Qin Lin: qing_lin1996{at}126.com; Yongjie Tang: cautyj{at}163.com; Yahui Gao: yahui.gao{at}scau.edu.cn; Shanjiang Zhao: zhaoshanjiang{at}caas.cn; Zhe Zhang: zhezhang{at}scau.edu.cn; Junting Du: jtdu{at}lc-bio.com; Chao Fang: cfang{at}lc-bio.com; Bingxing An: abx{at}qgg.au.dk; Bingjin Lin: bingjinlin1127{at}163.com; Haihan Zhang: hhzhang{at}hunau.edu.cn; Min Tian: mintian{at}qgg.au.dk; Jingjing Tian: jingjingtian{at}qgg.au.dk; Siqian Chen: sqchen1028{at}163.com; Wansheng Liu: wul12{at}psu.edu; Yanan Wang: wangyanan{at}mail.kiz.ac.cn; Mingshan Wang: wangmingshan{at}mail.kiz.ac.cn; Eveline M. Ibeagha-Awemu: eveline.ibeagha-awemu{at}agr.gc.ca; Richard P. M. A. Crooijmans: richard.crooijmans{at}wur.nl; Martijn F. L. Derks: martijn.derks{at}wur.nl; Marta Gòdia: marta.godia{at}wur.nl; Ole Madsen: ole.madsen{at}wur.nl; Hubert Pausch: hubert.pausch{at}usys.ethz.ch; Alexander S. Leonard: alexander.leonard{at}usys.ethz.ch; Laurent Frantz: laurent.frantz{at}gmail.com; David E. MacHugh: david.machugh{at}ucd.ie; John F. O’Grady: johnfrancis.ogrady{at}usys.ethz.ch; Iuliana Ionita-Laza: iuliana.laza{at}gmail.com; Xin Zhao: xin.zhao{at}mcgill.ca; Leluo Guan: leluo.guan{at}ubc.ca; Huaijun Zhou: hzhou{at}ucdavis.edu; Emilio Mármol Sánchez: emilio.marmol.sanchez{at}gmail.com; Monique G. P. van der Wijst: m.g.p.van.der.wijst{at}umcg.nl; Xubin Lu: lxb{at}yzu.edu.cn; Hui Jiang: dx120210160{at}stu.yzu.edu.cn; Zhangping Yang: yzp{at}yzu.edu.cn; Qien Yang: yangqien{at}nwipb.cas.cn, Qinyou Liu: qingyouliu{at}scau.edu.cn; Chuang Xu: xuchuang{at}cau.edu.cn; Moli Li: lml94520{at}cau.edu.cn; Yali Hou: houyali1210{at}gmail.com; Zhangyuan Pan: zhypan01{at}163.com; Yan Chen: chenyan{at}caas.cn; Ruidong Xiang: ruidong.xiang{at}agriculture.vic.gov.au; Mathew Littlejohn: mathew.littlejohn{at}lic.co.nz; Emily L. Clark: eclark{at}ebi.ac.uk; Wenfa Lyu: wenfa2004{at}163.com; Yuwen Liu: liuyuwen{at}caas.cn; Lin Jiang: jianglin{at}caas.cn; Peng Su: super96110{at}gmail.com; Xuexue Liu: Xuexue.liu{at}utoulouse.fr; Senlin Zhu: senlin_zhu{at}zju.edu.cn; Minghui Jia: jmhui{at}zju.edu.cn; Huizeng Sun: huizeng{at}zju.edu.cn; Bo Han: bohan{at}cau.edu.cn; Yi Zhang: yizhang{at}cau.edu.cn; Ying Yu: yuying{at}cau.edu.cn; Dongxiao Sun: sundx{at}cau.edu.cn; Yaokun Li: ykli{at}scau.edu.cn; Dewu Liu: dwliu{at}scau.edu.cn; Goutam Sahana: goutam.sahana{at}qgg.au.dk; Zexi Cai: zexi.cai{at}qgg.au.dk; Mogens Sandø Lund: mogens.lund{at}qgg.au.dk; John B. Cole: john.cole{at}uscdcb.com; Li Ma: lima{at}umd.edu; Jicai Jiang: jicai_jiang{at}ncsu.edu; Wenjian Li: liwenjian{at}wchscu.edu.cn; Yang Wu: yang.wu{at}wchscu.cn; Jianbin Li: msdljb{at}163.com; Jun Teng: tengjun0520{at}163.com; Qin Zhang: qzhang{at}sdau.edu.cn; The legend of Figure1 and part of author information has been revised. 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