数字农科院2.0

Genetic regulation of gene expression across multiple tissues in chickens

文献类型： 外文期刊

作者： Guan, Dailu;Bai, Zhonghao;Zhu, Xiaoning;Zhong, Conghao;Hou, Yali;Zhu, Di;Li, Houcheng;Lan, Fangren;Diao, Shuqi;Yao, Yuelin;Zhao, Bingru;Li, Xiaochang;Pan, Zhangyuan;Gao, Yahui;Wang, Yuzhe;Zou, Dong;Wang, Ruizhen;Xu, Tianyi;Sun, Congjiao;Yin, Hongwei;Teng, Jinyan;Xu, Zhiting;Lin, Qing;Shi, Shourong;Shao, Dan;Degalez, Fabien;Lagarrigue, Sandrine;Wang, Ying;Wang, Mingshan;Peng, Minsheng;Rocha, Dominique;Charles, Mathieu;Smith, Jacqueline;Watson, Kellie;Buitenhuis, Albert Johannes;Sahana, Goutam;Lund, Mogens Sando;Warren, Wesley;Frantz, Laurent;Larson, Greger;Lamont, Susan J.;Si, Wei;Zhao, Xin;Li, Bingjie;Zhang, Haihan;Luo, Chenglong;Shu, Dingming;Qu, Hao;Luo, Wei;Li, Zhenhui;Nie, Qinghua;Zhang, Xiquan;Xiang, Ruidong;Liu, Shuli;Zhang, Zhe;Zhang, Zhang;Liu, George E.;Cheng, Hans;Yang, Ning;Hu, Xiaoxiang;Zhou, Huaijun;Fang, Lingzhao

作者机构：

期刊名称： NATURE GENETICS

ISSN： 1061-4036

年卷期： 2025 年

页码：

收录情况： SCIE（2025版）

摘要： The chicken is a valuable model for understanding fundamental biology and vertebrate evolution and is a major global source of nutrient-dense and lean protein. Despite being the first non-mammalian amniote to have its genome sequenced, a systematic characterization of functional variation on the chicken genome remains lacking. Here, we integrated bulk RNA sequencing (RNA-seq) data from 7,015 samples, single-cell RNA-seq data from 127,598 cells and 2,869 whole-genome sequences to present a pilot atlas of regulatory variants across 28 chicken tissues. This atlas reveals millions of regulatory effects on primary expression (protein-coding genes, long non-coding RNA and exons) and post-transcriptional modifications (alternative splicing and 3 '-untranslated region alternative polyadenylation). We highlighted distinct molecular mechanisms underlying these regulatory variants, their context-dependent behavior and their utility in interpreting genome-wide associations for 39 chicken complex traits. Finally, our comparative analyses of gene regulation between chickens and mammals demonstrate how this resource can facilitate cross-species gene mapping of complex traits.

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