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<p>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.</p>

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Genetic regulation of gene expression across multiple tissues in chickens

  • 期刊论文

  • 发表日期：

    2025年4月8日

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

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.