Genetic regulation of gene expression across multiple tissues in chickens

Authors: GUAN, DAILU - University Of California, Davis; BAI, ZHONGHAO - Aarhus University; ZHU, XIAONING - China Agricultural University; ZHONG, CONGHAO - China Agricultural University; HOU, YALI - Chinese Academy Of Sciences; ZHU, DI - Aarhus University; FARMGTEX-CHICKENGTEX, CONSORTIUM - Collaborator; LI, HOUCHENG - Aarhus University; LAN, FANGREN - China Agricultural University; DIAO, SHUQI - South China Agricultural University; YAO, YUELIN - University Of Edinburgh; ZHAO, BINGRU - Nanjing Agricultural University; LI, XIAOCHANG - China Agricultural University; PAN, ZHANGYUAN - Chinese Academy Of Agricultural Sciences; GAO, YAHUI - South China Agricultural University; WANG, YUZHE - China Agricultural University; ZOU, DONG - Chinese Academy Of Sciences; WANG, RUIZHEN - Chinese Academy Of Sciences; XU, TIANYI - Chinese Academy Of Sciences; SUN, CONGJIAO - China Agricultural University; YIN, HONGWEI - Chinese Academy Of Agricultural Sciences; TENG, JINYAN - South China Agricultural University; XU, ZHITING - South China Agricultural Univerisity; LIN, QING - South China Agricultural Univerisity; SHI, SHOURONG - Chinese Academy Of Agricultural Sciences; SHAO, DAN - Chinese Academy Of Agricultural Sciences; DEGALEZ, FABIEN - Inrae; LAGARRIGUE, SANDRINE - Inrae; WANG, YING - University Of California, Davis; WANG, MINGSHAN - Chinese Academy Of Sciences; PENG, MINSHENG - Chinese Academy Of Sciences; ROCHA, DOMINIQUE - Inrae; CHARLES, MATHIEU - Inrae; SMITH, JACQUELINE - Roslin Institute; WATSON, KELLIE - Roslin Institute; BUITENHUIS, JOHANNES - Aarhus University; SAHANA, GOUTAM - Aarhus University; LUND, MOGENS - Aarhus University; WARREN, WESLEY - University Of Missouri; FRANTZ, LAURENT - Collaborator; LARSON, GREGER - University Of Oxford; LAMONT, SUSAN - Iowa State University; SI, WEI - Chinese Academy Of Agricultural Sciences; ZHAO, XIN - McGill University - Canada; LI, BINGJIE - Sruc-Scotland'S Rural College; ZHANG, HAIHAN - Hunan Agricultural University; LUO, CHENGLONG - Aarhus University; SHU, DINGMING - Guangdong Academy Of Agricultural Sciences; QU, HAO - South China Agricultural University; LUO, WEI - South China Agricultural University; LI, ZHENHUI - South China Agricultural University; NIE, QINGHUA - South China Agricultural University; ZHANG, XIQUAN - South China Agricultural University; XIANG, RUIDONG - Agriculture Victoria; LIU, SHULI - Westlake University; ZHANG, ZHE - South China Agricultural University; ZHANG, ZHANG - Chinese Academy Of Sciences; Liu, Ge; Cheng, Hans; YANG, NING - China Agricultural University; HU, XIAOXIANG - China Agricultural University; ZHOU, HUAIJUN - University Of California, Davis; FANG, LINGZHAO - Aarhus University

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/5/2025
Publication Date: 4/8/2025
Citation: Guan, D., Bai, Z., Zhu, X., Zhong, C., Hou, Y., Zhu, D., Chickengtex, C., Li, H., Lan, F., Diao, S., Yao, Y., Zhao, B., Li, X., Pan, Z., Gao, Y., Wang, Y., Zou, D., Wang, R., Xu, T., Sun, C., Yin, H., Teng, J., Xu, Z., Lin, Q., Shi, S., Shao, D., Degalez, F., Lagarrigue, S., Wang, Y., Wang, M., Peng, M., Rocha, D., Charles, M., Smith, J., Watson, K., Buitenhuis, J.A., Sahana, G., Lund, M.S., Warren, W., Frantz, L., Larson, G., Lamont, S. ., Si, W., Zhao, X., Li, B., Zhang, H., Luo, C., Shu, D., Qu, H., Luo, W., Li, Z., Nie, Q., Zhang, X., Xiang, R., Liu, S., Zhang, Z., Zhang, Z., Liu, G., Cheng, H.H., Yang, N., Hu, X., Zhou, H., Fang, L. 2025. Genetic regulation of gene expression across multiple tissues in chickens. Nature Genetics. 57:1298–1308. https://doi.org/10.1038/s41588-025-02155-9.
DOI: https://doi.org/10.1038/s41588-025-02155-9

Interpretive Summary: Comprehensive analyses of genetic regulatory variants will benefit our understanding of genetic bases for complex traits. We provided the first chicken Genotype-Tissue Expression atlas. These results fill our knowledge gaps and provide the foundation for incorporating new transcriptome insights into the future animal breeding program. Farmers, scientists, and policy planners who need improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical Abstract: Chicken, a modern descendant of dinosaurs, remains a valuable model for studying fundamental biology, vertebrate evolution and human diseases, as well as a major source of protein-rich food worldwide. Although it is the first non-mammalian amniote genome to be sequenced, the chicken genome still lacks a systematic characterization of the functional impacts of non-coding variants. Here, through integrating 7,015 RNA-Seq and 2,869 whole-genome sequence data, the Farm animal Genotype-Tissue Expression (FarmGTEx) project presents the pilot reference of regulatory variants in 28 chicken tissue transcriptomes, including millions of regulatory effects on primary expression (including protein-coding genes, lncRNA and exon) and post-transcriptional modifications (alternative splicing and 3’ untranslated region alternative polyadenylation). We explored the context-specificity of these regulatory variants, their underlying molecular mechanisms of actions, and their utility in interpreting adaptation and genome-wide associations of 108 chicken complex traits. We finally illustrated shared and lineage-specific features of gene regulation between chickens and mammals and how the FarmGTEx resource can help translate genetic findings between species.