The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues
Author:
Guan DailuORCID, Bai Zhonghao, Zhu Xiaoning, Zhong Conghao, Hou Yali, Lan Fangren, Diao Shuqi, Yao Yuelin, Zhao Bingru, Zhu Di, Li Xiaochang, Pan Zhangyuan, Gao Yahui, Wang Yuzhe, Zou DongORCID, Wang Ruizhen, Xu Tianyi, Sun Congjiao, Yin Hongwei, Teng JinyanORCID, Xu Zhiting, Lin Qing, Shi Shourong, Shao Dan, Degalez Fabien, Lagarrigue Sandrine, Wang Ying, Wang Mingshan, Peng Minsheng, Rocha DominiqueORCID, Charles Mathieu, Smith Jacqueline, Watson Kellie, Buitenhuis Albert Johannes, Sahana Goutam, Lund Mogens Sandø, 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, Zhang ZheORCID, Zhang Zhang, Liu George E.ORCID, Cheng Hans, Yang Ning, Hu Xiaoxiang, Zhou HuaijunORCID, Fang Lingzhao,
Abstract
AbstractChicken is a valuable model for understanding fundamental biology, vertebrate evolution and diseases, as well as a major source of nutrient-dense and lean-protein-enriched food globally. Although it is the first non-mammalian amniote genome to be sequenced, the chicken genome still lacks a systematic characterization of functional impacts of genetic variants. Here, through integrating 7,015 RNA-Seq and 2,869 whole-genome sequence data, the Chicken Genotype- Tissue Expression (ChickenGTEx) 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 tissue-sharing and context-specificity of these regulatory variants, their underlying molecular mechanisms of action, and their utility in interpreting adaptation and genome-wide associations of 108 chicken complex traits. Finally, we illustrated shared and lineage-specific features of gene regulation between chickens and mammals, and demonstrated how the ChickenGTEx resource can further assist with translating genetic findings across species.One-Sentence SummaryThe ChickenGTEx provides a multi-tissue reference of regulatory variants for chicken genetics and genomics, functional genomics, precision breeding, veterinary medicine, vertebrate evolution and even human biomedicine.
Publisher
Cold Spring Harbor Laboratory
Cited by
2 articles.
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