The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues

Guan, D.; Bai, Z.; Zhu, X.; Zhong, C.; Hou, Y.; Lan, F.; Diao, S.; Yao, Y.; Zhao, B.; Zhu, D.; 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, M.; Peng, M.; Rocha, D.; Charles, M.; Smith, J.; Watson, K.; Buitenhuis, A. J.; Sahana, G.; Lund, M. S.; Warren, W.; Frantz, L.; Larson, G.; Lamont, S. J.; Si, W.; Zhao, X.; Li, B.; Zhang, H.; Luo, C.; Shu, D.; Qu, H.; Luo, W.; Li, Z.; Nie, Q.; Zhang, X.; Zhang, Z.; Liu, G. E.; Cheng, H.; Yang, N.; Hu, X.; Zhou, H.; Fang

doi:10.1101/2023.06.27.546670

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bioRxiv · 10.1101/2023.06.27.546670

The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues

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Abstract

Chicken 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.

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Guan, D., Bai, Z., Zhu, X., Zhong, C., Hou, Y., Lan, F., Diao, S., Yao, Y., Zhao, B., Zhu, D., 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, M., Peng, M., Rocha, D., Charles, M., Smith, J., Watson, K., Buitenhuis, A. J., Sahana, G., Lund, M. S., Warren, W., Frantz, L., Larson, G., Lamont, S. J., Si, W., Zhao, X., Li, B., Zhang, H., Luo, C., Shu, D., Qu, H., Luo, W., Li, Z., Nie, Q., Zhang, X., Zhang, Z., Liu, G. E., Cheng, H., Yang, N., Hu, X., Zhou, H., Fang. 2023-06-29. The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues. https://doi.org/10.1101/2023.06.27.546670

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