Comprehensive multi‐tissue epigenome atlas in sheep: A resource for complex traits, domestication, and breeding
Comprehensive functional genome annotation is crucial to elucidate the molecular mechanisms of agronomic traits in livestock, yet systematic functional annotation of the sheep genome is lacking. Here, we generated 92 transcriptomic and epigenomic data sets from nine major tissues, along with whole-genome data from 2357 individuals across 29 breeds worldwide, and 4006 phenotypic data related to tail fat weight. We constructed the first multi-tissue epigenome atlas in terms of functional elements, chromatin states, and their functions and explored the utility of the functional elements in interpreting phenotypic variation during sheep domestication and improvement. Particularly, we identified a total of 753,723 nonredundant functional elements, with over 60% being novel. We found tissue-specific promoters and enhancers related to sensory abilities and immune response that were highly enriched in genomic regions influenced by domestication, while <i>longissimus dorsi</i> tissue-specific active enhancers and tail fat tissue-specific active promoters were highly enriched in genomic regions influenced by breeding and improvement. Notably, a variant, Chr13:51760995A>C, located in an enhancer region, was identified as a causal variant for tail fat deposition based on multi-layered data sets. Overall, this research provides foundational resources and a successful case for future investigations of complex traits in sheep through the integration of multi-omics data sets.
Authors
- Peng Hu (ORCID: https://orcid.org/0000-0002-0017-1948)
- Defu Tang (ORCID: https://orcid.org/0000-0002-8472-9311)
- Kai Huang (ORCID: https://orcid.org/0000-0003-2990-4655)
- Huibin Tian (ORCID: https://orcid.org/0000-0002-1294-0660)
- Jiangbo Cheng (ORCID: https://orcid.org/0000-0002-1281-5157)
- Yuanqing Feng (ORCID: https://orcid.org/0000-0001-9164-1628)
- Zhihua Jiang (ORCID: https://orcid.org/0000-0003-1986-088X)
- Deyin Zhang (ORCID: https://orcid.org/0000-0001-9587-084X)
- Peter Kalds
- Fang Nian
- Wanhong Li (ORCID: https://orcid.org/0000-0002-2155-6863)
- Xiuxiu Weng (ORCID: https://orcid.org/0000-0002-4832-5643)
- Lvfeng Yuan (ORCID: https://orcid.org/0000-0002-0625-7742)
- Xiaoxue Zhang (ORCID: https://orcid.org/0000-0002-3289-5393)
- Xiaolong Li (ORCID: https://orcid.org/0000-0002-6647-5565)
- Chong Li (ORCID: https://orcid.org/0000-0002-3802-1507)
- Yukun Zhang (ORCID: https://orcid.org/0000-0003-0729-3267)
- Yuan Zhao (ORCID: https://orcid.org/0009-0006-5649-6422)
- Quanzhong Xu
- Yunxia Zhao (ORCID: https://orcid.org/0000-0002-2253-2484)
- Liming Zhao (ORCID: https://orcid.org/0000-0001-7087-7383)
- Xiaobin Yang (ORCID: https://orcid.org/0000-0002-8475-1287)
- Chen Zheng (ORCID: https://orcid.org/0000-0002-8814-9971)
- Dan Xu (ORCID: https://orcid.org/0000-0002-0648-0100)
- Zongwu Ma (ORCID: https://orcid.org/0009-0001-8413-2937)
- Xiangpeng Yue (ORCID: https://orcid.org/0000-0003-1954-5273)
- Weimin Wang (ORCID: https://orcid.org/0009-0006-8513-0147)
- Xiaojuan Wang (ORCID: https://orcid.org/0000-0002-2246-4602)
Institutions
- Gansu Agricultural University (CN)
- Huazhong Agricultural University (CN)
- Lanzhou Veterinary Research Institute (CN)
- Chinese Academy of Agricultural Sciences (CN)
- Institute of Grassland Research (CN)
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems
- Shanghai Ocean University (CN)
- Washington State University (US)
- Lanzhou University (CN)
- University of Pennsylvania (US)
Publication Details
- Journal
- iMeta
- Published
- 2024-12-01
- DOI
- https://doi.org/10.1002/imt2.254
- Citations
- 15
- Primary Topic
- Epigenetics and DNA Methylation
- Type
- article
- Field-Weighted Citation Impact
- 3.51
Funders
- National Natural Science Foundation of China