Comprehensive multi-tissue epigenome atlas in sheep: A resource for complex traits, domestication, and breeding

IF 23.7 Q1 MICROBIOLOGY
iMeta Pub Date : 2024-12-15 DOI:10.1002/imt2.254
Deyin Zhang, Jiangbo Cheng, Xiaolong Li, Kai Huang, Lvfeng Yuan, Yuan Zhao, Dan Xu, Yukun Zhang, Liming Zhao, Xiaobin Yang, Zongwu Ma, Quanzhong Xu, Chong Li, Xiaojuan Wang, Chen Zheng, Defu Tang, Fang Nian, Xiangpeng Yue, Wanhong Li, Huibin Tian, Xiuxiu Weng, Peng Hu, Yuanqing Feng, Peter Kalds, Zhihua Jiang, Yunxia Zhao, Xiaoxue Zhang, Fadi Li, Weimin Wang
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Abstract

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 longissimus dorsi 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.

Abstract Image

绵羊综合多组织表观基因组图谱:复杂性状、驯化和育种的资源。
全面的功能基因组注释对于阐明家畜农艺性状的分子机制至关重要,但绵羊基因组的系统功能注释尚缺乏。在这里,我们生成了来自9个主要组织的92个转录组和表观基因组数据集,以及来自全球29个品种的2357个个体的全基因组数据,以及4006个与尾脂肪重量相关的表型数据。我们根据功能元件、染色质状态及其功能构建了首个多组织表观基因组图谱,并探索了功能元件在绵羊驯化和改良过程中解释表型变异的效用。特别是,我们确定了总共753,723个非冗余的功能元素,其中超过60%是新颖的。我们发现,与感觉能力和免疫应答相关的组织特异性启动子和增强子在驯化影响的基因组区域高度富集,而背最长肌组织特异性活性增强子和尾脂肪组织特异性活性启动子在育种和改良影响的基因组区域高度富集。值得注意的是,基于多层数据集,位于增强子区域的变体Chr13:51760995A>C被确定为尾部脂肪沉积的因果变异。总的来说,本研究通过整合多组学数据集,为未来研究绵羊复杂性状提供了基础资源和成功案例。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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CiteScore
10.80
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