By uniformly analyzing 723 RNA-seq data from 91 tissues and cell types, we built a comprehensive gene atlas and studied tissue specificity of genes in cattle. We demonstrated that tissue-specific genes significantly reflected the tissue-relevant biology, showing distinct promoter methylation and evolution patterns (e.g., brain-specific genes evolve slowest, whereas testis-specific genes evolve fastest). Through integrative analyses of those tissue-specific genes with large-scale genome-wide association studies, we detected relevant tissues/cell types and candidate genes for 45 economically important traits in cattle, including blood/immune system (e.g., CCDC88C) for male fertility, brain (e.g., TRIM46 and RAB6A) for milk production, and multiple growth-related tissues (e.g., FGF6 and CCND2) for body conformation. We validated these findings by using epigenomic data across major somatic tissues and sperm. Collectively, our findings provided novel insights into the genetic and biological mechanisms underlying complex traits in cattle, and our transcriptome atlas can serve as a primary source for biological interpretation, functional validation, studies of adaptive evolution, and genomic improvement in livestock.

中文翻译：

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对 723 个转录组的综合分析增强了对牛复杂性状的遗传和生物学解释。


通过统一分析来自 91 个组织和细胞类型的 723 个 RNA-seq 数据，我们构建了全面的基因图谱，并研究了牛基因的组织特异性。我们证明组织特异性基因显着反映了组织相关生物学，显示出不同的启动子甲基化和进化模式（例如，脑特异性基因进化最慢，而睾丸特异性基因进化最快）。通过对这些组织特异性基因与大规模全基因组关联研究的综合分析，我们检测了牛的45个重要经济性状的相关组织/细胞类型和候选基因，包括影响雄性生育能力的血液/免疫系统（例如CCDC88C）用于产奶的大脑（例如 TRIM46 和 RAB6A），以及用于身体构象的多种生长相关组织（例如 FGF6 和 CCND2）。我们通过使用主要体细胞组织和精子的表观基因组数据验证了这些发现。总的来说，我们的研究结果为牛复杂性状背后的遗传和生物学机制提供了新的见解，我们的转录组图谱可以作为生物学解释、功能验证、适应性进化研究和牲畜基因组改良的主要来源。