Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle

• DOI: 10.1101/gr.250704.119
• Publication Date: 2020-05-19T00:35:37Z
• Authors: Lingzhao Fang; Wentao Cai; Shuli Liu; Oriol Canela-Xandri; Yahui Gao; Jicai Jiang; Konrad Rawlik; Bingjie Li; Steven G. Schroeder; Benjamin D. Rosen; Cong-jun Li; Tad S. Sonstegard; Leeson J. Alexander; Curtis P. Van Tas...; Paul M. VanRaden; John B. Cole; Ying Yu; Shengli Zhang; Albert Tenesa; Li Ma; George E. Liu
• Keywords: Epigenomics; RNA-Seq; Genome-wide Association Study

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