Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.
National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
Nat Genet. 2022 Sep;54(9):1438-1447. doi: 10.1038/s41588-022-01153-5. Epub 2022 Aug 11.
Characterization of genetic regulatory variants acting on livestock gene expression is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here we build a Cattle Genotype-Tissue Expression atlas (CattleGTEx) as part of the pilot phase of the Farm animal GTEx (FarmGTEx) project for the research community based on 7,180 publicly available RNA-sequencing (RNA-seq) samples. We describe the transcriptomic landscape of more than 100 tissues/cell types and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 23 distinct tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multiomics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle.
研究家畜基因表达的遗传调控变异对于解释具有经济价值的性状的分子机制以及通过人工选择提高遗传增益率至关重要。在这里，我们构建了一个牛基因-组织表达图谱（CattleGTEx），作为 Farm animal GTEx（FarmGTEx）项目的试点阶段的一部分，为研究界提供了 7180 个公开可用的 RNA 测序（RNA-seq）样本。我们描述了 100 多种组织/细胞类型的转录组景观，并报告了 23 种不同组织中与基因表达和选择性剪接相关的数十万种遗传关联。我们评估了这些遗传调控效应的组织共享模式，并使用多组学数据对其进行功能注释。最后，我们使用全转录组关联和共定位分析将不同组织中的基因表达与 43 个经济重要性状联系起来，以破译牛的这些农艺性状的分子调控机制。
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