A comprehensive catalogue of regulatory variants in the cattle transcriptome-猫眼课题宝

DOI：

10.1101/2020.12.01.406280

发表时间：

2020-12

期刊：

bioRxiv

影响因子：

通讯作者：

中科院分区：

其他

文献类型：

作者：

Shuli Liu;Yahui Gao;O. Canela‐Xandri;Sheng Wang;Ying Yu;Wentao Cai;Bingjie Li;E. Pairo-Castineira;K. D'Mellow;K. Rawlik;Charley Xia;Yuelin Yao;Xiujin Li;Ze Yan;Congjun Li;B. Rosen;C. V. Van Tassell;P. Vanraden;Shengli Zhang;Li Ma;J. Cole;G. Liu;A. Tenesa;L. Fang

表征作用于家畜转录组的遗传调控变体对于解释经济价值性状的分子机制和通过人工选择提高遗传获得率是必不可少的。在这里，我们建立了一个牛基因型组织表达图谱（cGTEx，http：//cgtex.roslin.ed.ac.uk/）的研究社区的基础上，11,642 RNA序列从公开的数据集代表100多个牛组织。我们描述了跨组织的转录组的景观，并报告了24个主要组织的数十万个顺式和反式基因与基因表达和选择性剪接的关联。我们评估了这些基因调控效应在组织中的特异性/相似性，并使用多组学数据的组合对其进行功能注释。最后，我们使用大型全转录组关联研究（TWAS）将不同组织中的基因表达与43个经济重要性状联系起来，为支撑牛农艺性状的分子调控机制提供新的生物学见解。

Characterization of genetic regulatory variants acting on the transcriptome of livestock 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 (cGTEx, http://cgtex.roslin.ed.ac.uk/) for the research community based on 11,642 RNA sequences from publicly available datasets representing over 100 cattle tissues. We describe the landscape of the transcriptome across tissues and report hundreds of thousands of cis- and trans- genetic associations with gene expression and alternative splicing for 24 major tissues. We evaluate the specificity/similarity of these genetic regulatory effects across tissues, and functionally annotate them using a combination of multi-omics data. Finally, we link gene expression in different tissues to 43 economically important traits using a large transcriptome-wide association study (TWAS) to provide novel biological insights into the molecular regulatory mechanisms underpinning agronomic traits in cattle.

A comprehensive catalogue of regulatory variants in the cattle transcriptome

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