A multi-tissue atlas of regulatory variants in cattle: Cattle Genotype-Tissue Expression Atlas

Shuli Liu, Yahui Gao, Oriol Canela-Xandri, Sheng Wang, Ying Yu, Wentao Cai, Bingjie Li, Ruidong Xiang, Amanda Chamberlain, Erola Pairo-Castineira, Kenton D'Mellow, Konrad Rawlik, Charley Xia, Yuelin Yao, Pau Navarro, Dominique Rocha, Xiujin Li, Ze Yan, Congjun Li, Benjamin D. RosenCurtis P Van Tassell, Paul M. Vanraden, Shengli Zhang, Li Ma, John B. Cole, George E Liu, Albert Tenesa, Lingzhao Fang

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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.

Original languageEnglish
Pages (from-to)1438-1447
JournalNature Genetics
Issue number9
Early online date11 Aug 2022
Publication statusPublished - 1 Sept 2022

Keywords / Materials (for Non-textual outputs)

  • Cattle
  • expression QTLs
  • GWAS
  • RNA-Seq
  • TWAS


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