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. Rosen; Curtis P Van Tassell; Paul M.  Vanraden; Shengli Zhang; Li  Ma; John B.  Cole; George E Liu; Albert Tenesa; Lingzhao Fang

doi:10.1038/s41588-022-01153-5

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 journal › Article › peer-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 language	English
Pages (from-to)	1438-1447
Journal	Nature Genetics
Volume	54
Issue number	9
Early online date	11 Aug 2022
DOIs	https://doi.org/10.1038/s41588-022-01153-5
Publication status	Published - 1 Sept 2022

Keywords / Materials (for Non-textual outputs)

Cattle
expression QTLs
GWAS
RNA-Seq
TWAS

Access to Document

10.1038/s41588-022-01153-5

59583_4_merged_1655920711Accepted author manuscript, 15.5 MBLicence: Creative Commons: Attribution (CC-BY)

TRAIN@Ed: Transnational Research and Innovation Network at Edinburgh
Gorjanc, G., Bell, C., Duncan, A., Farrington, S., Florian, L., Forde, M., Hickey, J., Lacka, E., Ma, T., Mcneill, G., Medina-Lopez, E., Rosser, S., Rossi, R., Sabanis, S., Szpruch, L., Tenesa, A., Wake, D., Williamson, B. & Yang, Y.
EU government bodies, Non-EU industry, commerce and public corporations
1/11/19 → 19/04/23
Project: Research
Understanding disease through environmental-wide association studies
Tenesa, A., Canela Xandri, O., Rawlik, K. & Sudlow, C.
MRC
1/08/17 → 31/07/20
Project: Research

Cite this

Liu, S., Gao, Y., Canela-Xandri, O., Wang, S., Yu, Y., Cai, W., Li, B., Xiang, R., Chamberlain, A., Pairo-Castineira, E., D'Mellow, K., Rawlik, K., Xia, C., Yao, Y., Navarro, P., Rocha, D., Li, X., Yan, Z., Li, C., ... Fang, L. (2022). A multi-tissue atlas of regulatory variants in cattle: Cattle Genotype-Tissue Expression Atlas. Nature Genetics, 54(9), 1438-1447. https://doi.org/10.1038/s41588-022-01153-5

@article{11ab5731bf9241a19f0d8d516172c48e,

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

abstract = "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.",

keywords = "Cattle, expression QTLs, GWAS, RNA-Seq, TWAS",

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

year = "2022",

month = sep,

day = "1",

doi = "10.1038/s41588-022-01153-5",

language = "English",

volume = "54",

pages = "1438--1447",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Publishing Group",

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Liu, S, Gao, Y, Canela-Xandri, O, Wang, S, Yu, Y, Cai, W, Li, B, Xiang, R, Chamberlain, A, Pairo-Castineira, E , D'Mellow, K , Rawlik, K, Xia, C, Yao, Y, Navarro, P, Rocha, D, Li, X, Yan, Z, Li, C, Rosen, BD, Van Tassell, CP, Vanraden, PM, Zhang, S, Ma, L, Cole, JB, Liu, GE, Tenesa, A & Fang, L 2022, 'A multi-tissue atlas of regulatory variants in cattle: Cattle Genotype-Tissue Expression Atlas', Nature Genetics, vol. 54, no. 9, pp. 1438-1447. https://doi.org/10.1038/s41588-022-01153-5

TY - JOUR

T1 - A multi-tissue atlas of regulatory variants in cattle

T2 - Cattle Genotype-Tissue Expression Atlas

AU - Liu, Shuli

AU - Gao, Yahui

AU - Canela-Xandri, Oriol

AU - Wang, Sheng

AU - Yu, Ying

AU - Cai, Wentao

AU - Li, Bingjie

AU - Xiang, Ruidong

AU - Chamberlain, Amanda

AU - Pairo-Castineira, Erola

AU - D'Mellow, Kenton

AU - Rawlik, Konrad

AU - Xia, Charley

AU - Yao, Yuelin

AU - Navarro, Pau

AU - Rocha, Dominique

AU - Li, Xiujin

AU - Yan, Ze

AU - Li, Congjun

AU - Rosen, Benjamin D.

AU - Van Tassell, Curtis P

AU - Vanraden, Paul M.

AU - Zhang, Shengli

AU - Ma, Li

AU - Cole, John B.

AU - Liu, George E

AU - Tenesa, Albert

AU - Fang, Lingzhao

PY - 2022/9/1

Y1 - 2022/9/1

N2 - 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.

AB - 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.

KW - Cattle

KW - expression QTLs

KW - GWAS

KW - RNA-Seq

KW - TWAS

U2 - 10.1038/s41588-022-01153-5

DO - 10.1038/s41588-022-01153-5

M3 - Article

SN - 1061-4036

VL - 54

SP - 1438

EP - 1447

JO - Nature Genetics

JF - Nature Genetics

IS - 9

ER -

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

Abstract / Description of output

Keywords / Materials (for Non-textual outputs)

Access to Document

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Projects

TRAIN@Ed: Transnational Research and Innovation Network at Edinburgh

Understanding disease through environmental-wide association studies

Cite this