A multi-tissue atlas of regulatory variants in cattle

Shuli Liu; Yahui Gao; Oriol Canela-Xandri; Sheng Wang; Ying Yu; Wentao Cai; Bingjie Li; Ruidong Xiang; Amanda J 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

Shuli Liu, Yahui Gao, Oriol Canela-Xandri, Sheng Wang, Ying Yu, Wentao Cai, Bingjie Li, Ruidong Xiang, Amanda J 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^*

^*Corresponding author af dette arbejde

Center for Kvantitativ Genetik og Genomforskning, Aarhus - Center for Kvantitativ Genetik og Genomforskning, Foulum

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

101 Citationer (Scopus)

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.

Originalsprog	Engelsk
Tidsskrift	Nature Genetics
Vol/bind	54
Nummer	9
Sider (fra-til)	1438-1447
Antal sider	10
ISSN	1061-4036
DOI	https://doi.org/10.1038/s41588-022-01153-5
Status	Udgivet - sep. 2022

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7613894/pdf/EMS157770.pdfLicens: CC BY

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Liu, S., Gao, Y., Canela-Xandri, O., Wang, S., Yu, Y., Cai, W., Li, B., Xiang, R., Chamberlain, A. J., 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. Nature Genetics, 54(9), 1438-1447. https://doi.org/10.1038/s41588-022-01153-5

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title = "A multi-tissue atlas of regulatory variants in cattle",

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.",

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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 Chamberlain, {Amanda J} 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,

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

language = "English",

volume = "54",

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Liu, S, Gao, Y, Canela-Xandri, O, Wang, S, Yu, Y, Cai, W, Li, B, Xiang, R, Chamberlain, AJ, 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', Nature Genetics, bind 54, nr. 9, s. 1438-1447. https://doi.org/10.1038/s41588-022-01153-5

TY - JOUR

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

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 J

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

Y1 - 2022/9

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 - Animals

KW - Cattle/genetics

KW - Gene Expression Regulation

KW - Phenotype

KW - Quantitative Trait Loci/genetics

KW - Sequence Analysis, RNA

KW - Transcriptome/genetics

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U2 - 10.1038/s41588-022-01153-5

DO - 10.1038/s41588-022-01153-5

M3 - Journal article

C2 - 35953587

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

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