Evidence map›Paper›PMID 35953587›Full record

ArticleNature genetics2022

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 and 18 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 156 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
156citing papers in PubMed, 2 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

156 citing papers in PubMed, 2 syntheses or guidelines pooled it.

  1. Pooled it
  2. Sequence-based GWAS meta-analyses for beef production traits.Genetics, selection, evolution : GSE · 2023
    Pooled it
  3. Article
  4. Review
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  10. Integrated Analysis ofBiomolecules · 2026
    Article
  11. Review
  12. Article
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  14. Article
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  16. Article
  17. Review
  18. Pan-tissue transcriptomic profiling of dairy cattle.Journal of animal science and biotechnology · 2026
    Article
  19. Role ofZoological research · 2026
    Article
  20. Article

96 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

28 authors.

Shuli Liu *Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.
Yahui Gao *Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.
Oriol Canela-Xandri *MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.ORCID http://orcid.org/0000-0003-4601-6289
Sheng Wang *State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Ying Yu *National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.ORCID http://orcid.org/0000-0002-4524-0791
Wentao CaiInstitute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China.
Bingjie LiScotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK.
Ruidong XiangFaculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville, Victoria, Australia.ORCID http://orcid.org/0000-0002-1584-7605
Amanda J ChamberlainAgriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, Australia.ORCID http://orcid.org/0000-0002-9395-1299
Erola Pairo-CastineiraMRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.ORCID http://orcid.org/0000-0002-2423-3090
Kenton D'MellowMRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
Konrad RawlikThe Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.ORCID http://orcid.org/0000-0002-0010-370X
Charley XiaThe Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.
Yuelin YaoMRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
Pau NavarroMRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.ORCID http://orcid.org/0000-0001-5576-8584
Dominique RochaINRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France.
Xiujin LiGuangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
Ze YanNational Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
Congjun LiAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.ORCID http://orcid.org/0000-0003-1389-9820
Benjamin D RosenAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.ORCID http://orcid.org/0000-0001-9395-8346
Curtis P Van TassellAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.ORCID http://orcid.org/0000-0002-8416-2087
Paul M VanradenAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.
Shengli ZhangNational Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
Li MaDepartment of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.ORCID http://orcid.org/0000-0003-1038-1081
John B ColeAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.ORCID http://orcid.org/0000-0003-1242-4401
George E LiuAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA. George.Liu@usda.gov.
Albert TenesaMRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK. Albert.Tenesa@ed.ac.uk.ORCID http://orcid.org/0000-0003-4884-4475
Lingzhao FangAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA. lingzhao.fang@qgg.au.dk.ORCID http://orcid.org/0000-0003-1103-3679

Funding

Biotechnology and Biological Sciences Research Council BBS/E/D/10002070Biotechnology and Biological Sciences Research Council BBS/E/D/30002275Medical Research Council MR/P015514/1Medical Research Council MR/R025851/1
6 · The paper itself

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.

Indexed as

Quantitative Trait LociTranscriptomeAnimalsCattleGene Expression RegulationPhenotypeSequence Analysis, RNA

Identifiers

PMID35953587
PMCPMC7613894

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.