A compendium of genetic regulatory effects across pig tissues

The PigGTEx Consortium

doi:10.1038/s41588-023-01585-7

A compendium of genetic regulatory effects across pig tissues

The PigGTEx Consortium

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

37 Citations (Scopus)

Abstract

The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.

Original language	English
Journal	Nature Genetics
Volume	56
Issue	1
Pages (from-to)	112-123
Number of pages	12
ISSN	1061-4036
DOIs	https://doi.org/10.1038/s41588-023-01585-7
Publication status	Published - Jan 2024

Keywords

Animals
Gene Expression Profiling
Gene Expression Regulation
Genotype
Humans
Phenotype
Sequence Analysis, RNA
Swine/genetics

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10.1038/s41588-023-01585-7Licence: CC BY

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title = "A compendium of genetic regulatory effects across pig tissues",

abstract = "The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.",

keywords = "Animals, Gene Expression Profiling, Gene Expression Regulation, Genotype, Humans, Phenotype, Sequence Analysis, RNA, Swine/genetics",

author = "Jinyan Teng and Yahui Gao and Hongwei Yin and Zhonghao Bai and Shuli Liu and Haonan Zeng and Lijing Bai and Zexi Cai and Bingru Zhao and Xiujin Li and Zhiting Xu and Qing Lin and Zhangyuan Pan and Wenjing Yang and Xiaoshan Yu and Dailu Guan and Yali Hou and Keel, {Brittney N.} and Rohrer, {Gary A.} and Lindholm-Perry, {Amanda K.} and Oliver, {William T.} and Maria Ballester and Daniel Crespo-Piazuelo and Raquel Quintanilla and Oriol Canela-Xandri and Konrad Rawlik and Charley Xia and Yuelin Yao and Qianyi Zhao and Wenye Yao and Liu Yang and Houcheng Li and Huicong Zhang and Wang Liao and Tianshuo Chen and Peter Karlskov-Mortensen and Sheng Wang and Guosheng Su and Goutam Sahana and Lund, {Mogens Sand{\o}} and Ole Madsen and Yonglun Luo and Lin Lin and Zhe Zhang and Pinghua Li and Li Ma and Qin Zhang and Bingjie Li and Zhe Zhang and Lingzhao Fang and {The PigGTEx Consortium}",

note = "Publisher Copyright: {\textcopyright} 2024, The Author(s).",

year = "2024",

month = jan,

doi = "10.1038/s41588-023-01585-7",

language = "English",

volume = "56",

pages = "112--123",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Research",

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TY - JOUR

T1 - A compendium of genetic regulatory effects across pig tissues

AU - Teng, Jinyan

AU - Gao, Yahui

AU - Yin, Hongwei

AU - Bai, Zhonghao

AU - Liu, Shuli

AU - Zeng, Haonan

AU - Bai, Lijing

AU - Cai, Zexi

AU - Zhao, Bingru

AU - Li, Xiujin

AU - Xu, Zhiting

AU - Lin, Qing

AU - Pan, Zhangyuan

AU - Yang, Wenjing

AU - Yu, Xiaoshan

AU - Guan, Dailu

AU - Hou, Yali

AU - Keel, Brittney N.

AU - Rohrer, Gary A.

AU - Lindholm-Perry, Amanda K.

AU - Oliver, William T.

AU - Ballester, Maria

AU - Crespo-Piazuelo, Daniel

AU - Quintanilla, Raquel

AU - Canela-Xandri, Oriol

AU - Rawlik, Konrad

AU - Xia, Charley

AU - Yao, Yuelin

AU - Zhao, Qianyi

AU - Yao, Wenye

AU - Yang, Liu

AU - Li, Houcheng

AU - Zhang, Huicong

AU - Liao, Wang

AU - Chen, Tianshuo

AU - Karlskov-Mortensen, Peter

AU - Wang, Sheng

AU - Su, Guosheng

AU - Sahana, Goutam

AU - Lund, Mogens Sandø

AU - Madsen, Ole

AU - Luo, Yonglun

AU - Lin, Lin

AU - Zhang, Zhe

AU - Li, Pinghua

AU - Ma, Li

AU - Zhang, Qin

AU - Li, Bingjie

AU - Zhang, Zhe

AU - Fang, Lingzhao

AU - The PigGTEx Consortium

PY - 2024/1

Y1 - 2024/1

N2 - The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.

AB - The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.

KW - Animals

KW - Gene Expression Profiling

KW - Gene Expression Regulation

KW - Genotype

KW - Humans

KW - Phenotype

KW - Sequence Analysis, RNA

KW - Swine/genetics

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U2 - 10.1038/s41588-023-01585-7

DO - 10.1038/s41588-023-01585-7

M3 - Journal article

C2 - 38177344

AN - SCOPUS:85181452836

SN - 1061-4036

VL - 56

SP - 112

EP - 123

JO - Nature Genetics

JF - Nature Genetics

IS - 1

ER -

A compendium of genetic regulatory effects across pig tissues

Abstract

Keywords

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