A compendium of genetic regulatory effects across pig tissues
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Author
Teng, Jinyan
Gao, Yahui
Yin, Hongwei
Bai, Zhonghao
Liu, Shuli
Zeng, Haonan
The PigGTEx Consortium
Bai, Lijing
Cai, Zexi
Zhao, Bingru
Li, Xiujin
Xu, Zhiting
Lin, Qing
Pan, Zhangyuan
Yang, Wenjing
Yu, Xiaoshan
Guan, Dailu
Hou, Yali
Keel, Brittney N.
Rohrer, Gary A.
Lindholm-Perry, Amanda K.
Oliver, William T.
Publication date
2024-01-04ISSN
1061-4036
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.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
57 - Biological sciences in general
Pages
34
Publisher
Nature Research
Is part of
Nature Genetics
Citation
Teng, Jinyan, Yahui Gao, Hongwei Yin, Zhonghao Bai, Shuli Liu, Haonan Zeng, Lijing Bai, et al. 2024. “A Compendium of Genetic Regulatory Effects across Pig Tissues.” Nature Genetics 56:112-123. doi:10.1038/s41588-023-01585-7.
Grant agreement number
EC/H2020/801215/EU/TRAIN@Ed/TRAINEd
EC/H2020/817998/EU/The regulatory GENomE of SWine and CHicken: functional annotation during development/GENE-SWitCH
Program
Genètica i Millora Animal
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2555]
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Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/