Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues
Author
Acloque, Hervé
González-Rodríguez, Olga
Mongellaz, Mayrone
Mercat, Marie-José
Bink, Marco C A M
Huisman, Abe E
Publication date
2023-06-24ISSN
2047-217X
Abstract
Background
In humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. To discover genetic polymorphisms affecting the duodenum, liver, and muscle transcriptomes of 300 pigs from 3 different breeds (Duroc, Landrace, and Large White), we performed expression GWAS between 25,315,878 polymorphisms and the expression of 13,891 genes in duodenum, 12,748 genes in liver, and 11,617 genes in muscle.
Results
More than 9.68 × 1011 association tests were performed, yielding 14,096,080 significantly associated variants, which were grouped in 26,414 expression quantitative trait locus (eQTL) regions. Over 56% of the variants were within 1 Mb of their associated gene. In addition to the 100-kb region upstream of the transcription start site, we identified the importance of the 100-kb region downstream of the 3′UTR for gene regulation, as most of the cis-regulatory variants were located within these 2 regions. We also observed 39,874 hotspot regulatory polymorphisms associated with the expression of 10 or more genes that could modify the protein structure or the expression of a regulator gene. In addition, 2 motifs (5′-GATCCNGYGTTGCYG-3′ and a poly(A) sequence) were enriched across the 3 tissues within the neighboring sequences of the most significant single-nucleotide polymorphisms in each cis-eQTL region.
Conclusions
The 14 million significant associations obtained in this study are publicly available and have enabled the identification of expression-associated cis-, trans-, and hotspot regulatory variants within and across tissues, thus shedding light on the molecular mechanisms of regulatory variations that shape end-trait phenotypes.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
575 - General genetics. General cytogenetics
Pages
14
Publisher
Oxford University Press
Is part of
GigaScience
Citation
Crespo-Piazuelo, Daniel, Hervé Acloque, Olga González-Rodríguez, Mayrone Mongellaz, Marie-José Mercat, Marco C A M Bink, Abe E Huisman, Yuliaxis Ramayo-Caldas, Juan Pablo Sánchez, and Maria Ballester. 2022. "Identification Of Transcriptional Regulatory Variants In Pig Duodenum, Liver, And Muscle Tissues". Gigascience 12. doi:10.1093/gigascience/giad042.
Grant agreement number
EC/H2020/817998/EU/The regulatory GENomE of SWine and CHicken: functional annotation during development/GENE-SWitCH
EC/ / /EU/Accelerating genome to phenome research for farmed animals in Europe/EuroFAANG
MICIU-FEDER/Programa Estatal de promoción del talento y su empleabilidad en I+D+I/RYC2019-027244-I/ES/Metagenomics and integrative biology tools to improve sustainable livestock systems/
Program
Genètica i Millora Animal
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2850]
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/