| Title: |
Exploring the Landscape of Local and Distant Intra-vs. Inter-Chromosomal eQTLs Using TensorQTL and GCTA: A case study from 459 Liver Transcriptomes of Aged Laying Hens |
| Authors: |
Hubert, Alexandre; Degalez, Fabien; Allain, Coralie; Burlot, Thierry; Calvez, Louis; Gòdia, Marta; Lagoutte, Laetitia; Lebez, Bénédicte; Lecerf, Frédéric; Madsen, Ole; Zerjal, Tatiana; Pitel, Frédérique; Emily, Mathieu; Allais, Sophie; Lagarrigue, Sandrine |
| Contributors: |
Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage Rennes (PEGASE); Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro); NOVOGEN; Groupe Grimaud; Wageningen University and Research Wageningen (WUR); Génétique Animale et Biologie Intégrative (GABI); AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE); Génétique Physiologie et Systèmes d'Elevage (GenPhySE); École nationale vétérinaire de Toulouse (ENVT); Institut National Polytechnique (Toulouse) (Toulouse INP); Communauté d'universités et établissements de Toulouse (Comue de Toulouse)-Communauté d'universités et établissements de Toulouse (Comue de Toulouse)-Institut National Polytechnique (Toulouse) (Toulouse INP); Communauté d'universités et établissements de Toulouse (Comue de Toulouse)-Communauté d'universités et établissements de Toulouse (Comue de Toulouse)-École nationale supérieure agronomique de Toulouse (ENSAT, INP-ENSAT, AgroToulouse, INP-AgroToulouse); Communauté d'universités et établissements de Toulouse (Comue de Toulouse)-Communauté d'universités et établissements de Toulouse (Comue de Toulouse)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole d'Ingénieurs de Purpan (EI Purpan); Communauté d'universités et établissements de Toulouse (Comue de Toulouse); Institut de Recherche Mathématique de Rennes (IRMAR); Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes); Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut Agro Rennes Angers; ANR-20-CE20-0029,EFFICACE,Analyse du contrôle génétique de différents caractères sur de longues carrières de production, chez la poule pondeuse(2020); European Project: 101000236,H2020-SFS-2018-2020,H2020-SFS-2020-2,GEroNIMO(2021) |
| Source: |
PAG33 ; https://hal.inrae.fr/hal-05560651 ; PAG33, Jan 2026, San diego (Californie), United States. https://plan.core-apps.com/pag33/abstract/2907311f-56dd-4348-bf69-ca2da809ea0f ; https://intlpag.org/PAG33/ |
| Publisher Information: |
CCSD |
| Publication Year: |
2026 |
| Collection: |
Université Toulouse III - Paul Sabatier: HAL-UPS |
| Subject Terms: |
[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics |
| Subject Geographic: |
San diego (Californie); United States |
| Description: |
International audience ; Expression quantitative trait loci (eQTL) mapping is a key approach in understanding how genetic variants influence gene expression and phenotypic variability. In this study, we compared the performance of two eQTL mapping tools: GCTA, widely used for quantitative traits, and TensorQTL, a recent method applied in human GTEx datasets. We assessed their performance in terms of eGene discovery, concordance, and computational efficiency using a large liver transcriptomic dataset from aged laying hens. Sustaining egg production in aging hens likely depends on efficient lipid synthesis, not only because yolk formation requires a large lipid supply, but also because lipids provide precursors for hormones and signaling molecules controlling ovulation and egg production. The liver is the central organ of lipid metabolism, making it a suitable tissue to investigate eQTLs influencing reproductive longevity. We investigated the genetic regulation of gene expression in the liver of 459 aged laying hens (90 weeks of age) from a single pure line, generating one of the largest eQTL datasets in livestock. Gene expression levels were derived from RNA-seq data that were inverse-normal transformed before association testing. Both GCTA and TensorQTL were used to map two types of eQTLs: i) local eQTLs defined as associations between an eGene and SNPs within ±500kb of its transcription start site (TSS), and ii) distant eQTLs defined as associations outside this region, including those on different chromosomes. To ensure robust detection, a 1Mb region was considered as an eQTL when at least five SNPs within a 100kb window exceeded a significance threshold and were in linkage disequilibrium (LD≥0.5). Bonferroni correction was applied to account for multiply testing considering 11,830 variables, and for distant eQTLs, 4,442 independent SNPs. Overall, 5,254 of the 11,830 genes expressed in the liver were regulated by at least one local eQTL across both methods. TensorQTL detected more eGenes (5,231) than GCTA ... |
| Document Type: |
conference object |
| Language: |
English |
| Relation: |
info:eu-repo/grantAgreement//101000236/EU/GEroNIMO: Genome and Epigenome eNabled breedIng in MOnogastrics/GEroNIMO |
| Availability: |
https://hal.inrae.fr/hal-05560651; https://hal.inrae.fr/hal-05560651v1/document; https://hal.inrae.fr/hal-05560651v1/file/Abstract_eQTL.pdf |
| Rights: |
https://creativecommons.org/licenses/by/4.0/ ; info:eu-repo/semantics/OpenAccess |
| Accession Number: |
edsbas.2AFA5BA1 |
| Database: |
BASE |