Genetic variability of transcript abundance in pig peri-mortem skeletal muscle: eQTL localized genes involved in stress response, cell death, muscle disorders and metabolism
| Autor: | Laurence Liaubet, Pascale Le Roy, Valérie Lobjois, J. Glénisson, Thomas Faraut, Francis Benne, Magali SanCristobal, J. Pires, Nathalie Iannuccelli, Aurélie Tircazes, Annie Robic, Pierre Cherel |
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| Přispěvatelé: | Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut des Technologies Avancées en sciences du Vivant (ITAV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Centro de Investigação Operacional (CIO), Universidade de Lisboa (ULISBOA), Génétique Animale (GARen), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST-Ecole Nationale Supérieure Agronomique de Rennes-IFR140, France Hybride, Hendrix Genetics, Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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)-Ecole Nationale Supérieure Agronomique de Rennes, This project received financial support from the French Ministry of Research in the framework of the PG ASG program. We thank the INRA Animal Genetics Department for post-doctoral financial help. The microarray annotation and the database with BASE software is managed by SIGENAE computer group (Systeme d'information du projet d'analyse des genomes des animaux d'elevage, http://www.sigenae.org) and especially Philippe Bardou for GEO submission. We thank Julien Thia-Ah-Fat (master student) for help and Daphne Goodfellow for the English revision. Our special thanks to Francis Hatey who initiated this project with Pierre Cherel., Liaubet, Laurence |
| Jazyk: | angličtina |
| Rok vydání: | 2011 |
| Předmět: |
Male
pig MESH: Cell Death Transcription Genetic Swine muscle [SDV]Life Sciences [q-bio] Adipose tissue Inbred strain Cluster Analysis MESH: Animals MESH: Genetic Variation MESH: Stress Physiological MESH: Swine Oligonucleotide Array Sequence Analysis Genetics Regulation of gene expression 0303 health sciences MESH: Muscle Skeletal Cell Death system biology cochon Chromosome Mapping muscle squelettique systems biology 04 agricultural and veterinary sciences eqtl MESH: Gene Expression Regulation Phenotype medicine.anatomical_structure Female Research Article Biotechnology biologie des systèmes lcsh:QH426-470 lcsh:Biotechnology Quantitative Trait Loci MESH: Molecular Sequence Annotation Muscle disorder Biology MESH: Phenotype 03 medical and health sciences genetical genomics transcriptome genetical genomic Stress Physiological lcsh:TP248.13-248.65 Genetic variation medicine Animals Genetic variability Muscle Skeletal 030304 developmental biology MESH: Transcription Genetic MESH: Transcriptome 0402 animal and dairy science Genetic Variation Skeletal muscle Molecular Sequence Annotation 040201 dairy & animal science MESH: Cluster Analysis MESH: Quantitative Trait Loci MESH: Male lcsh:Genetics Gene Expression Regulation Expression quantitative trait loci MESH: Oligonucleotide Array Sequence Analysis MESH: Chromosome Mapping MESH: Female |
| Zdroj: | BMC Genomics BMC Genomics, BioMed Central, 2011, 12, pp.548. ⟨10.1186/1471-2164-12-548⟩ BMC Genomics, BioMed Central, 2011, 12 (november), pp.548. ⟨10.1186/1471-2164-12-548⟩ BMC Genomics, Vol 12, Iss 1, p 548 (2011) BMC Genomics november (12, online), Non paginé. (2011) |
| ISSN: | 1471-2164 |
| DOI: | 10.1186/1471-2164-12-548⟩ |
| Popis: | Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access; International audience; BACKGROUND: The genetics of transcript-level variation is an exciting field that has recently given rise to many studies. Genetical genomics studies have mainly focused on cell lines, blood cells or adipose tissues, from human clinical samples or mice inbred lines. Few eQTL studies have focused on animal tissues sampled from outbred populations to reflect natural genetic variation of gene expression levels in animals. In this work, we analyzed gene expression in a whole tissue, pig skeletal muscle sampled from individuals from a half sib F2 family shortly after slaughtering. RESULTS: QTL detection on transcriptome measurements was performed on a family structured population. The analysis identified 335 eQTLs affecting the expression of 272 transcripts. The ontologic annotation of these eQTLs revealed an over-representation of genes encoding proteins involved in processes that are expected to be induced during muscle development and metabolism, cell morphology, assembly and organization and also in stress response and apoptosis. A gene functional network approach was used to evidence existing biological relationships between all the genes whose expression levels are influenced by eQTLs. eQTLs localization revealed a significant clustered organization of about half the genes located on segments of chromosome 1, 2, 10, 13, 16, and 18. Finally, the combined expression and genetic approaches pointed to putative cis-drivers of gene expression programs in skeletal muscle as COQ4 (SSC1), LOC100513192 (SSC18) where both the gene transcription unit and the eQTL affecting its expression level were shown to be localized in the same genomic region. This suggests cis-causing genetic polymorphims affecting gene expression levels, with (e.g. COQ4) or without (e.g. LOC100513192) potential pleiotropic effects that affect the expression of other genes (cluster of trans-eQTLs). CONCLUSION: Genetic analysis of transcription levels revealed dependence among molecular phenotypes as being affected by variation at the same loci. We observed the genetic variation of molecular phenotypes in a specific situation of cellular stress thus contributing to a better description of muscle physiologic response. In turn, this suggests that large amounts of genetic variation, mediated through transcriptional networks, can drive transient cell response phenotypes and contribute to organismal adaptative potential. |
| Databáze: | OpenAIRE |
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