P3029 Identification of regulatory genes involved in longissimus dorsi transcriptomic differences between pig genotypes
Notice bibliographique
Résumé
Iberian pig production is based on both purebred Iberian (IB) and crossbred Duroc X Iberian (DUxIB) pigs. These two genetic types show important differences in growth, fattening and tissue composition. This study was conducted to assess Longissimus dorsi muscle gene expression profiles and to identify regulatory genes potentially responsible for gene expression and phenotypic differences between pig genotypes. Nine IB and 10 DUxIB piglets were slaughtered at birth, and 7 IB and 10 DUxIB were slaughtered at 4 mo of age (growing stage). Carcass traits were measured and samples from Longissimus dorsi were taken to study intramuscular fat (IMF) content and composition and to analyze the muscle transcriptome with RNA-seq technology. Differences in growth and fatness patterns were observed between genotypes. Genetic type significantly affected expression of 261 genes (P < 0.01 and Fold change > 1.5) at birth and 113 genes at growing stage. To understand the molecular mechanisms underlying gene expression differences between IB and IBxDU, a regulatory gene examination was conducted following three different approaches. Identification of regulators was based on biological data mining (Ingenuity Pathways Analysis software), coexpression data (Regulatory Impact Factor study) and differential expression data (DE regulators). Regulatory genes identified at both ages were deemed to have a deeper impact in the final phenotype. Some of the genes were closely related to muscle development (MYOD1, BHLHE40 and HDAC2) and adipogenesis and fat accumulation (NFKBIA, ATF4 or CEBPA). Regulators identified in more than one approach were considered to be the most robust results. In newborns, these regulators were mainly involved in muscle cell differentiation (MEF2C, MEF2D, MYOG, SOX4) and protein degradation (CREB3L1, HSF1 and CREBBP), thus playing a role in muscle development. FOS and FOXO regulatory genes control muscle differentiation but also adipogenic genes expression and IMF accumulation. In growing animals, three regulators were identified by complementary approaches, being involved in the regulation of the cell cycle (EN1 and IRF2) and lipid metabolism (EN1 and TCF7L2). Moreover, a functional analysis was performed combining the DE and the regulators studies information. Several pathways were enriched at both stages. Among them, pathways involved in adipocyte differentiation and protein degradation (the PPAR signaling, the adipogenesis, the Wnt and the unfolded protein response) are of special relevance. The present work identifies regulatory genes potentially involved in differences in metabolism and productive traits between IB and IBxDU pigs.
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Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,001 | 0,001 |
| Bibliométrie | 0,001 | 0,001 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,001 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,001 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,005 | 0,002 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».