PhD grants "Genomic study of the interactions between muscular and digestive metabolisms: role in the control of energy reserves in broiler chickens" (SSBCV)

• 36 months doctoral funding (October 2021 to September 2024)
• Keywords

transcriptome, genetics, muscle, glycogen, digestion, chicken

• Profile and skills required

Master or proven skills in bioinformatics applied to biology. Good ability to lead multidisciplinary approaches. Laboratory experience would be an advantage.

Niveau de français requis: Intermédiaire supérieur: Vous pouvez utiliser la langue de manière efficace et vous exprimer précisément.

Niveau d'anglais requis: Intermédiaire supérieur: Vous pouvez utiliser la langue de manière efficace et vous exprimer précisément.

• Project description

In chicken, glycogen reserves play a determining role in muscle integrity and meat quality. While there is a strong genetic determinism of this trait, the genes and mutations at the origin of its variation remain to be elucidated as well as the biological pathways involved. Recently, several studies in humans and mice have shown a link between muscle function and intestinal microbiota, highlighting the role of digestive function and nutrient assimilation in the development of muscle phenotypes such as glycogen reserves. This dialogue between the digestive sphere and muscle metabolism will be studied within a unique genetic model of two divergent chicken lines selected for the ultimate pH of the breast, reflecting the muscle glycogen reserves. The experimental approach will consist in an integrated analysis of muscle and digestive transcripts obtained by RNAseq, as well as phenotypes measured on the same animals. It will aim on the one hand to better understand the biological processes related to the digestion, absorption, transport and metabolic use of nutrients associated with the variability of glycogen reserves, and on the other hand to detect genetic polymorphisms that may contribute to their regulation.

• References

Adetunji MO, Lamont SJ, Abasht B, Schmidt CJ (2019) Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data. PLoS ONE 14(9): e0216838.

Beauclercq S, Hennequet-Antier C, Praud C, Godet E, Collin A, Tesseraud S, Métayer-Coustard S, Bourin M, Moroldo M, Martins F, Lagarrigue S, Le Bihan-Duval E, Berri C. Muscle transcriptome analysis reveals molecular pathways and biomarkers involved in extreme ultimate pH and meat defect occurrence in chicken. Sci Rep. 2017 Jul 25;7(1):6447.

Beauclercq S, Nadal-Desbarats L, Hennequet-Antier C, Collin A, Tesseraud S, Bourin M, Le Bihan-Duval E, Berri C. Serum and Muscle Metabolomics for the Prediction of Ultimate pH, a Key Factor for Chicken-Meat Quality. J Proteome Res. 2016 Apr 1;15(4):1168-78.

Hawley JA. Microbiota and muscle highway - two way traffic. Nat Rev Endocrinol. 2020 Feb;16(2):71-72.

Le Bihan-Duval E, Debut M, Berri CM, Sellier N, Santé-Lhoutellier V, Jégo Y, Beaumont C. Chicken meat quality: genetic variability and relationship with growth and muscle characteristics. BMC Genet. 2008 Aug 18;9:53.

Le Bihan-Duval E, Hennequet-Antier C, Berri C, Beauclercq SA, Bourin MC, Boulay M, Demeure O, Boitard S. Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL. BMC Genomics. 2018 Apr 25;19(1):294.

Nay K, Jollet M, Goustard B, Baati N, Vernus B, Pontones M, Lefeuvre-Orfila L, Bendavid C, Rué O, Mariadassou M, Bonnieu A, Ollendorff V, Lepage P, Derbré F, Koechlin-Ramonatxo C. Gut bacteria are critical for optimal muscle function: a potential link with glucose homeostasis. Am J Physiol Endocrinol Metab. 2019 Jul 1;317(1):E158-E171.

Pampouille E, Hennequet-Antier C, Praud C, Juanchich A, Brionne A, Godet E, Bordeau T, Fagnoul F, Le Bihan-Duval E, Berri C. Differential expression and co- expression gene network analyses reveal molecular mechanisms and candidate biomarkers involved in breast muscle myopathies in chicken. Sci Rep. 2019 Oct 17;9(1):14905.

Praud C, Jimenez J, Pampouille E, Couroussé N, Godet E, Le Bihan-Duval E, Berri C. Molecular Phenotyping of White Striping and Wooden Breast Myopathies in Chicken. Front Physiol. 2020 Jun 24;11:633.

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