Mots-Clés

Systems biology Biostatistics Bioinformatics Data Integration

Description

Working environment:
A post-doc position is available at GDEC, Clermont-Ferrand starting at the earliest convenience and funded as part of the industrial chair UCA/Limagrain (I-SITE CAP2025 pole of excellence). The research work will be conducted in the Plant Immunity and Multistress team (ex-MDC), whose projects are dedicated to elucidating the mechanisms of natural immunity in bread wheat and assessing the impact of environmental factors on their expression. To this end, the team employs multidisciplinary methodologies, integrating genetics, genomics, biochemistry, molecular physiology, plant pathology,
agronomy, and biostatistics within a comprehensive systems biology framework. The post-doc will integrate the work dedicated to the characterization of the molecular and physiological determinants of wheat to a combination of biotic and abiotic stress (leader L.Bonhomme, PR UCA). He/she will set up systems biology approaches that will aim to analyze and predict the plant adjustments in a holistic or reductionist manner using large -omics and phenotypic datasets. Project objectives and missions: Climate change is not only forcing plants to cope with extreme stresses, but will also encourage the recurrence of complex and simultaneous disturbances to their abiotic and biotic environment. Still largely underestimated, the impact of these combinations of stresses particularly threatens the performance of cropping systems, with major consequences for the expression of natural immunity mechanisms and the ability of plants to adjust to their environment. Multiple evidences already demonstrated that these combinations of stresses mobilize determinants that cannot be predicted from knowledge acquired on isolated stresses. Identifying the specific processes and mechanisms of these stress combinations represents a real opportunity to diversify breeding tools for crop varieties better adapted
to expected climatic scenarios. With our extensive knowledge of the molecular and physiological determinants controlling FHB susceptibility in wheat, the aim of this post-doc position will be to set up original integrative approaches, using descriptive and predictive statistics, to provide new knowledge on this complex dual-biologic systems in changing environmental conditions exploiting diverse -omics data. This will make it possible to open new insights in system biology of combined stress responses in plants and will guide the understanding of the non-trivial dynamic models of gene networks in plant stress response and their respective contribution to the plant phenotype. This work will benefit from all the means necessary for the full realization of the project, such as access to computer resources (storage, calculation) available at the “MésoCentre” computing facility in Clermont-Ferrand.

Profile:
Highly motivated candidates with a PhD degree and having a strong background in biostatistics (data mining, interpretation, data aggregation...) and bioinformatics are encouraged to apply. Previous experience with analyzing integrative biology is required. The candidates should also have good communication skills evidenced by scientific publications. Ability to work in a team environment is required.

Technical skills:
Master in bioanalyses, biostatistics and bioinformatics or a related field with relevant expertise in the project
topics. Experience with R tools are mandatory as well as with high throughput data analysis, management
and integration. Programming skills appreciated.

Significant publications on the topic:
F. Rocher, S. Dou, G. Philippe, M.L. Martin, P. Label, T. Langin, L. Bonhomme. 2024. Integrative systems biology of wheat susceptibility to Fusarium graminearum uncovers a conserved gene regulatory network and identifies master regulators targeted by fungal core-effectors. BMC Biology 22, 53.

L. Adamik, T. Langin, L. Bonhomme. 2023. A generic part of specific combined responses to biotic and abiotic stresses in crops: Overcoming multifaceted challenges towards new opportunities. Frontiers in Plant Science 14:1140808.
F. Rocher, T. Alouane, G. Philippe, M.-L. Martin, P. Label, T. Langin, L. Bonhomme. 2022. Fusarium graminearum infection strategy in wheat involves a highly conserved genetic program that controls the expression of a core effectome. Int. Journal of Molecular Science 23, 1914.

T. Alouane, H. Rimbert, J. Bormann, G.A. González-Montiel, S. Loesgen, W. Schäfer, M. Freitag, T. Langin, L. Bonhomme. 2021. Comparative Genomics of eight Fusarium graminearum strains with contrasting aggressiveness reveals an expanded open pangenome and extended effector content signatures. Int. Journal of Molecular Science 22, 6257.

F. Fabre, S. Urbach, S. Roche, T. Langin, L. Bonhomme. 2021. Proteomics-Based Data Integration of Wheat Cultivars Facing Fusarium graminearum Strains Revealed a Core-Responsive Pattern Controlling Fusarium Head Blight. Frontiers in Plant Science 12:644810.

Project Title: Systems biology and predictive modeling of multistress responses in wheat Head of the Scientific Project: Ludovic Bonhomme (UCA)