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24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

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Axis 3: Data integration and ecophysiological modeling

The team pursues the objective to integrate data knowledge from different levels of biological organization and to integrate the genetic control in operating models that make the links between the plant and its environment.

Multi-scale data regulation.

In tomato, (collaboration with the group of F. Carrari, Argentina), we are integrating several genome expression data (proteome, RNAseq, miRNA, methylation in leaf and fruit) with metabolome and phenotypes in the 8 MAGIC and four F1 hybrids to study their relationships and inheritance.

In the EU Traditom project we will contribute to the development and characterization of a large database of phenotypic descriptors for European traditional tomato varieties (~1400 varieties, including 120 French accessions), which will also be characterized at the metabolome and genotypic levels. We will also integrate consumer preferences, sensory and metabolome profiles in a set of accessions including traditional varieties and their modern counterparts to model consumer preferences.

Relevant Publications

Kanso, H., B. Quilot-Turion, et al. (2020). Reducing a model of sugar metabolism in peach to catch different patterns among genotypes. Mathematical Biosciences 321: 108321.

Constantinescu D, M Memmah, G Vercambre, M Génard, V Baldazzi, M Causse, E Albert, B Brunel, P Valsesia and N Bertin (2016) Model-Assisted Estimation of the Genetic Variability in Physiological Parameters Related to Tomato Fruit Growth under Contrasted Water Conditions. Frontiers Plant Sci7:1841. doi:  10.3389/fpls.2016.01841

Bevacqua, D., Quilot-Turion, B., Bolzoni, L. (2018). A Model for Temporal Dynamics of Brown Rot Spreading in Fruit Orchards. Phytopathology, PHYTO-07-17-025. , DOI : 10.1094/PHYTO-07-17-0250-R

Desnoues, E., Génard, M., Quilot-Turion, B., Baldazzi, V. (2018). A kinetic model of sugar metabolism in peach fruit reveals a functional hypothesis of markedly low fructose-to-glucose ratio phenotype. The Plant Journal, 1-34.

Desnoues, E., Baldazzi, V., Génard, M., Mauroux, J.-B., Lambert, P., Confolent, C., Quilot-Turion, B. (2016). Dynamic QTLs for sugars and enzyme activities provide an overview of genetic control of sugar metabolism during peach fruit development. Journal of Experimental Botany, 67 (11), 3419-3431.

Prunus ideotypes design.

The reflection on the design of low-input production systems, optimizing of Genotype x Environment x Management (GxExM) interactions to design ideotypes is conducted collectively, with ecophysiologists and modelers from PSH unit. The challenge pursued is be to progress in the integration of the genetic control (gene linkage, effects, pleiotropy, epistasis…) in the process-based models.  The integration of knowledge about the brown-rot system (from the PhD work of L. Lino) into the ‘Virtual Fruit’ model will be pursued in order to further develop an integrated model to reason GxExM interactions. Particular attention will be given to the collaboration with UR PSH unit aiming at developing optimization methods adapted to explore discrete landscapes such as the allele space controlling the parameters of an ecophysiological model.


Relevant Publications

Barrasso, C., M.-M. Memah, et al. (2019). Model-based QTL detection is sensitive to slight modifications in model formulation. PloS one 14(10): e0222764.

Quilot-Turion, B., Génard, M., Valsesia, P., Memmah, M.-M. (2016). Optimization of Allelic Combinations Controlling Parameters of a Peach Quality Model. Frontiers in Plant Science, 20 (7).