Model-Assisted Estimation of the Genetic Variability in Physiological Parameters Related to Tomato Fruit Growth under Contrasted Water Conditions

Abstract

Drought stress is a major abiotic stress threatening plant and crop productivity. In case of fleshy fruits, understanding mechanisms governing water and carbon accumulations and identifying genes, QTLs and phenotypes, that will enable trade-offs between fruit growth and quality under Water Deficit (WD) condition is a crucial challenge for breeders and growers. In the present work, 117 recombinant inbred lines of a population of Solanum lycopersicum were phenotyped under control and WD conditions. Plant water status, fruit growth and composition were measured and data were used to calibrate a process-based model describing water and carbon fluxes in a growing fruit as a function of plant and environment. Eight genotype-dependent model parameters were estimated using a multiobjective evolutionary algorithm in order to minimize the prediction errors of fruit dry and fresh mass throughout fruit development. WD increased the fruit dry matter content (up to 85%) and decreased its fresh weight (up to 60%), big fruit size genotypes being the most sensitive. The mean normalized root mean squared errors of the predictions ranged between 16–18% in the population. Variability in model genotypic parameters allowed us to explore diverse genetic strategies in response to WD. An interesting group of genotypes could be discriminated in which (i) the low loss of fresh mass under WD was associated with high active uptake of sugars and low value of the maximum cell wall extensibility, and (ii) the high dry matter content in control treatment (C) was associated with a slow decrease of mass flow. Using 501 SNP markers genotyped across the genome, a QTL analysis of model parameters allowed to detect three main QTLs related to xylem and phloem conductivities, on chromosomes 2, 4, and 8. The model was then applied to design ideotypes with high dry matter content in C condition and low fresh mass loss in WD condition. The ideotypes outperformed the RILs especially for large and medium fruit-size genotypes, by combining high pedicel conductance and high active uptake of sugars. Interestingly, five small fruit-size RILs were close to the selected ideotypes, and likely bear interesting traits and alleles for adaptation to WD.

Putting primary metabolism into perspective to obtain better fruits

“…Overall, with the development of high-performance computing, progress in FBA and enzyme-based kinetic models and the expansion of process-based dynamic models, the time has come to integrate isolated models into a multi-scale model framework covering gene regulatory networks, activities and properties of enzymes, metabolic pathways and their compartmentalization, and plant growth. Thanks to a multi-disciplinary approach within the plant sciences (Zhu et al, 2016;Chew et al, 2017b;Marshall-Colon et al, 2017), such multi-scale models for both crops and fruits could lead to ideotype design by picking the right parameters and could eventually allow breeding to be accelerated (Long et al, 2015;Constantinescu et al, 2016;Zhu et al, 2016;Chenu et al, 2017).…”

Organ-wide and ploidy-dependent regulations both contribute to cell size determination: evidence from a computational model of tomato fruit

“…Six parameters have been selected for calibration based on a previous sensitivity analysis (Constantinescu et al, 2016), whereas the others have been fixed to the original values (Baldazzi et al, 2013;Fishman and Génard, 1998;Liu et al,…”

Variability of structural and functional traits of vascular tissues in tomato: modeling, histology and flow-MRI investigations

“…A modeling approach of water flow through the pedicel and within the fruit suggested that water importation in the young growing tomato could be limited mainly by the pedicel resistance and the phloem conductivity, linked to sap viscosity (Bussières 2002 ;Bussières et al, 2011). In agreement, a study on the design of tomato fruit ideotypes adapted to WD based on the Virtual Fruit model (Fishman and Génard, 1998 ;Liu et al, 2007) led to the hypothesis that the conductance of the vascular tissues in the pedicel could be an interesting adaptation trait (Constantinescu et al, 2016). The Virtual Fruit model is a biophysical model of fruit expansion, which has been further extended to describe the longitudinal water fluxes in the pedicel and both longitudinal and radial water fluxes in the fruit (Hall et al, 2013).…”