Quantitative Genetics and Functional-Structural Plant Growth Models: Simulation of Quantitative Trait Loci Detection for Model Parameters and Application to Potential Yield Optimization

TL;DR

This study integrates genetics into a functional-structural plant growth model to improve QTL detection for traits and optimize yield, demonstrating enhanced accuracy when using model parameters over phenotypic traits.

Contribution

It introduces a novel approach combining genetic modeling with a growth model to identify fundamental traits for QTL detection and yield optimization.

Findings

QTL detection is more accurate when using model parameters than phenotypic traits.

The approach successfully identified parameters linked to yield optimization.

GreenLab model effectively represents genotype x environment interactions.

Abstract

Background and Aims: Prediction of phenotypic traits from new genotypes under untested environmental conditions is crucial to build simulations of breeding strategies to improve target traits. Although the plant response to environmental stresses is characterized by both architectural and functional plasticity, recent attempts to integrate biological knowledge into genetics models have mainly concerned specific physiological processes or crop models without architecture, and thus may prove limited when studying genotype x environment interactions. Consequently, this paper presents a simulation study introducing genetics into a functional-structural growth model, which gives access to more fundamental traits for quantitative trait loci (QTL) detection and thus to promising tools for yield optimization. Methods: The GreenLab model was selected as a reasonable choice to link growth model parameters to QTL. Virtual genes and virtual chromosomes were defined to build a simple genetic model that drove the settings of the species-specific parameters of the model. The QTL Cartographer software was used to study QTL detection of simulated plant traits. A genetic algorithm was implemented to define the ideotype for yield maximization based on the model parameters and the associated allelic combination. Key Results and Conclusions: By keeping the environmental factors constant and using a virtual population with a large number of individuals generated by a Mendelian genetic model, results for an ideal case could be simulated. Virtual QTL detection was compared in the case of phenotypic traits - such as cob weight - and when traits were model parameters, and was found to be more accurate in the latter case. The practical interest of this approach is illustrated by calculating the parameters (and the corresponding genotype) associated with yield optimization of a GreenLab maize model. The paper discusses the potentials of GreenLab to represent environment x genotype interactions, in particular through its main state variable, the ratio of biomass supply over demand.