From QTLs to Adaptation Landscapes: Using Genotype-To-Phenotype Models to Characterize GxE Over Time

Genotype by environment interaction (GxE) for the target trait, e.g. yield, is an emerging property of agricultural systems and results from the interplay between a hierarchy of secondary traits involving the capture and allocation of environmental resources during the growing season. This hierarchy of secondary traits ranges from basic traits that correspond to response mechanisms/sensitivities, to intermediate traits that integrate a larger number of processes over time and therefore show a larger amount of GxE. Traits underlying yield differ in their contribution to adaptation across environmental conditions and have different levels of GxE. Here, we provide a framework to study the performance of genotype to phenotype (G2P) modeling approaches. We generate and analyze response surfaces, or adaptation landscapes, for yield and yield related traits, emphasizing the organization of the traits in a hierarchy and their development and interactions over time. We use the crop growth model APSIM-wheat with genotype-dependent parameters as a tool to simulate non-linear trait responses over time with complex trait dependencies and apply it to wheat crops in Australia. For biological realism, APSIM parameters were given a genetic basis of 300 QTLs sampled from a gamma distribution whose shape and rate parameters were estimated from real wheat data. In the simulations, the hierarchical organization of the traits and their interactions over time cause GxE for yield even when underlying traits do not show GxE. Insight into how GxE arises during growth and development helps to improve the accuracy of phenotype predictions within and across environments and to optimize trial networks. We produced a tangible simulated adaptation landscape for yield that we first investigated for its biological credibility by statistical models for GxE that incorporate genotypic and environmental covariables. Subsequently, the simulated trait data were used to evaluate statistical genotype-to-phenotype models for multiple traits and environments and to characterize relationships between traits over time and across environments, as a way to identify traits that could be useful to select for specific adaptation. Designed appropriately, these types of simulated landscapes might also serve as a basis to train other, more deep learning methodologies in order to transfer such network models to real-world situations.