Integrating molecular and physiological approaches to quantify genetic controls for wheat development and improve phenotyping

Abstract Disentangling genotype×environment (G×E) controls of flowering time requires phenotypes that link molecular regulation, developmental physiology, and environment. Here, we integrated time-resolved measurements of apical development, final leaf number, and expression of the flowering-time genes VRN1, VRN2, and VRN3 across contrasting temperature and photoperiod regimes in six wheat genotypes spanning a wide range of developmental sensitivities. By combining controlled-environment phenotyping with concurrent gene-expression profiling, we show that environmentally driven variation in final leaf number is coherently explained by shifts in the timing of key apical transitions and associated VRN gene-expression dynamics. These integrated datasets were used to parameterize and interrogate the Cereal Anthesis Molecular Phenology (CAMP) model, enabling direct comparison between observed foliar gene-expression time courses and modelled gene activity. While overall developmental responses were well captured by the model, systematic differences between observed and modelled gene-expression patterns highlight the importance of distinguishing foliar expression from apical regulatory activity, as well as differences in temporal scaling. Building on this framework, we present a phenotyping protocol based on final leaf number responses to defined temperature and photoperiod treatments that delivers unconfounded developmental phenotypes explicitly linked to underlying genetic regulation.