Temporal GWAS and QTL mapping of UAV-derived digital canopy height reveals stage-specific genetic effects in bread wheat.

Dissecting the temporal genetic architecture of crop growth requires phenotyping platforms that combine high throughput with fine temporal resolution. Here, we combined multi-season RGB-UAV phenotyping with temporal GWAS and QTL mapping to resolve stage-specific genetic effects on canopy height in bread wheat. An elite panel of 174 cultivars and a recombinant inbred line population of 162 lines were monitored across three growing seasons (2021-2024) in southern Italy. Digital canopy height was extracted from plot-level 3D point clouds at multiple percentile levels and validated against ground measurements (R 2 = 0.89-0.98; RMSE = 0.07-0.20 m). Temporal modelling of fitted height trajectories generated both whole-height and growth-rate traits; growth-rate associations consistently preceded whole-height associations by 100-200 growing degree days (GDD), capturing the onset of genetic effects on elongation earlier than cumulative height. An apparent tillering plateau separated two phases of genetic control: an early phase linked to vernalization ( Vrn ) and photoperiod ( Ppd ) loci and a later phase linked to gibberellin-related dwarfing genes ( Rht ), a sequence consistent with published expression profiles. Recurrent loci converged on five chromosomal regions, and candidate-gene prioritization highlighted a small set of regulators, including DELLA and TB1-like genes. Overall, temporal UAV phenotyping, and especially the contrast between whole-height and growth-rate traits, resolves when successive developmental loci become detectable on the canopy, providing a framework to dissect the dynamic genetic control of plant height.