Structural and coding variation in PHYTOCHROMES A and C underlies differences in flowering time and shade avoidance in wheat

Plant architecture and developmental timing are influenced by light availability, especially in high-density cropping systems, where canopy shading modifies both light intensity and spectral quality. Despite their ecological and agronomical importance, the genetic basis of these responses in wheat remains poorly understood. Here, using a Recombinant Inbred Lines (RILs) population, we investigated phenological and morphological traits under sunlight and simulated canopy shade. We identify a major QTL on chromosome 5A with light-dependent allelic effects, indicating genotype-by-environment variation in developmental responses. This QTL corresponds to a structural rearrangement, consistent with an inversion in the wild emmer reference genome encompassing PHYTOCHROME C (PHYC-A) and VERNALIZATION-1 (VRN-A1), as well as coding polymorphism in PHYC-A. Analysis of a tetraploid wheat diversity panel further showed that natural variation at PHYC-A and an early stop codon in the BB genome copy of PHYTOCHROME A (PHYA-B) on chromosome 4B are associated with differences in heading time. Functional analysis using TILLING-derived phytochrome mutants confirms distinct and complementary roles for PHYA and PHYC in regulating flowering time, plant height, and leaf elongation under simulated canopy shade. These findings highlight the contribution of phytochrome variation to developmental plasticity under canopy-like light environment, thereby extending model insights to agronomically relevant conditions.