PHYA and PHYC as Candidate Loci for Flowering Time and Developmental Plasticity 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 identified 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 that suppresses recombination and maintains a haplotype block at a flowering locus including PHYTOCHROME C (PHYC-A) and VERNALIZATION-1 (VRN-A1). Analysis of a tetraploid wheat diversity panel further showed that natural variation at PHYC-A interacted with VRN-A1 to regulate heading time, with the effect of PHYC-A being substantially stronger in winter VRN-A1 backgrounds. This epistatic interaction likely reflects PHYC's role in modulating the circadian phase of photoperiod-pathway genes. Additionally, we found an early stop codon in the BB genome copy of PHYTOCHROME A (PHYA-B) on chromosome 4B associated with delayed heading, supported by TILLING-derived phytochrome mutants that reveal distinct and complementary roles for PHYA and PHYC in regulating flowering time, plant height, and leaf elongation under simulated canopy shade. Our findings highlight the potential contribution of phytochrome variation to wheat development under canopy-like light environment, thereby extending model insights to agronomically relevant conditions.