Lodging is a major factor limiting wheat yield improvement under high-density cultivation and is closely associated with canopy low light conditions caused by close planting. Canopy light limitation under close planting can suppress stem lignification and weaken mechanical strength, yet the structural and metabolic basis of this response remains insufficiently resolved. A two-season field-embedded pot experiment compared sparse planting (SP), close planting (CP), and close planting with supplemental lighting (CP + L), integrating physiological, mechanical, biochemical, transcriptomic, and metabolomic analyses. Compared with SP, CP reduced the net photosynthetic rate of the third to fifth leaves by 24.59–26.43%, decreased stem diameter and breaking moment, and increased the lodging index. Total lignin content declined by 36.34%, and the G-type lignin-derived aldehyde showed the greatest reduction, resulting in a 33.82% increase in the S/G ratio. Transcriptomic and metabolomic analyses indicated coordinated attenuation of photosynthetic carbon fixation, secondary cell wall formation, and phenylpropanoid-related processes under CP. These changes were accompanied by lower activities of PAL, 4CL, C4H, and CCR and reduced accumulation of hydroxycinnamic acid derivatives and monolignol-related intermediates. Gene–metabolite and TF–structural gene analyses identified treatment-dependent co-variation patterns within the phenylpropanoid pathway. Supplemental lighting increased leaf photosynthetic rates by 20.56–27.39% and partially restored lignin-related enzyme activities, molecular responses, total lignin content, and stem mechanical performance without changing planting density. Close planting was associated with reduced basal stem strength, lower lignification, and attenuation of phenylpropanoid–lignin metabolism. The partial recovery under CP + L supports an important contribution of within-canopy light availability to these responses. These findings highlight canopy light management as a potential strategy for improving wheat lodging resistance under high-density cultivation.
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