Integrated anatomical, biochemical and transcriptomic analysis provide new insights into the photosynthetic regulation and source capacity of Coffea arabica under prolonged differential shading

Shade cultivation is generally considered more suitable for coffee growth and development. However, to date, systematic studies on the response of Coffea arabica under multi-gradient shading conditions remain scarce, and, in particular, no comprehensive analysis of the molecular regulatory mechanisms has been reported. This study focused on evaluating the phenotypic, photosynthetic physiological, energy metabolic, and molecular responses of Coffea arabica under four shade conditions (25%, 40%, 65%, and 90% shade degree), with no-shade condition as the control. The results indicate that shading induced leaf size and color adjustment but exhibited a distinct threshold effect, whereas palisade tissue and spongy tissue showed significant structural plasticity across treatments. Coffee exhibited optimal photosynthetic performance under light- and moderate- shade (25%-40% shading), with the net photosynthetic rate reaching 16.443 μmol·m -2 ·s -1 . Under severe shade (90% shading), despite pronounced non-stomatal limitations, high light use efficiency sustained energy output and redox-related metabolic balance, with selective accumulation of TCA cycle intermediates and an apparent shift toward fermentative metabolism, as indicated by lactate accumulation. Transcriptomic analysis revealed that the number of differentially expressed genes increased markedly with shade intensity, with functional enrichment predominantly in pathways such as ribosome, starch and sucrose metabolism, and plant hormone signal transduction. WGCNA identified six co-regulatory networks containing 38 candidate hub genes associated with ribosome biogenesis repression, organellar metabolic reprogramming, auxin transduction, and redox homeostasis maintenance. These findings reveal a shade adaptation syndrome of Coffea arabica as a facultative shade species, providing an integrative phenotypic, physiological, metabolic, and molecular framework for shade management optimization in coffee agroforestry systems.