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

Coffea arabica shows optimal photosynthetic performance under 25%–40% shading, with net photosynthetic rate reaching 16.443 μmol m-2·s-1, while 90% shade triggers redox and metabolic reprogramming.

• Why it matters: Multi-gradient shading responses and the molecular regulatory mechanisms in Coffea arabica are not well characterized, limiting evidence-based shade management in coffee agroforestry.
• What they did: Plants were grown under four shade degrees (25%, 40%, 65%, 90%) plus a no-shade control, and integrated anatomical, physiological, energy-metabolism, and transcriptomic analyses were performed.
• The result: Differential expression rose with shade intensity, WGCNA defined six co-regulatory networks with 38 hub genes linked to ribosome biogenesis repression, auxin transduction, and redox homeostasis, supporting a facultative shade adaptation syndrome.

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