African rice (Oryza glaberrima) has adapted to challenging environments and is a promising source of genetic variation. We analysed dynamics of photosynthesis and morphology in a reference set of 155 O. glaberrima accessions. Plants were grown in an agronomy glasshouse to late tillering stage. Photosynthesis induction from darkness and the decrease in low light was measured by gas exchange and chlorophyll fluorescence along with root and shoot biomass, stomatal density and leaf area. Steady state and kinetic responses were modelled. We describe extensive natural variation in O. glaberrima for steady state, induction and reduction responses of photosynthesis that has value for gene discovery and crop improvement. Principle component analyses indicated key clusters of plant biomass, kinetics of photosynthesis (CO2 assimilation, A) and photoprotection induction and reduction (measured by Non Photochemical Quenching, NPQ), consistent with diverse adaptation. Accessions also clustered according to countries with differing water availability, stomatal conductance (gs), A and NPQ and indicating that dynamic photosynthesis has adaptive value in O.glaberrima. Kinetics of NPQ, A and gs showed high correlation with biomass and leaf area. We conclude that dynamic photosynthetic traits and NPQ are important within O.glaberrima and we highlight NPQ kinetics and NPQ under low light.

High light intensities raise photosynthetic and plant growth rates but can cause damage to photosynthetic machinery. The likelihood and severity of deleterious effects is reduced by a set of photoprotective mechanisms, one key process being the controlled dissipation of energy from chlorophyll within photosystem II (PSII) known as non-photochemical quenching (NPQ). Although ubiquitous, the role of NPQ in plant productivity is important because it momentarily reduces the quantum efficiency of photosynthesis. Rice plants overexpressing and deficient in the gene encoding a central regulator of NPQ, the protein PsbS, were used to assess the effect of protective effectiveness of NPQ (pNPQ) at the canopy scale. Using a combination of 3-dimensional reconstruction, modelling, chlorophyll fluorescence and gas exchange, the influence of altered NPQ capacity on the distribution of pNPQ was explored. A higher phototolerance in the lower layers of a canopy was found, regardless of genotype, suggesting a mechanism for increased protection for leaves that experience relatively low ligh intensities interspersed with brief periods of high light. Relative to wild-type plants, PsbS overexpressors have a reduced risk of photoinactivation and early growth advantage, demonstrating that manipulating photoprotective mechanisms can impact both subcellular mechanisms and whole canopy function.