**1. Introduction**

In nature, light energy supply for plant photosynthesis varies strongly in both amplitude and frequency. How plants respond to dynamic light environments is still poorly understood. This has many reasons, among them being that for most experiments, plants are grown under standard, highly controlled, and uniform light regimes (U). However, plant responses strongly depend on the environment that plants have acclimated to, as they adjust their metabolism to cope most efficiently with the prevailing condition. Several recent studies focused on the model plant *Arabidopsis thaliana* (hereafter: Arabidopsis) under dynamic light [1–3], but these were restricted to few accessions only and thus did not assess the effects of genetic factors. The study of a larger set of genotypes is warranted, also because photosynthesis shows great intraspecific variation in Arabidopsis [4,5], and variation on the genetic level has been shown to translate more strongly into phenotypic variation under fluctuating light regimes (FL; [6]). Using genome-wide association mapping, natural variation in the photosynthetic response to high light could be linked to several quantitative trait loci [5], supporting the notion that in Arabidopsis, traits linked to photosynthesis are heritable.

Compared to U, FL with the same average intensity often reduces plant growth [7–10], although exceptions exist [11]. There are at least two reasons for this reduction. Firstly, photosynthesis responds nonlinearly to light, i.e., at higher light intensities the rate of photosynthesis is limited by its capacity for CO2 fixation, in turn leading to the activation of photoprotective mechanisms that dissipate absorbed light energy as heat, and resulting in a decrease in photosynthetic efficiency (reviewed by [12]). Leaves under FL, in contrast to U, are generally exposed to light periods during which photosynthesis is saturated. Secondly, photosynthesis generally lags behind rapid changes in light intensity, but the loss in CO2 fixation after an increase in light intensity typically exceeds any gains in CO2 fixation after a decrease (though see [13] for a further discussion on the role of post-illumination CO2 fixation). The latter is partially connected to the slow relaxation of photoprotective mechanisms in low light [14].

Theoretically, plant growth is linked to how quickly photosynthesis can switch between protective mechanisms in high light and highly efficient light capture and conversion in shade periods [14]. Insufficient protection in high light causes photooxidative damage [15], while overprotection can result in low rates of photosynthesis through a reduction in the operating efficiency of PSII (ΦPSII), particularly in shade periods when light availability limits the rate of photosynthesis [16]. Non-photochemical quenching (NPQ) is a central photoprotective mechanism in plants [17]. Most NPQ is rapidly reversible, and is controlled by the proton concentration of the lumen (reviewed by [12]). Light-driven electron transport from water to NADPH along the thylakoid localized electron transport chain is coupled to the transfer of protons from the stroma into the lumen. Protons then exit the lumen via the ATP synthase, thereby providing the energy required for ATP synthesis. In high light conditions, when downstream metabolic reactions are limiting, the proton concentration in the lumen rises, as efflux via the ATP synthase is restricted [18,19]. Above a threshold, the proton concentration in the lumen induces a reorganization of the PSII supercomplex via protonating key amino acid residues of the PsbS protein and activates the violaxanthin-deepoxidase (VDE), both of which are important for maximum pH-dependent quenching, which is also referred to as energy-dependent quenching (qE, reviewed by [12]). Under prolonged stress conditions, photoinhibitory quenching (qI) is induced, which coincides with oxidative damage to the D1 protein of photosystem II [17]. Such damage also causes an increased Chl *a* fluorescence of dark acclimated plants and is reflected as a decrease in Fv/Fm, which is a measure of the maximum quantum efficiency of PSII. However, reductions of Fv/Fm are often only observed under relatively harsh conditions, whereas NPQ and ΦPSII already respond to milder stresses.

While the rapid response of photosynthesis to high light is comparably well studied on the molecular level (reviewed by [12]), much less is known about molecular mechanisms that allow photosynthesis to rapidly adjust to low light periods. Only recently, it was shown that plants contain at least one molecular player that accelerates the response of photosynthesis to shade periods [16,19]. Furthermore, the capacity for NPQ can be upregulated in Arabidopsis acclimated to FL [1,20], but it is not known whether (i) such an upregulation might reduce ΦPSII, particularly in shade periods, during which this reduction could reduce photosynthetic efficiency and growth and (ii) whether natural genetic variation exists for these phenomena. We hypothesized that (i) NPQ would be upregulated and ΦPSII would be decreased in low light in plants grown under FL compared to U, (ii) dark-adapted Fv/Fm would be largely unaffected by FL relative to U, (iii) growth would be reduced under FL compared to U, and that (iv) large differences for the extent of these changes between FL and U would become apparent between genotypes. To test these hypotheses, we grew 36 natural accessions of Arabidopsis (Table 1) under U and FL and next to their growth and development assessed ΦPSII and NPQ under low light, as well as dark-adapted Fv/Fm.


**Table 1.** Full names and abbreviations (as used in the figures) of Arabidopsis accessions. Accessions are sorted by the fluctuating light (FL) experiment they were used in. Information on country of origin, latitude, and number of leaves at flowering was accessed on the 1001 genomes website (https://1001genomes.org/). nd = not determined.
