*2.1. Chlorophyll a Fluorescence*

Twenty-six accessions (i.e., 72%) showed significantly reduced values of ΦPSII when grown under FL as compared to growth under U (Figure 1A). No accession showed increased ΦPSII under FL. NPQ was significantly increased in 13 (36%) of the FL-grown accessions (Figure 1B), and none of the FL-grown accessions showed significantly reduced NPQ. Maximum quantum efficiency of photosystem II (Fv/Fm), measured in dark-adapted leaves, showed a very different pattern compared to ΦPSII and NPQ: of the ten accessions showing a significant effect of FL on Fv/Fm, six FL-grown accessions showed significantly enhanced Fv/Fm, while four others showed significantly reduced Fv/Fm (Figure 1C).

## *2.2. Growth and Development*

Projected leaf area (PLA) and the number of visible leaves were assessed as proxies for growth and development, respectively. PLA of plants was significantly reduced when grown under FL as compared to U in 22 (61%) accessions (Figure 2A). On average, PLA was reduced by 36% across all accessions, meaning that the reduction in PLA was not only significant for many accessions, but also substantial (although PLA showed a large coefficient of variation: 42.3%). However, one accession, Hs-0, had a strongly increased PLA (74%) under FL compared to U (Figure 2A). Of the 12 accessions that showed significant treatment effects on the number of visible leaves, FL decreased leaf number in nine cases, but increased it in another three cases (among which was Hs-0; Figure 2B). Finally, to

account for the possibility that differences in projected leaf area may be caused by differences in the number of leaves, average leaf size was determined by dividing projected leaf area by leaf number (Figure 2C). When expressed this way, 24 (67%) FL-grown accessions showed significant reductions in average leaf size, most of which overlapped with those showing reduced PLA. Hs-0 again displayed a significant increase in average leaf size when grown under FL. Two other accessions, Tsu-0 and Cen-0, showed larger growth- and development-related parameters under FL, albeit to a lesser extent than Hs-0. While for Tsu-0 this did not correlate with treatment effects on Chl *a* fluorescence data, Cen-0, like Hs-0, showed positive growth and development despite reduced ΦPSII and increased NPQ in FL as compared to U (Figures 1 and 2). Accession Col-0 had been grown in both experiments: ΦPSII, leaf area, leaf number and average leaf area were all significantly reduced in FL-grown Col-0, compared to Col-0 under uniform irradiance, in both experiments (Figures 1 and 2). NPQ was significantly increased under FL in Col-0 in Exp. 1 but not in Exp. 2, although data showed the same tendency (Figure 1B). Similarly, Fv/Fm was significantly reduced in FL-treated Col-0 in Exp. 1 but not in Exp. 2, however it tended to be reduced (Figure 1C). Altogether, these data suggest that similar conclusions could be drawn from both FL experiments, reassuring us of the repeatability of the experimental setup used.

**Figure 1.** Chlorophyll *a* fluorescence analysis of 36 Arabidopsis accessions acclimated to uniform (U; yellow boxes) and fluctuating light intensities (FL; blue boxes), grown in two different experiments. (**A**) photosystem II operating efficiency (ΦPSII), (**B**) non-photochemical quenching (NPQ), and (**C**) photosystem II maximum quantum efficiency (Fv/Fm). ΦPSII and NPQ were measured at 90 μmol m−<sup>2</sup> s<sup>−</sup>1, whereas Fv/Fm was measured on dark-adapted leaves. Bars depict interquartile range (IQR; 25th–75th percentile) and median (thick line inside bar), whiskers depict data up to 1.5 × IQR, dots outside whiskers depict outliers (>1.5 × IQR). In the case of significant differences between average values under U and FL, these are shown for a given accession as: \*\*\* = *p* < 0.001, \*\* = *p* < 0.01 and \* = *p* < 0.05 (n = 5–7).

**Figure 2.** Growth and development of 36 Arabidopsis accessions acclimated to uniform (U; yellow boxes) and fluctuating light intensities (FL; blue boxes), grown in two different experiments. (**A**) Projected leaf area, (**B**) number of visible leaves and (**C**) average leaf size. Values were obtained from chlorophyll *a* fluorescence pictures. Bars depict interquartile range (IQR; 25th–75th percentile) and median (thick line inside bar), whiskers depict data up to 1.5 × IQR, dots outside whiskers depict outliers (>1.5 × IQR). In the case of significant differences between average values under U and FL, these are shown for a given accession as: \*\*\* = *p* < 0.001, \*\* = *p* < 0.01 and \* = *p* < 0.05 (n = 5–7).

We observed a large trait variation across accessions and treatments (Figures 1 and 2). For example, projected leaf area for a given accession ranged from 1.4 to 8.0 cm2 (Figure 2A), resulting in a coefficient of variation (CV) of 42.3%. Average leaf size varied to a slightly lesser degree (35.9% CV; Figure 2C), while leaf number per plant displayed a comparably low CV of 10.3% (Figure 2B). Of the chlorophyll *a* fluorescence traits, NPQ showed the largest variation (0.38–0.82; 19.2% CV; Figure 1B) while ΦPSII (0.42–0.66; 9.0% CV; Figure 1A) varied comparably less. In contrast to these values, Fv/Fm showed a very small variation of only 0.8% CV (Figure 1C).
