## Materials and Methods
### Simultaneous Measurement Using Both PAM and FLD-LISP Methods  
Figure 1 shows a schematic diagram of the setup for the measurement of ChIF parameters using PAM and FLD-LISP. The experiments were carried out from 10 a.m. to 3 p.m. from August to October in an experimental room. Plants were moved from the growth chamber to the experimental room for adaptation at least one week before the experiments and were kept in the experimental room during the experiments. Air temperature in the experimental room was controlled but not recorded, however the leaf temperature was monitored by sensors attached to the JUNIOR-B leaf clip. The solar lightentered through glass where its PPFD could have been variable by incident conditions via glass and cloudiness. In summer in Japan, the maximum solar light at a right-angled surface to the incident light can exceed 2000 umol m\({}^{-2}\) s\({}^{-1}\), so the incident light via glass reached about 2000 umol m\({}^{-2}\) s\({}^{-1}\) in this experiment. The change from dark to light was carried out by rapid movement of a black box shown in Figure 1. The focal point (measurement area, white circle on the leaf) of fibre-HR2000+ was set at a distance of 2 mm from that of the fibre-PAM (light blue filled circle) to avoid the influence of saturation pulse light and shadow of the fibre-PAM. A time chart of the ChLF measurement using a combination of PAM and FLD-LISP methods is presented in Figure 2A. The set of sequential experiments included (i) dark adaptation of the clipped leaf area of the sample plant for 20 min; (ii) PAM measurement of maximum ChLF (Fm) during dark adaptation through switched on blue LED saturation pulse light (SL\({}_{\text{PAM}}\)); (iii) after 50 s of the PAM measurement, FLD measurement of Fm using a HR2000+ spectrometer on red laser saturation pulse light (SL\({}_{\text{RL}}\)); (iv) exposure to solar light for about 5 min; (v) PAM measurement of steady-state ChLF (Fs) and maximum ChLF (Fm') during the light adaptation; (vi) after 20 s of the PAM measurement, FLD measurement of Fs and Fm' using the HR2000+ spectrometer; and (vii) FLD measurement of the non-fluorescent reference (90% White Card) after about 20 s under solar light, immediately. The (v) and (vi) procedures were repeated 3 to 4 times at intervals of 40 s and it was found that the change in solar PPFD was negligible during the experiment. Several measures were taken throughout the FLD measurements to improve the Fm, Fm', and F\({}_{\text{S}}\) retrieval accuracies. First, optimal wavelength bands were selected for the mean values of radiant intensities (Ma, Mb, Mc, and Md) (See Section 2.4 and [65]). Second, in procedures (iii) and (vi) outlined above, Fm and Fm' were given by the mean value of three peak points during 0.6 s SL\({}_{\text{RL}}\) illumination and F\({}_{\text{S}}\) was calculated by averaging data during 10 s before the SL\({}_{\text{RL}}\) illumination using a median filter. It is known that the deviation in SIF retrieval using the FLD method is intrinsic to the method (not to the spectral resolution of the instrument, which is very high in this case) and linked to the reflectance spectral shape [67]. However, a sequence of measurements within a day would be consistent (despite the offset) since the chlorophyll content does not substantially vary and the reflectance remains mostly stable. However, there will be deviations from one date to another where the chlorophyll content has changed, thus increasing the variance and  
Figure 1: Schematic diagram for the measurement of ChLF (Chlorophyll Fluorescence) parameters using PAM (Pulse Amplitude-Modulated) and FLD-LISP (Fraunhofer Line Depth and Laser-Induced Saturation Pulse) methods. The focal point (measurement area, white circle on leaf) of fibre-HR2000+ was set at a distance of 2 mm from that of the fibre-PAM (light blue filled circle) to avoid the influence of saturation pulse light and shadow of the fibre-PAM. Red filled area on the leaf is the footprint of the red laser beam.