## 2 Materials and Methods
### Leaf Level Measurements
#### 2.2.1 Fluorescence and Reflectance Measurements  
The fluorescence and reflectance spectra of the leaves were measured under standardized conditions in the laboratory to facilitate intercomparability of results. These measurements were conducted using two separate spectrometers: a USB2000+ (Ocean Optics Inc., Orlando, FL, USA) for spectral fluorescence measurements and an ASD Hand-Held (ASD Inc., Boulder, CO, USA) for reflectance measurements with an integrating sphere. Note that canopy-level spectral measurements were conducted using two additional spectrometers coupled to a UAV (see below). Spectral fluorescence measurements were conducted with a USB-2000+ spectrometer (range (R): 300-1100 nm, sampling interval (SI): 0.5 nm, full width at half maximum (FWHM): 1.5-1.8 nm). Attached to the spectrometer was a bifurcated reflectance probe (R600-7 VIS-125F, Ocean Optics Inc., Orlando, FL, USA) and fiber holder (RPH-1, Ocean Optics Inc., Orlando, FL, USA) used to conduct spectral measurements in the nadir position in order to maximize the fluorescence signal. The probe was connected to a filter carrier housing an OD4 short-pass 650 nm filter (Edmund Optics, Barrington, NJ, USA) to remove 99.99% of radiation above 650 nm and facilitate the measurement of spectral fluorescence. Figure 2: Experimental setup and underlying logic of the study. The dynamics of leaf and canopy-level traits in response to fertilization, water stress, and canopy development were measured. Subsequently, we characterize the relationships between leaf and canopy-level traits and spectral indices, investigating and discussing the mechanisms that underlie the relationships at each scale. Finally, the filter carrier is connected to a halogen light source (HL-2000, Ocean Optics Inc., Orlando, FL, USA) through a fiber optic bundle. Prior to spectral measurements, leaves were cut from shoots and dark acclimated for 20 min at room temperature. Spectral measurements were conducted at an integration time of 300 ms, and a dark current (DC) measurement was conducted prior to ChIP measurements and subtracted from the subsequent spectra. While this measurement technique allowed us to record the whole fluorescence spectra of the leaf, we only used the average of three measurements in the range from 685.110 nm to 685.780 nm and from 759.700 nm to 760.350 nm to represent F685 and F760, respectively (Figure 3A). For better comparability between leaf and canopy scale results, the 760 nm region was used for analysis instead of the 740 nm peak region. Further details on the measurement setup and protocol can be found in [PERSON] et al. [50]. Separately, a different subset of leaves was used to measure leaf directional-hemispherical reflectance spectra and estimate a range of reflectance indices (Table 3). Measurements were conducted using a RTS-3 ZC Integrating Sphere (ASD Inc., Boulder, CO, USA) equipped with a halogen light (10 W, 6 V, Model 64225, Osram, Munich, Germany) coupled to an ASD Hand-Held Spectrometer (R: 325-1075 nm, SI: 1.6 nm, FWHM: 3.5 nm). Measurements were conducted at an integration time of 540 ms, and 10 spectra were averaged. A DC measurement was recorded before and after the measurements and subtracted from the spectra. Leaf directional-hemispherical reflectance factors were obtained by factoring the DC-corrected spectra obtained with the sample by those obtained using a Spectralon(r) panel (Labsphere, North Sutton, NH, USA) after [PERSON] et al. [51]. \begin{table}
\begin{tabular}{c c c} \hline \hline
**Vegetation Index** & **Equation** & **Reference** \\ \hline NDVI & \(NDVI=\frac{8660-8660}{860+R660}\) & [PERSON] et al. [11] \\ \hline MTCI & \(MTCI=\frac{8753-8709}{8709-8681}\) & [PERSON] [52] \\ \hline Red edge & \(Red\)\(edge=R_{712\text{nm}}-722\text{mm}\) & [PERSON] et al. [53] \\ \hline PRI & \(PRI=\frac{8531-8570}{8531+8570}\) & [PERSON] et al. [30] \\ \hline CCI & \(CCI=\frac{8531-8645}{8531+8645}\) & [PERSON] et al. [31] \\ \hline \hline \end{tabular}
\end{table} 
Table 3: Vegetation indices used in this study.