## 4 Discussion
### Further Understanding the Relationship Between SIF and the PSII Operating Efficiency
Further, when the local time changed, the contribution of the same leaf site to canopy SIF was not at the same magnitude, which resulted in a nonlinear relationship between the SIF and \(F^{\prime}_{q}/F^{\prime}_{m}\). Considering that the \(F^{\prime}_{q}/F^{\prime}_{m}\) can be calculated as the product of \(F^{\prime}_{v}/F^{\prime}_{m}\) and \(F^{\prime}_{q}/F^{\prime}_{v}\), its nonlinear relationship with \(F^{\prime}_{q}/F^{\prime}_{m}\) should be affected by the diurnal dynamics of \(F^{\prime}_{v}/F^{\prime}_{m}\) and \(F^{\prime}_{q}/F^{\prime}_{v}\). From images of the leaf chlorophyll fluorescence, \(F^{\prime}_{v}/F^{\prime}_{m}\) clearly showed heterogeneity over time both in soybean and sweet potato, which means that the maximum quantum efficiency of the PSII photochemistry was not even across the leaf and not stable in a day. That is, the capacity of the light-harvesting of antennae in PSII at different sites was discrepant and also changed with the solar time. It should be noted that, although \(F^{\prime}_{q}/F^{\prime}_{v}\) in soybean did not always show large variations in a day, the sweet potato results of \(F^{\prime}_{q}/F^{\prime}_{v}\) showed similar patterns of heterogeneity to \(F^{\prime}_{v}/F^{\prime}_{m}\). This finding suggested that the proportion of PSII centers that are open also affected the diurnal dynamics of the PSII operating efficiency. Thus, the nonlinear relationship between the \(F^{\prime}_{q}/F^{\prime}_{m}\) and SIF was intrinsically determined by the status of the maximum quantum efficiency of the PSII photochemistry and the proportion of PSII centers that were open. Previous studies have indicated that autumn senescent plants rapidly down-regulate photosynthesis accompanied by pigment decomposition to protect the photosynthetic apparatus from the damage of more light energy [42]. Our results also support the dynamics of photosynthesis when plants are in autumn senescence. It should be noted that the yield of full-wavelength SIF at 650-850 nm should be the best proxy for indicating the proportion of APAR that was used for dissipating as SIF [39]. However, the SIF yield was only measured at 760 nm in our study, which cannot well indicate the full SIF efficiency at all. This may be another reason for the nonlinear relationship between the SIF efficiency at 760 nm (Fy760) and the photosynthetic efficiency (\(F^{\prime}_{q}/F^{\prime}_{m}\)). This nonlinear relationship between the SIF efficiency and photosynthetic efficiency is related to the gene expression and plastic responses of the photosynthetic apparatus. Specific sets of genes (known as those nuclear genes encoding the chlorophyll a/b-binding proteins, an enzyme catalyzing the first committed step of anthocyanin biosynthesis and the small subunit of ribulose bisphosphate carboxylase) mediate the etiolation and abscission of leaves, which may alter the relationship between SIF efficiency and photosynthetic efficiency [43]. This was demonstrated by our finding that Fy760 of soybean and sweet potato with different pigment contents showed different relationships with \(F^{\prime}_{q}/F^{\prime}_{m}\) (Figure 4a,b). The expressions of such genes may be further regulated by circadian rhythms; for example, the genes encoding the chlorophyll a/b-binding proteins may be upregulated at dawn and downregulated before sunset [44]. This means that circadian rhythms may be another factor in altering the relationship between the SIF efficiency and photosynthetic efficiency. Circadian rhythms also affect their relationship by controlling the stomatal opening, photosynthetic light harvesting, and photosynthetic efficiency [45]. Furthermore, it has been suggested that the reorganization of the photosynthetic apparatus during fall and winter allows Scots pine to maintain a large fraction of chlorophyll in a quenched, photo-protected state, allowing the rapid recovery of photosynthesis in the spring [43]. This might also explain our observed pattern that SIF efficiency and photosynthetic efficiency is not linear.