Research Online Research Online Extending Fluspect to simulate xanthophyll driven leaf reflectance Extending Fluspect to simulate xanthophyll driven leaf reflectance dynamics dynamics

Abstract The xanthophyll cycle regulates the energy flow to photosynthetic reaction centres of plant leaves. Changes in the de-epoxidation state (DEPS) of xanthophyll cycle pigments can be observed as changes in the leaf absorption of light with wavelengths between 500 to 570 nm. These spectral changes can be a good remote sensing indicator of the photosynthetic efficiency, and are traditionally quantified with a two-band physiologically based optical index, the Photochemical Reflectance Index (PRI). In this paper, we present an extension of the plant leaf radiative transfer model Fluspect (Fluspect-CX) that reproduces the spectral changes in a wide band of green reflectance: a radiative transfer analogy to the PRI. The idea of Fluspect-CX is to use in vivo specific absorption coefficients for two extreme states of carotenoids, representing the two extremes of the xanthophyll de-epoxidation, and to describe the intermediate states as a linear mixture of these two states. The 'photochemical reflectance parameter' (Cx) quantifies the relative proportion of the two states. Fluspect-CX simulates leaf chlorophyll fluorescence (ChlF) excitation-emission matrices, as well as reflectance (R) and transmittance (T) spectra as a function of leaf structure, pigment contents and Cx. We describe the calibration of the model and test its performance using various experimental datasets. Furthermore, we retrieved Cx from optical measurements of various datasets. The retrieved Cx correlates well with xanthophyll DEPS (R2=0.57), as well with non-photochemical quenching (NPQ) of fluorescence (R2=0.78). The correlation with NPQ enabled us to incorporate Fluspect-CX in the model SCOPE to scale the processes to the canopy level. Introducing the dynamic green reflectance into a radiative transfer model provides new means to study chlorophyll fluorescence and PRI dynamics on leaf and canopy scales, which is crucial for the remote sensing. Abstract The xanthophyll cycle regulates the energy ﬂow to photosynthetic reaction centres of plant leaves. Changes in the de-epoxidation state ( DEPS ) of xanthophyll cycle pigments can be observed as changes in the leaf absorption of light with wavelengths between 500 to 570 nm. These spectral changes can be a good remote sensing indicator of the photosynthetic eﬃciency, and are traditionally quantiﬁed with a two-band physiologically based optical index, the Photochemical Reﬂectance Index (PRI). In this paper we present an extension of the plant leaf radiative transfer model Fluspect (Fluspect-CX) that reproduces the spectral changes in a wide band of green reﬂectance: a radiative transfer analogy to the PRI. The idea of Fluspect-CX is to use in vivo speciﬁc absorption coeﬃcients for two extreme states of carotenoids, representing the two extremes of the xanthophyll de-epoxidation, and to describe the intermediate states as a linear mixture of these two states. The ’photochemical reﬂectance parameter’ ( C x ) quantiﬁes the relative proportion of the two states. Fluspect-CX simulates leaf chlorophyll ﬂuorescence (ChlF) excitation-emission pigment contents and C x . We describe the calibration of the model and test its performance using various experimental datasets. Furthermore, we retrieved C x from optical measurements of various datasets. The retrieved C x correlates well with xanthophyll DEPS (R 2 =0.57), as well with non-photochemical quenching (NPQ) of ﬂuorescence (R 2 =0.78). The correlation with NPQ enabled us to incorporate Fluspect-CX in the model SCOPE to scale the processes to the canopy level. Introducing the dynamic green reﬂectance into a radiative transfer model provides new means to study chlorophyll ﬂuorescence and PRI dynamics on leaf and canopy scales, which is crucial for the remote sensing.