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Chlorophyll a (Chl a) has an asymmetrical molecular organization, which dictates its orientation and the location of the pigment in the mature photosynthetic apparatus. Although Chl a fluorescence (ChlF) is widely accepted as a proxy for plant photosynthetic performance under countless stress conditions and across species, a mechanistic understanding of this causality is missing. Since water plays a much greater role than solvent for the photosynthetic machinery, elucidating its influence on Chl a may explain the reliable reflection of plant stress response in the ChlF signal. We examine the effect of hydration from well-watered to lethal drought on ChlF imagery results across morphologically diverse species to begin testing the impact of molecular scale hydration of Chl a on ChlF. Our results support a conceptual model where water is an integral part of the photosystems' structure and directly influences Chl a behavior leading to changes in the energy partitioning and ultimately in ChlF.

Crop improvement is crucial to ensuring global food security under climate change, and hence there is a pressing need for phenotypic observations that are both high throughput and improve mechanistic understanding of plant responses to environmental cues and limitations. In this study, chlorophyll a fluorescence light response curves and gas-exchange observations are combined to test the photosynthetic response to moderate drought in four genotypes of Brassica rapa. The quantum yield of PSII (ϕ(PSII)) is here analyzed as an exponential decline under changing light intensity and soil moisture. Both the maximum ϕ(PSII) and the rate of ϕ(PSII) decline across a large range of light intensities (0–1,000 μmol photons m(−2) s(−1); β(PSII)) are negatively affected by drought. We introduce an alternative photosynthesis model (β(PSII) model) incorporating parameters from rapid fluorescence response curves. Specifically, the model uses β(PSII) as an input for estimating the photosynthetic electron transport rate, which agrees well with two existing photosynthesis models (Farquhar-von Caemmerer-Berry and Yin). The β(PSII) model represents a major improvement in photosynthesis modeling through the integration of high-throughput fluorescence phenotyping data, resulting in gained parameters of high mechanistic value.

Genomic prediction is used to parameterize canopy growth of a process-based whole-plant model. The updated model formalizes components of genotype by environment interaction (G×E)., Dynamic process-based plant models capture complex physiological response across time, carrying the potential to extend simulations out to novel environments and lend mechanistic insight to observed phenotypes. Despite the translational opportunities for varietal crop improvement that could be unlocked by linking natural genetic variation to first principles-based modeling, these models are challenging to apply to large populations of related individuals. Here we use a combination of model development, experimental evaluation, and genomic prediction in Brassica rapa L. to set the stage for future large-scale process-based modeling of intraspecific variation. We develop a new canopy growth submodel for B. rapa within the process-based model Terrestrial Regional Ecosystem Exchange Simulator (TREES), test input parameters for feasibility of direct estimation with observed phenotypes across cultivated morphotypes and indirect estimation using genomic prediction on a recombinant inbred line population, and explore model performance on an in silico population under non-stressed and mild water-stressed conditions. We find evidence that the updated whole-plant model has the capacity to distill genotype by environment interaction (G×E) into tractable components. The framework presented offers a means to link genetic variation with environment-modulated plant response and serves as a stepping stone towards large-scale prediction of unphenotyped, genetically related individuals under untested environmental scenarios.

Climate models predict widespread increases in both drought intensity and duration in the next decades. Although water deficiency is a significant determinant of plant survival, limited understanding of plant responses to extreme drought impedes forecasts of both forest and crop productivity under increasing aridity. Drought induces a suite of physiological responses; however, we lack an accurate mechanistic description of plant response to lethal drought that would improve predictive understanding of mortality under altered climate conditions. Here, proxies for leaf cellular damage, chlorophyll a fluorescence, and electrolyte leakage were directly associated with failure to recover from drought upon rewatering in Brassicarapa (genotype R500) and thus define the exact timing of drought-induced death. We validated our results using a second genotype (imb211) that differs substantially in life history traits. Our study demonstrates that whereas changes in carbon dynamics and water transport are critical indicators of drought stress, they can be unrelated to visible metrics of mortality, i.e. lack of meristematic activity and regrowth. In contrast, membrane failure at the cellular scale is the most proximate cause of death. This hypothesis was corroborated in two gymnosperms (Picea engelmannii and Pinus contorta) that experienced lethal water stress in the field and in laboratory conditions. We suggest that measurement of chlorophyll a fluorescence can be used to operationally define plant death arising from drought, and improved plant characterization can enhance surface model predictions of drought mortality and its consequences to ecosystem services at a global scale.

A growing body of evidence demonstrates a significant relationship between cellular redox state and circadian rhythms. Each day these two vital components of plant biology influence one another, dictating the pace for metabolism and physiology. Diverse environmental stressors can disrupt this condition and, although plant scientists have made significant progress in re-constructing functional networks of plant stress responses, stress impacts on the clock-redox crosstalk is poorly understood. Inter-connected phenomena such as redox state and metabolism, internal and external environments, cellular homeostasis and rhythms can impede predictive understanding of coordinated regulation of plant stress response. The integration of circadian clock effects into predictive network models is likely to increase final yield and better predict plant responses to stress. To achieve such integrated understanding, it is necessary to consider the internal clock not only as a gatekeeper of environmental responses but also as a target of stress syndromes. Using chlorophyll fluorescence as a reliable and high-throughput probe of stress coupled to functional genomics and metabolomics will provide insights on the crosstalk across a wide range of stress severity and duration, including potential insights into oxidative stress response and signaling. We suggest the efficiency of photosystem II in light conditions (Fv′/Fm′) to be the most dynamic of the fluorescence variables and therefore the most reliable parameter to follow the stress response from early sensing to mortality.

The circadian clock regulates many aspects of leaf gas supply and biochemical demand for CO2 20 , and is hypothesized to improve plant performance. Yet the extent to which the clock may regulate the efficiency of photosystem II (PSII) and photoprotective mechanisms such as heat dissipation remains largely unexplored. Based on measurements of chlorophyll a fluorescence, we estimated the maximum efficiency of photosystem II in light (Fv'/Fm') and heat dissipation by non-photochemical quenching (NPQ). We further dissected total NPQ into its main components, qE (pH-dependent quenching), qT (state-transition quenching) and qI (quenching related to photoinhibition), in clock mutant genotypes of Arabidopsis thaliana, the cognate wild-type genotypes, and a panel of recombinant inbred lines (RILs) expressing quantitative variation in clock period. Compared to mutants with altered clock function, we observed that wild-type genotypes with clock period lengths of approximately 24 hr had both higher levels of Fv'/Fm ', indicative of improved PSII function, and reduced NPQ, suggestive of lower stress on PSII light harvesting complexes. In the RILs, genetic variances were significant for Fv'/Fm' and all three components of NPQ, with qE explaining the greatest proportion of NPQ. Bivariate tests of association and structural equation models of hierarchical trait relationships showed that quantitative clock variation was empirically associated with Fv'/Fm' and NPQ, with qE mediating the relationship with gas exchange. The results demonstrate significant segregating variation for all photoprotective components, and suggest the adaptive significance of the clock may partly derive from its regulation of the light reactions of photosynthesis and of photoprotective mechanisms. Key words: Arabidopsis thaliana, circadian rhythms, chlorophyll a fluorescence, maximum efficiency of PSII, non-photochemical quenching

Based on the examination and quantitative comparison of the approaches used to assess the energy partitioning in photosystem II, the unified method was proposed to calculate the contribution of the components of nonphotochemical quenching.

In highlight stress conditions, the mechanism of non-photochemical quenching (NPQ) of chlorophyll fluorescence is triggered at the chloroplast level. This process allows thermal quenching of the excessive excitation energy and it is strictly related to the efficiency of the xanthophyll cycle. Nowadays, the utilization of the nuclear magnetic resonance (NMR) spectroscopy provides a powerful complementary way for the identification and quantitative analysis of plant metabolites either in vivo or in tissue extracts. Seeing that the oxidative damage caused by light stress in plants and the consequent involvement of pigments are widely studied, NMR spectroscopy can be utilized to compare crude leaf extract at different levels of light stress, allowing an analysis of these compounds. In this paper, the identification of possible relationships between light stress and 1H NMR signal variations is discussed. The analysis of the 1H NMR (1D) spectra of two agronomic species (Spinacia oleracea and Beta vulgaris) exposed to different light intensities is presented. In particular, change in carotenoids and xanthophylls signals are analyzed.

Non-photochemical quenching (NPQ) of chlorophyll a fluorescence and leaf gas-exchange were investigated in relation to the chlorophyll and carotenoid content, and the xanthophyll cycles in wild type tomato (Solanum lycopersicum, L. cv Red Setter (RS)) and in two transgenic lines (UO and UU) over-expressing β-carotene hydroxylase. Potted plants were grown in a glasshouse under low light (LL, 100 μmol m−2 s−1) or high light (HL, 300 μmol m−2 s−1). The maximum quantum efficiency of photosystems II (PSII) photochemistry in dark-adapted leaves (Fv/Fm) was higher than 0.82 in all treatments while photosynthetic CO2 assimilation (A) was higher than 14 μmol m−2 s−1, and stomatal conductance (gs) higher than 0.4 mol m−2 s−1 in HL plants, indicating no effects induced by the genetic modification. Chlorophyll content and composition changed little, whereas transgenic plants had up to 47% higher total carotenoid content than wild type plants. Violaxanthin was the most abundant carotenoid in transgenic plants, with more than 2-fold higher content than the average 0.586 mg g−1 found in RS plants. Transgenic plants had similar light-induced steady-state NPQ compared to wild type plants, but had slower dark relaxation because of the decreased de-epoxydation state index due to the higher violaxanthin accumulation, despite the higher zeaxanthin content.