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Kromdijk, J.

Publications and source records attributed to Kromdijk, J..

At least 19 recordsLinked to original sources

From Field Photosynthesis to Genetic Architecture: Insights from the First Dedicated Photosynthesis Hackathon

Photosynthesis is among the most consequential yet genetically complex traits in crop plants, and translating its natural variation into actionable genomic targets remains a central challenge for breeding climate-resilient varieties. To start addressing this, researchers are generating increasingly large, multi-environment field photosynthesis datasets. Yet, these data have been structurally under-analysed since their inception. Here we report the outcomes of the first dedicated hackathon focused on computational mining of such field data held in Accra, Ghana, in March 2026. Bringing together data scientists, plant physiologists, geneticists, and breeders from Europe and Africa, these interdisciplinary teams used photosynthetic data collected with hand-held fluorometers to genome-wide marker data across four crop species: cowpea (Vigna unguiculata), barley (Hordeum vulgare), common bean (Phaseolus vulgaris), and potato (Solanum tuberosum). Despite using different species and methods, independent teams identified the same three key findings. First, mechanism-informed feature engineering and dynamic modelling recover genetic signals that are not detected or discarded in standard analysis pipelines, resulting in traits with improved heritability and meaningful associations with yield. Secondly, machine learning methods proved effective at uncovering genetic associations, with temporally resolved features substantially outperforming single time-point measurements. Third, raw chlorophyll fluorescence and absorbance traces consistently contained more information and predictive power than the extracted parameters currently used. A defining feature of this event was having experimentalists and data scientists working together, enabling AI approaches to be grounded in domain knowledge and biological mechanisms rather than relying on data alone.

plant biology↗

The controlled spectrum of plant form and function

Dimension reduction techniques with plant traits have suggested the existence of independent acquisitive-conservative spectra in leaves and roots across diverse plants. However, this finding may be due to third-variable effects that can alter the fundamental dimensionality of plant trait variation. Using a dimension reduction approach that controls for third-variable effects, we show that the acquisitive-conservative axis is not confined within an organ, but acts at the whole plant level.

ecology↗

KineticGP: a computational framework for genomic prediction of leaf photosynthesis traits

Crop traits are the integrated outcome of genetic factors, environment effects, and their complex interactions, rendering accurate prediction from genetic markers alone a challenging problem. Here we present KineticGP, a computational framework that combines genomic prediction with genotype-specific kinetic models of C4 photosynthesis to make predictions of leaf photosynthesis traits across genotypes from a multiple parent advanced generation intercross maize population. Using genetic markers and gas exchange measurements from three field seasons, we show that KineticGP outperforms a baseline genomic prediction model for photosynthesis rate at saturating light by 86% for unseen genotypes across two seen seasons. In addition, KineticGP allowed surveying the genetic variability in enzyme kinetic parameters that can be used to raise targets for improvement of photosynthesis. The approach paves the way for interrogating and integrating the dynamic interactions between genotype and environment to improve the prediction accuracy of photosynthetic traits.

systems biology↗

Kinetic parameter prediction using neural networks identifies limitations to C4 photosynthesis

Large-scale kinetic models of photosynthesis enable time-resolved predictions of traits related to this key process, and provide the means to identify factors limiting photosynthesis. However, their use is currently limited by the lack of efficient approaches to estimate the hundreds of genotype-specific kinetic parameters. Here, we present C4TUNE, an artificial neural network, which can efficiently predict parameters of a large-scale photosynthesis model from photosynthesis response curves. C4TUNE was trained on a biologically-relevant synthetic dataset comprising matched samples of parameters and response curves obtained using a C4 photosynthesis kinetic model. To speed up the training of C4TUNE, we devised a surrogate neural network to predict photosynthesis response curves directly from the model parameters and environmental inputs. Given response curves as input, we showed that over 99% of the parameter vectors predicted by C4TUNE could be used directly in simulation of the kinetic model and resulted in excellent fits. Finally, we applied C4TUNE to predict parameters for a population of 68 maize genotypes across two seasons. The predicted genotype-specific parameters allowed pinpointing factors that limit photosynthetic efficiency, validated using simulations. Therefore, the use of C4TUNE presents a fast and precise approach for parameter prediction based on minimal datasets.

bioinformatics↗

Generalizability of machine learning models for plant traits using hyperspectral reflectance data: The case of maize

Hyperspectral reflectance provides rapid and precise phenotyping of plants in a non-destructive manner both in field and well-controlled settings. The resulting data have been used to devise machine learning (ML) models for paired measurements of different traits in diverse plants and crops. Yet, despite advances in using of hyperspectral data to reliably predict crop traits of interest, there are pressing issues concerning the training of ML models, the aggregation of data from crop field trials, and the generalizability of the models in different prediction settings. We collected hyperspectral reflectance data along with 25 anatomical, gas exchange, and chlorophyll fluorescence traits from 320 recombinant inbred lines of a maize Multi-Parent Advanced Generation Inter-Cross population grown across three consecutive seasons. We use these data to systematically: (1) compare the performance of representative ML models for different traits, including slow fluorescence kinetics whose predictability by hyperspectral data has not yet been investigated, (2) evaluate the ML model performance in prediction scenarios concerning unseen genotypes, unseen seasons, and the combination thereof, (3) investigate the effects of data aggregation of ML model performance. These problems are addressed in a rigorous nested cross-validation setting that provides a template for adequate assessment of performance of ML models for diverse crop traits considering the particularities of the experimental design. Significance statementWe present a comprehensive evaluation of hyperspectral reflectance for predicting 25 physiological traits, including fluorescence kinetics, in maize across three seasons using rigorous nested cross-validation. By comparing ML models, prediction scenarios, and data aggregation strategies, our study reveals trait-specific limits of generalizability and offers a robust framework for deploying hyperspectral data in breeding applications.

plant biology↗

Mutation of a conserved stromal C-terminus threonine residue of Photosystem II subunit S slows down NPQ induction and speeds up relaxation.

In order to prevent damage by excess light, photosystem antennae can switch to an energy dissipative mode (termed non-photochemical quenching, NPQ). In higher plants, this switch is facilitated by the presence of Photosystem II subunit S (PsbS) protein, which was discovered 25 years ago. While the role of PsbS in induction of NPQ was soon found to require protonation of key glutamate residues facing the thylakoid lumen, a complete understanding of how NPQ is subsequently initiated is still lacking. Recent work on Norway spruce suggests that reversible phosphorylation at a few key residues of PsbS may coincide with the induction of a sustained dissipative state. Here we used Arabidopsis thaliana mutant lines to assess the functional implications of phosphorylation at threonine-259, one of the implicated phosphorylatable residues. Using a set of residue changes expressed in the background of PsbS knock-out mutant, npq4, we show that neither phosphomimetic, phosphosubstitution, nor phosphonull complementations could rescue NPQ activity to the level of the unperturbed protein. Instead, all residue substitutions at threonine-259 gave rise to significantly impaired induction and accelerated NPQ recovery, while protein accumulation and thylakoid membrane localisation were not affected. We suggest that these results are consistent with a role for the C-terminus in the propensity or stability of hydrophobic interactions between PsbS monomers to form homodimers, or between PsbS and other LHCII proteins to initiate the quenched state. HighlightReversible phosphorylation of threonine-259 on PsbS has previously been suggested to play a role in sustained NPQ during cold-acclimation in evergreen conifers. Here we show that both phosphomimetic and phosphonull substitutions at T259 lead to significantly impaired NPQ induction and faster recovery, which may be explained by their impact on hydrophobic interactions between PsbS and other LHCII proteins.

plant biology↗

High throughput screen of NPQ in sorghum shows highly polygenic architecture of photoprotection

O_LINatural genetic variation in photosynthesis and photoprotection within crop germplasm represents an untapped resource for crop improvement. Sorghum bicolor (sorghum) is one of the worlds most widely grown crops, yet the genetic basis of photoprotection in sorghum is not well understood. C_LIO_LIThis study examined genetic variation in non-photochemical quenching traits by screening a field-grown panel of 861 genetically diverse natural sorghum accessions across two years. C_LIO_LIBroad-sense heritability ranged between 0.3 to 0.65 across different chlorophyll fluorescence parameters. A combination of genome- and transcriptome-wide (GWAS and TWAS) identification of genetic correlates with the observed trait variation uncovered a complex genetic architecture of many significant small-effect loci. An ensemble approach based on GWAS and TWAS results and the covariance between different fluorescence parameters was used to identify 110 unique candidate genes. C_LIO_LIThe resulting high-confidence candidates reveal novel genetic associations with photoprotection and offer resources for further genetic studies and crop genomic improvement efforts. C_LI

plant biology↗

Metabolite profiling reveals slow and uncoordinated adjustment of C4 photosynthesis to sudden changes in irradiance

In the field plants continually experience changes in irradiance. Research in C3 species has revealed that whilst the Carbon-Benson cycle (CBC) adjusts rapidly to changing irradiance, there is substantial loss of photosynthesis efficiency due to slow adjustment of energy dissipation and stomatal conductance. Less is known about the impact of changing irradiance on photosynthetic efficiency in C4 species. We have subjected maize to a sudden increase or decrease of irradiance in the non-saturating range and performed time-resolved measurement of photosynthetic rate and profiling of metabolites from the CBC, the CO2-concentrating mechanism (CCM), photorespiration and end-product biosynthesis. After a decrease in irradiance, photosynthesis is transiently buffered by energy delivered by transformations in the large pools of metabolites that are involved in intercellular shuttles. During the subsequent decline in photosynthesis, metabolism transitions to a sub-optimal state for photosynthesis in low irradiance, from which it takes several minutes to recover. One reason is that the large pools of metabolites that facilitate intercellular shuttles run down too far and it takes time to build them up again. After an increase in irradiance, there is a long delay until a new steady rate of photosynthesis is achieved. The delay is partly due to regulation of enzymes in the CBC and CCM, but also to the need to build up large pools of metabolites to drive intercellular shuttles. In addition, in both transitions, transient imbalances between the pumping and utilization of CO2 lead to increased back-leakage of CO2 or to photorespiration, further decreasing photosynthetic efficiency.

plant biology↗

Sub-optimal temperature leads to tighter coupling between photosynthetic electron transport and CO2 assimilation under fluctuating light in maize.

The C4 carbon concentrating pathway promotes high CO2 assimilation rates. To keep C4 photosynthesis energetically efficient, electron transport reactions and downstream biochemistry need to be carefully balanced. Here we use a combination of non-invasive measurements and metabolic profiling to study the efficiency of C4 photosynthesis in maize under two conditions that can lead to decoupling between electron transport and carbon assimilation: fluctuating light and suboptimal temperature. Measurements were performed for three fluctuating light regimes and three temperatures, providing the most detailed study to date of the interaction between fluctuating light and suboptimal temperature on the photosynthetic performance of maize, an important global crop. At room temperature, CO2 assimilation rates were decoupled from photosynthetic electron transport under fluctuating light regimes, in contrast to tight coordination observed under constant light. This decoupling was underpinned by metabolic flexibility and buffering by large pools of C4 transfer metabolites. Surprisingly, at sub-optimal temperatures, CO2 assimilation rates became more tightly coupled to photosynthetic electron transport rates under fluctuating light regimes. This appeared to be caused by strong feedback downregulation of electron transport and a stronger degree of light-saturation of CO2 assimilation at low temperature. Low temperature impacted carbon assimilation rates more strongly than metabolite pools or intercellular metabolite distribution, which could reflect negative effects on diffusional metabolite transfer through plasmodesmata. Altogether, these results show that maize is able to maintain energetic efficiency by buffering light transitions under room temperature, as well as avoid oxidative damage by strongly downregulating electron transfer under short-term exposure to low temperature. One-sentence summaryAnalysis of maize CO2 assimilation under fluctuating light shows significant decoupling from photosynthetic electron transport at room temperature, supported by metabolic flexibility and buffering by large pools of C4 transfer metabolites, but tight coordination is restored under suboptimal temperature due to enhanced feedback regulation of electron transport and a stronger degree of light saturation of CO2 assimilation.

plant biology↗

Faster relaxation of nonphotochemical quenching (NPQ) in C4 than in C3 species

Acceleration of photoprotective non-photochemical quenching (NPQ) responses to changes in light intensity has been suggested as a strategy to enhance crop yield. Despite many key crops utilising C4 photosynthesis, our current understanding of NPQ overwhelmingly comes from C3 species. Using a series of experiments on three phylogenetically controlled C3 and C4 comparisons, we show that NPQ relaxation is faster in C4 species. Temporal analysis of NPQ relaxation in leaves infiltrated with inhibitors to block proton motive force formation or xanthophyll de-epoxidation showed that the faster relaxation observed in C4 species is driven by a greater contribution of energy-dependent quenching (qE) to overall NPQ. We show that the C4-associated enhancement of qE is linked to altered regulation of lumen pH in C4 species, reflecting increases in cyclic electron flow and membrane proton conductivity to meet the increased ATP demands of the C4 pathway. Indeed, in two of the three tested C4 species, NPQ relaxation became significantly slower and statistically indistinguishable from paired C3 species when ATP and NADPH consumption was suppressed by performing measurements in CO2-free air. Altogether, our results suggest that NPQ responses in C4 species may already be optimised to maintain high photosynthetic efficiency in the fluctuating light conditions typically found within C4 canopies. Given the intrinsically faster NPQ in C4 photosynthesis, further acceleration of NPQ may have limited scope to enhance crop photosynthetic efficiency. Significance StatementAcceleration of non-photochemical quenching has been proposed as a means to enhance crop photosynthetic efficiency in C3 species but whether this strategy has potential in C4 species, which include several major crops, remains unclear. We use three phylogenetically paired C3 and C4 species to show that NPQ relaxation is significantly faster in species with the C4 pathway, possibly aiding the maintenance of photosynthetic efficiency in fluctuating light environments. As a result, accelerating the rate of NPQ relaxation in C4 crops may have a more limited scope to enhance photosynthesis.

plant biology↗

Extensive photophysiological variation in wild barley is linked to environmental origin

O_LIIntraspecific variation between crop wild relatives (CWRs) represents a source of untapped genetic diversity for crop improvement. At the same time, improving photosynthesis in crops has the potential to enhance yield. Thus, exploring variation for photophysiology within CWRs is an important, yet underexplored, research area. C_LIO_LIWe describe a common garden experiment where 320 wild barley accessions were grown across two seasons. A photophysiology phenotyping pipeline was employed to quantify >30 traits within this diversity panel. Population genetics, genome-wide association analyses (GWAS) and deep phenotyping were performed to address local adaptation hypotheses. C_LIO_LIHeritable variation was detected across this photophysiological spectrum, with genotype-by-environment (GxE) interactions being prevalent. Evidence for local adaptation was observed in the form of subpopulation differences, signals of selection, and allele frequency variation associated to markers identified via GWAS. Phenotyping of representative accessions across distinct water availabilities highlighted a role for stomatal conductance (gs) in adaptation to dry environments. C_LIO_LIWe identified substantial variation in key photosynthesis-associated traits in a CWR closely related to barley, an economically important crop species. Our results demonstrate that this variation is partially due to local adaptation, where plasticity in gs appears important for maintaining photosynthesis and biomass accumulation in water restricted conditions. C_LI

plant biology↗

Chloroplast-derived hydrogen peroxide coordinates photosynthesis with stomatal opening

Stomatal pores on plant leaves control the entry point of carbon into the terrestrial biosphere and concomitant release of water vapour into the atmosphere. Stomatal aperture changes need to be coordinated with photosynthesis to balance carbon gain against water loss. Despite this importance, molecular signals underpinning this coordination, and the cell types from which such signals originate, remain poorly understood. Here we show that chloroplast-derived H2O2 coordinates stomatal movements with photosynthesis. Specifically, when H2O2 scavenging is compromised in the cytosolic ascorbate peroxidase1 (apx1) mutant, stomatal opening is increased. This is rescued when photosynthetic H2O2 production derived from plastoquinol is reduced either genetically or pharmacologically. Furthermore, cell-specific complementation of APX1 in the apx1 mutant demonstrated that H2O2 signals from both guard cells and mesophyll cells contribute significantly to stomatal movements. Altogether, our findings identify H2O2 as a key photosynthesis-derived signal underpinning effective coordination between stomatal conductance and photosynthesis, a key prerequisite for terrestrial plant life, and may inspire new strategies to enhance photosynthetic water use efficiency in crop species.

plant biology↗

In vivo analysis of the relationship between CP26 and qE-type NPQ via higher-order Arabidopsis cp26 mutants

CP26 is a monomeric minor light-harvesting complex of PSII (LHCII) protein that connects major LHCII trimers to the PSII core in photosynthetic thylakoid membranes. Previous studies have proposed that CP26 is not only involved in light harvesting but could also be involved in non-photochemical quenching (NPQ). Here, we analyzed higher-order Arabidopsis cp26 mutants using biophysical and pharmacological approaches to investigate the nature of NPQ and its relationship to known NPQ regulators (PSII subunit S (PsbS), the xanthophyll-converting enzyme VDE and the pH gradient across the thylakoid membrane). Maximum PSII quantum efficiencies (Fv/Fm) and chlorophyll fluorescence lifetimes in the dark were significantly lower in cp26 mutants, confirming that CP26 deficiency leads to a sustained quenched state even in the absence of light. Destabilized PSII-LHCII supercomplexes as observed with native PAGE analysis are the likely cause for this pre-quenched state, without other antenna proteins being able to rescue this phenotype. Further analyses revealed that cp26 mutants exhibit modest (single mutant) to highly significant (double mutants) reductions in overall NPQ capacity, which do not directly rely on PsbS and VDE (although the effect is more pronounced when these qE components are altered) but depend on thylakoid lumen acidification and protonation of protein residues. Together, these results show that the NPQ component lacking in cp26 mutants acts independently of qE and qZ and is induced in a slower phase of NPQ induction that most likely relies on pH-dependent conformational changes.

plant biology↗

The genetic basis of dynamic non-photochemical quenching and photosystem II efficiency in fluctuating light reveals novel molecular targets for maize (Zea mays) improvement

Maize (Zea mays L.) is a major global crop species which uses C4 photosynthesis. Although C4 is typically considered to be more efficient than C3 photosynthesis, especially under warmer and drier conditions, there is substantial evidence that its efficiency can still be further improved, which may benefit crop performance. Improving photosynthetic efficiency via targeted manipulation of non-photochemical quenching has focused on a limited set of genes that are known to be important determinants of the NPQ response in C3 plants. The C4 pathway may alter NPQ responses but only relatively few studies have explored genetic variation in NPQ kinetics in species that perform C4 photosynthesis. In addition, studies of NPQ responses in field-grown plants of either C3 or C4 species are especially limited. Here we apply high-definition phenotyping of NPQ responses and photosynthetic efficiency and quantitative trait locus (QTL) mapping using a field-grown maize Multi-parent Advanced Generation Inter-Cross (MAGIC) population, which combines the allelic diversity of eight contrasting inbred lines. We find substantial and consistent variation for dynamic NPQ and PSII efficiency for two subsequent field seasons. Further exploration of candidate genes within three major QTL regions identified a strong impact of allelic variation in expression of the minor PSII antenna protein CP24 (LHCB6) on a major QTL for NPQ and efficiency of PSII photochemistry on chromosome 10.

plant biology↗

Illuminating stomatal responses to red light: establishing the role of Ci-dependent vs -independent mechanisms

The stomatal response to red light appears to link stomatal conductance (gs) with photosynthetic rates. Initially, it was suggested that changes in intercellular CO 2 (Ci) provide the main cue via a Ci- dependent response. However, evidence for Ci-independent mechanisms suggests an additional, more direct relationship with photosynthesis. While both Ci-dependent and -independent mechanisms clearly function in stomatal red-light responses, little is known regarding their relative contribution. The present study aimed to quantify the relative magnitude of Ci-dependent and - independent mechanisms on the stomatal red-light response, to characterise their interplay and to assess the putative link between plastoquinone (PQ) redox state and Ci-independent stomatal responses. Red light response curves measured at a range of Ci values for wild-type Arabidopsis thaliana (Col-0) and the CO2 hyposensitive mutant, ca1ca4, allowed deconvolution of Ci-dependent and -independent pathways. Surprisingly, we observed that both mechanisms contribute equally to stomatal red-light responses, but Ci-independent stomatal opening is suppressed at high Ci. The present data are also consistent with the involvement of PQ redox in coordinating Ci-independent stomatal movements. Overall, it seems that while Ci-independent mechanisms are distinct from responses to Ci, interplay between these two pathways is important to facilitate effective coordination between gs and photosynthesis. HighlightBy controlling intercellular CO2 (Ci) at a range of values across red-light response curves, we demonstrate independent and interactive roles of Ci-dependent and -independent pathways in coordinating stomatal red-light responses.

plant biology↗

Leaf excision has minimal impact on photosynthetic parameters across crop functional types

Photosynthesis is increasingly becoming a recognised target for crop improvement. Phenotyping photosynthesis-related traits on field-grown material is a key bottleneck to progress here due to logistical barriers and short measurement days. Many studies attempt to overcome these challenges by phenotyping excised leaf material in the laboratory. To date there are no demonstrated examples of the representative nature of photosynthesis measurements performed on excised leaves relative to intact leaves in crops. Here, we tested whether standardised leaf excision on the day prior to phenotyping impacted a range of common photosynthesis-related traits across crop functional types using tomato (C3-dicot), barley (C3-monocot), and maize (C4-monocot). Potentially constraining aspects of leaf physiology that could be forecasted to impair photosynthesis in excised leaves, namely leaf water potential and abscisic acid accumulation, were not different between intact and excised leaves. We also observed non-significant differences in spectral reflectance and chlorophyll fluorescence traits between the treatments across the three species. However, we did observe some significant differences between gas exchange and photosynthetic capacity associated traits across all three species. This study represents a useful reference for those who perform measurements of this nature and the differences reported should be considered in associated experimental design and statistical analyses. HighlightAcross the main photosynthesis functional types (C3-dicot, C3-monot, and C4-monot) of major crops (tomato, barley, and maize), measurements of photosynthetic parameters demonstrate few, but important, differences when measured on excised relative to intact leaves.

plant biology↗

Compartmentation of photosynthesis gene expression between mesophyll and bundle sheath cells of C4 maize is dependent on time of day

Compared with the ancestral C3 state, C4 photosynthesis enables higher rates of photosynthesis as well as improved water and nitrogen use efficiencies. In both C3 and C4 plants rates of photosynthesis increase with light intensity and so are maximal around midday. We report that in the absence of light or temperature fluctuations, photosynthesis in maize peaks in the middle of the subjective photoperiod. To investigate molecular processes associated with these changes, we undertook RNA-sequencing of maize mesophyll and bundle sheath strands over a 24-hour time-course. Cell-preferential expression of C4 cycle genes was strongest between six and ten hours after dawn when rates of photosynthesis were highest. For the bundle sheath, DNA motif enrichment and gene co-expression analyses suggested members of the DOF and MADS-domain transcription factor families mediate diurnal fluctuations in C4 gene expression, and trans-activation assays in planta confirmed their ability to activate promoter fragments from bundle sheath expressed genes. The work thus identifies transcriptional regulators as well as peaks in cell-specific C4 gene expression coincident with maximum rates of photosynthesis in the maize leaf at midday.

plant biology↗

Lessons from relatives: C4 photosynthesis enhances CO2 assimilation during the low-light phase of fluctuations.

Despite the global importance of species with C4 photosynthesis, there is a lack of consensus regarding C4 performance under fluctuating light. Contrasting hypotheses and experimental evidence suggest that C4 photosynthesis is either less, or more efficient in fixing carbon under fluctuating light than the ancestral C3 form. Two main issues were identified that may underly the lack of consensus: neglect of evolutionary distance between selected C3 and C4 species and use of contrasting fluctuating light treatments. To circumvent these issues, we compared photosynthetic responses to fluctuating light across three independent phylogenetically controlled comparisons between C3 and C4 species from Alloteropsis, Flaveria, and Cleome genera under 21% and 2% O2. Leaves were subjected to repetitive stepwise changes in light intensity (800 and 100 {micro}mol m-2 s-1 PFD) with three contrasting durations: 6, 30 and 300 seconds. These experiments reconcile the opposing results found across previous studies showing that 1) stimulation of CO2 assimilation in C4 species during the low light phase was both stronger and more sustained than in C3 species; 2) CO2 assimilation patterns during the high light phase were genus-specific rather than impacted by photosynthetic pathway; and 3) the duration of each light step in the fluctuation regime can strongly influence experimental outcomes. One sentence significance statementComparing photosynthesis in three pairs of closely related C3 and C4 species across three fluctuating light regimes showed that C4 photosynthesis has a systematic advantage under the low light phase not related to suppression of photorespiration, while the comparative efficiency under the high light phase was not determined by photosynthetic pathway.

plant biology↗