Photosynthesis is acknowledged as a potential target to increase crop yield. Improved photosynthesis may be achieved by conventional breeding, exploiting the available natural genetic variation for photosynthesis traits. This approach is challenging for crops due to limitations in high-throughput photosynthesis phenotyping, the highly polygenic nature of photosynthesis, and its strongly dynamic response to environmental changes. Recent advancements in phenomics make accurate and detailed photosynthesis phenotyping more feasible, with the model species Arabidopsis thaliana paving the way for applications in crops. In this study, we examined photosynthesis parameters over time in the global Arabidopsis HapMap diversity panel exposed to three conditions: optimal nutrient supply, low phosphorus supply and low nitrogen supply. Combined with two previous studies on photosynthesis in response to low temperature, and to a one-step change in irradiance from low light to high light, five high-quality datasets were systematically analysed using the same approach (with one million-maker set, uni- and multi-variate analyses). Our findings emphasize the genetic complexity of photosynthesis, detecting hundreds of significant quantitative trait loci, only a small number of which are robust, and of which most are condition specific. Robust loci, found in multiple conditions, exemplify those suited for conferring higher all-round photosynthesis, and targets for marker-assisted selection, contributing to environmental resilience, while the multitude of small-effect conditional loci suggest that genomic selection approaches may be more suited to improve crop photosynthesis.

BACKGROUND AND AIMS:The Brassiceae tribe encompasses many economically important crops and exhibits high intra- and interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event (Br-α, ~15.9 Mya), differential lineage diversification and genomic changes contributed to an array of divergence in morphology, biochemistry and physiology underlying photosynthesis-related traits. Here, the C3 species Hirschfeldia incana is studied because it displays high photosynthetic rates in high-light conditions. Our aim was to elucidate the evolution that gave rise to the genome of H. incana and its high-photosynthesis traits. METHODS:We reconstructed a chromosome-level genome assembly for H. incana (Nijmegen, v.2.0) using nanopore and chromosome conformation capture (Hi-C) technologies, with 409 Mb in size and an N50 of 52 Mb (a 10× improvement over the previously published scaffold-level v.1.0 assembly). The updated assembly and annotation were subsequently used to investigate the WGT history of H. incana in a comparative phylogenomic framework from the Brassiceae ancestral genomic blocks and related diploidized crops. KEY RESULTS:Hirschfeldia incana (x = 7) shares extensive genome collinearity with Raphanus sativus (x = 9). These two species share some commonalities with Brassica rapa and Brassica oleracea (A genome, x = 10 and C genome, x = 9, respectively) and other similarities with Brassica nigra (B genome, x = 8). Phylogenetic analysis revealed that H. incana and R. sativus form a monophyletic clade in between the Brassica A/C and B genomes. We postulate that H. incana and R. sativus genomes are results of hybridization or introgression of the Brassica A/C and B genome types. Our results might explain the discrepancy observed in published studies regarding phylogenetic placement of H. incana and R. sativus in relationship to the 'triangle of U' species. Expression analysis of WGT retained gene copies revealed sub-genome expression divergence, probably attributable to neo- or sub-functionalization. Finally, we highlight genes associated with physio-biochemical-anatomical adaptive changes observed in H. incana, which are likely to facilitate its high-photosynthesis traits under high light. CONCLUSIONS:The improved H. incana genome assembly, annotation and results presented in this work will be a valuable resource for future research to unravel the genetic basis of its ability to maintain a high photosynthetic efficiency in high-light conditions and thereby improve photosynthesis for enhanced agricultural production.

Plants employ non-photochemical quenching (NPQ) to protect their photosynthetic apparatus from photodamage. The response latency of NPQ following changes in light intensity is thought to significantly decrease photosynthetic efficiency. The amount of NPQ is commonly quantified from chlorophyll-fluorescence techniques using the Stern-Volmer equation, which requires fully closed reaction centres (RCs) of photosystem II, yielding NPQ in the absence of photochemical quenching ( NPQ Closed ). However, in nature, NPQ and photochemical quenching are normally present simultaneously. Therefore, to obtain a full understanding of this process, NPQ should also be explored when the RCs are open. Here we developed two methodologies to obtain NPQ in the presence of photochemistry ( NPQ Open ) using both fluorescence lifetime and fluorescence yield measurements. A detailed comparison in Arabidopsis thaliana plants reveals that the value of NPQ Open is ~35% lower than that of NPQ Closed . This difference is consistently observed across all measurements and is seen both upon closing ( NPQ Open → NPQ Closed ) and upon reopening ( NPQ Closed → NPQ Open ) of the RCs. We show that this difference can be explained by the presence of RC-induced 'instantaneous' switching of the NPQ quenching rate. This means that, in plants, NPQ is much more economical than is widely believed, it is large when its presence is needed, and it decreases instantaneously when the need disappears.

Far-red light (FR) alone drives photosynthesis poorly, but when combined with shorter wavelengths it enhances photosynthesis beyond the sum of their individual effects-a phenomenon known as the Emerson enhancement effect. This effect is well-established for narrowband PAR-FR mixtures, and recent results show it also occurs within broadband "white" light, though the spectra investigated differed from those observed under natural conditions. In this study, we used simulated sun and foliar shade spectra (SUN and SHADE) during growth and measurements of mature tomato leaves to determine quantum yield for CO2 assimilation (ΦCO2) on an absorbed light basis under SUN and SHADE, 17 narrowband irradiances, and combinations of SUN or SHADE with the 17 narrowband irradiances. Enhancement was calculated for each of the 53 unique spectra by comparing predicted and measured ΦCO2. This study shows that a 23% enhancement occurs in the simulated SHADE spectrum light and involves the whole spectrum, and in the simulated SUN spectrum enhancement is absent. Further enhancement was observed when narrowband irradiances were added to the SUN or SHADE spectra. The exclusion of the far-red region (> 700 nm) by PAR-based light intensity measurement is particularly problematic in natural, far-red-rich, canopy environments where far-red has surprising photosynthetic utility.

When light absorption exceeds photochemical quenching, plants activate non-photochemical quenching (NPQ) to dissipate excess energy as heat. Recently, we have developed a novel multivariate pipeline for NPQ induction analysis. Applying this pipeline to NPQ induction curves of several Arabidopsis thaliana NPQ genotypes, overturns the long-held belief that zeaxanthin (Zx) accelerates NPQ induction upon light-adaptation. We demonstrate that the observed acceleration is solely due to the action of PsbS. Our approach allows the synergistic inter-relationships between PsbS and Zx to be unambiguously explored. Specifically, we applied our analysis to dark- and light-adapted wild-type (wt), Zx-lacking (npq1), Zx-rich (npq2) and PsbS-lacking (npq4) A. thaliana. Only the PsbS-dependent quenching in npq2, wt and npq1 plants exhibited faster induction kinetics following light adaptation. Changes in the Zx-levels (npq1 → wt → npq2) lead to changes in the overall amplitudes of the PsbS-components, revealing a Zx-driven amplification of PsbS-dependent quenching. In the presence of PsbS (npq2/wt), Zx also provides its own distinct contribution to NPQ. Together, this reveals the distinct roles of Zx in NPQ and the multilayered synergistic relationship between PsbS and Zx. Combined with mutant genotypes, our unique analysis is an invaluable toolkit to answer mechanistic questions and will allow different NPQ models to be experimentally explored.

An increase in global demand for crop‐based products necessitates an increased crop yield. Optimizing photosynthesis, which is sensitive to environmental fluctuations, offers a promising strategy to improve crop yield and resilience. Photosynthetic responses often lag behind changes in irradiance, resulting in the loss of potential carbon gain. Additionally, global warming is accompanied by unexpected chilling spells, further affecting photosynthesis. Thus, developing chilling‐resilient crops and optimizing photosynthetic responses to fluctuating light is critical. This can be achieved by identifying genetic markers associated with desirable photosynthetic traits in plant populations. However, the combined effect of chilling and photosynthetic responses to fluctuating light remains unexplored, and there is a lack in populations designed to explore these responses. Thus, exploration needs to be done in pre‐existing populations where there is phenotypic variation in photosynthetic responses and in how chilling affects these responses within parental lines. This study examined the variation in photosynthetic responses of the parental lines of a Multi‐parent‐Advanced‐Generation Inter‐Cross (MAGIC) population of tomato ( Solanum lycopersicum ) under fluctuating light and suboptimal temperatures. Photosynthetic responses to step increases and step decreases in irradiance were measured using modulated chlorophyll fluorescence and the effect of lowered temperature (14°C) on these responses was investigated. The results showed variation in the kinetics of the response of quantum efficiency of PSII (Φ PSII ) to step changes in irradiance under control and chilling conditions. Chilling had a minimal effect on the photosynthetic responses of some parental lines, indicating resilience to chilling. These findings highlight the potential of exploring genetic components to breed climate‐resilient crops.

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Photosynthesis underpins life on Earth, serving as the primary energy source while regulating global carbon and water cycles, thereby shaping climate and vegetation. Advancing photosynthesis research is essential for improving crop productivity and refining photosynthesis models across scales, ultimately addressing critical global challenges such as food security and environmental sustainability. This minireview synthesizes a selection of recent advancements presented at the 2nd European Congress of Photosynthesis Research, focusing on improving photosynthesis efficiency and modelling across the scales. We explore strategies to optimize light harvesting and carbon fixation, leading to canopy level improvements. Alongside synthetic biology, we examine recent advances in harnessing natural variability in key photosynthetic traits, considering both methodological innovations and the vast reservoir of opportunities they present. Additionally, we highlight unique insights gained from plants adapted to extreme environments, offering pathways to improve photosynthetic efficiency and resilience simultaneously. We emphasize the importance of a holistic approach, integrating dynamic modeling of metabolic processes to bridge these advancements. Beyond photosynthesis improvements, we discuss the progress of improving photosynthesis simulations, particularly through improved parametrization of mesophyll conductance, crucial for enhancing leaf-to-global scale simulations. Recognizing the need for greater interdisciplinary collaboration to tackle the grand challenges put on photosynthesis research, we highlight two initiatives launched at the congress-an open science platform and a dedicated journal for plant ecophysiology. We conclude this minireview with a forward-looking outline, highlighting key next steps toward achieving meaningful improvements in photosynthesis, yield, resilience and modeling.

Background The development and physiology of plants are influenced by light intensity and its changes. Despite the significance of this phenomenon, there is a lack of understanding regarding the processes light regulates. This lack of understanding is partly due to the complexity of plant’s responses, but also due to the limited availability of light setups capable of producing specific light patterns. Results While unraveling the complexities of plant responses will require further studies, this research proposes a simple method to implement dynamic light setups. In this study, we introduce two distinct electronic circuits that are cost-effective and enable the control of a dimmable power supply. Conclusion This method enables the generation of intricate light patterns and rapid intensity fluctuations, providing a means to investigate how plants respond and develop when exposed to dynamic light conditions.

Photosynthesis is the only yield-related trait not yet substantially improved by plant breeding. Previously, we have established H. incana as the model plant for high photosynthetic light-use efficiency (LUE). Now we aim to unravel the genetic basis of this trait in H. incana, potentially contributing to the improvement of photosynthetic LUE in other species. Here, we compare its transcriptomic response to high light with that of Arabidopsis thaliana, Brassica rapa, and Brassica nigra, 3 fellow Brassicaceae members with lower photosynthetic LUE. We built a high-light, high-uniformity growing environment, in which the plants developed normally without signs of stress. We compared gene expression in contrasting light conditions across species, utilizing a panproteome to identify orthologous proteins. In-depth analysis of 3 key photosynthetic pathways showed a general trend of lower gene expression under high-light conditions for all 4 species. However, several photosynthesis-related genes in H. incana break this trend. We observed cases of constitutive higher expression (like antenna protein LHCB8), treatment-dependent differential expression (as for PSBE), and cumulative higher expression through simultaneous expression of multiple gene copies (like LHCA6). Thus, H. incana shows differential regulation of essential photosynthesis genes, with the light-harvesting complex as the first point of deviation. The effect of these expression differences on protein abundance and turnover, and ultimately the high photosynthetic LUE phenotype is relevant for further investigation. Furthermore, this transcriptomic resource of plants fully grown under, rather than briefly exposed to, a very high irradiance, will support the development of highly efficient photosynthesis in crops.

Photoprotection in plants includes processes collectively known as nonphotochemical quenching (NPQ), which quench excess excitation-energy in photosystem II. NPQ is triggered by acidification of the thylakoid lumen, which leads to PsbS-protein protonation and violaxanthin de-epoxidase activation, resulting in zeaxanthin accumulation. Despite extensive study, questions persist about the mechanisms of NPQ. We have set up a novel analytical pipeline to disentangle NPQ induction curves measured at many light intensities into a limited number of different kinetic components. To validate the method, we applied it to Chl-fluorescence measurements, which utilised the saturating-pulse methodology, on wild-type (wt) and zeaxanthin-lacking (npq1) Arabidopsis thaliana plants. NPQ induction curves in wt and npq1 can be explained by four components ( α , β , γ and δ ). The fastest two ( β and γ ) correlate with pH difference formed across the thylakoid membrane in wt and npq1. In wt, the slower component ( α ) appears to be due to the formation of zeaxanthin-related quenching whilst for npq1, this component is 'replaced' by a slower component ( δ ), which reflects a photoinhibition-like process that appears in the absence of zeaxanthin-induced quenching. Expanding this approach will allow the effects of mutations and other abiotic-stress factors to be directly probed by changes in these underlying components.

Efforts to improve photosynthetic performance are increasingly employing natural genetic variation. However, genetic variation in the organellar genomes (plasmotypes) is often disregarded due to the difficulty of studying the plasmotypes and the lack of evidence that this is a worthwhile investment. Here, we systematically phenotyped plasmotype diversity using Arabidopsis thaliana as a model species. A reanalysis of whole-genome resequencing data of 1,541 representative accessions shows that the genetic diversity among the mitochondrial genomes is eight times lower than among the chloroplast genomes. Plasmotype diversity of the accessions divides the species into two major phylogenetic clusters, within which highly divergent subclusters are distinguished. We combined plasmotypes from 60 A. thaliana accessions with the nuclear genomes (nucleotypes) of four A. thaliana accessions to create a panel of 232 cytonuclear genotypes (cybrids). The cybrid plants were grown in a range of different light and temperature conditions and phenotyped using high-throughput phenotyping platforms. Analysis of the phenotypes showed that several plasmotypes alone or in interaction with the nucleotypes have significant effects on photosynthesis and that the effects are highly dependent on the environment. Moreover, we introduce Plasmotype Association Studies (PAS) as a method to reveal plasmotypic effects. Within A. thaliana, several organellar variants can influence photosynthetic phenotypes, which emphasizes the valuable role this variation has on improving photosynthetic performance. The increasing feasibility of producing cybrids in various species calls for further research into how these phenotypes may support breeding goals in crop species.

Improving photosynthesis, the fundamental process by which plants convert light energy into chemical energy, is a key area of research with great potential for enhancing sustainable agricultural productivity and addressing global food security challenges. This perspective delves into the latest advancements and approaches aimed at optimizing photosynthetic efficiency. Our discussion encompasses the entire process, beginning with light harvesting and its regulation and progressing through the bottleneck of electron transfer. We then delve into the carbon reactions of photosynthesis, focusing on strategies targeting the enzymes of the Calvin-Benson-Bassham (CBB) cycle. Additionally, we explore methods to increase carbon dioxide (CO2) concentration near the Rubisco, the enzyme responsible for the first step of CBB cycle, drawing inspiration from various photosynthetic organisms, and conclude this section by examining ways to enhance CO2 delivery into leaves. Moving beyond individual processes, we discuss two approaches to identifying key targets for photosynthesis improvement: systems modeling and the study of natural variation. Finally, we revisit some of the strategies mentioned above to provide a holistic view of the improvements, analyzing their impact on nitrogen use efficiency and on canopy photosynthesis.

Climate-resilient crops are crucial for meeting global food demand and increasing crop productivity. Photosynthesis, a crucial process, is impacted by environmental changes such as temperature and irradiance. Photosynthesis and stomatal opening often lag behind these changes, resulting in a loss in Light Use Efficiency (LUE). Temperature variations also affect photosynthesis, with a decrease below the optimal threshold resulting in a decrease in photosynthetic efficiency. To enhance photosynthetic LUE, understanding plant responses to environmental changes is essential. This study examines the short-term responses of four tomato genotypes to irradiance fluctuations using chlorophyll fluorescence and the effects of transient cold stress. The results show genotype-to-genotype variation in the maximum quantum efficiency of PSII, the kinetics of the quantum efficiency of PSII’s response to step changes in irradiance, and steady-state values of ΦPSII, which is used as a stand-in for photosynthetic efficiency. The control conditions were measured at 24°C and the cold stress conditions at 14°C. The fact that ΦPSII responds dynamically to step decrease and increase in irradiance and how cold impacts these responses illustrates the way tomato genotypes are impacted by cold stress. It also reveals how the genotypes adapt to cold exposure and recover once the cold stress is reversed. Highlight This study investigates the adaptation and recovery of four tomato genotypes to irradiance fluctuations and transient cold stress, highlighting the importance of climate-resilient crops for food demand. ### Competing Interest Statement The authors have declared no competing interest.

ABSTRACTThe Brassiceae tribe encompasses many economically important crops and exhibits high intraspecific and interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event (Br-α, ∼15.9 million years ago), different lineages and species underwent differential chromosomal rearrangements (diploidization) leading to diverse patterns of gene retention and loss (fractionation). Lineage diversification and genomic changes contributed to an array of divergence in morphology, biochemistry, and physiology underlying photosynthesis-related traits. The C3speciesHirschfeldia incanais studied as it displays high photosynthetic rates under high-light conditions. We present an improved chromosome-level genome assembly forH. incana(Nijmegen, v2.0) using nanopore and chromosome conformation capture (Hi-C) technologies, with 409Mb in size and an N50 of 52Mb (a 10× improvement over the previously published scaffold-level v1.0 assembly). The updated assembly and annotation allowed to investigate the WGT history ofH. incanain a comparative phylogenomic framework from the Brassiceae ancestral genomic blocks and related diploidized crops.Hirschfeldia incana(x=7) shares extensive genome collinearity withRaphanus sativus(x=9). These two species share some commonalities withBrassica rapaandB. oleracea(A genome, x=10 and C genome, x=9, respectively) and other similarities withB. nigra(B genome, x=8). Phylogenetic analysis revealed thatH. incanaandR. sativusform a monophyletic clade in between theBrassicaA/C and B genomes. We postulate thatH. incanaandR. sativusgenomes are results of reciprocal hybridization combinations of theBrassicaA/C and B genome types. Our results might explain the discrepancy observed in published studies regarding phylogenetic placement ofH. incanaandR. sativusin relation to the “Triangle of U” species. Expression analysis of WGT retained gene copies revealed sub-genome expression divergence, likely due to neo- or sub-functionalization. Finally, we highlighted genes associated with physio-biochemical-anatomical adaptive changes observed inH. incanawhich likely facilitate its high-photosynthesis traits under high light.

Abstract Using the GECROS model, we simulated the effect of improvements in photosynthesis a range of growth parameters, including yield, and on the εc (the conversion efficiency of absorbed solar energy to the chemical energy of biomass) and εi (the efficiency of solar energy interception or absorption by the canopy) parameters of the Monteith crop growth equation, for wheat and potato (which use C3 photosynthesis) and maize (which uses C4 photosynthesis). In the case of the C3 crops, the improvements in photosynthesis were via 20% increases in the parameters Vcmax (carboxylation capacity of Rubisco), Jmax (electron transport capacity), Sc/o (Rubisco specificity), κ2LL (efficiency of converting incident light into electron transport) and gm (mesophyll conductance), while for the C4 crop, it was via 20% increase in Vcmax, Jmax and Sc/o and a 20% decrease in gbs (the conductance that controls the leak of CO2 from the bundle sheath cells in C4 leaves). The changes were applied individually and in combination. The responses were modelled using climate data collected over a 10‐year period from 66 sites around Europe. Improvements in photosynthesis did result in increases in yield but with considerable variation between the parameters that were adjusted. The greatest increases were obtained for increases in Jmax and κ2LL (up to an average 11% increase for total plant biomass), and these increases were found across all Europe. Increases in both these parameters have a predominant effect on the light‐use efficiency for subsaturating irradiances. Improvements in the other parameters produced smaller increases.

To meet the increasing global demand for food, feed, fibre and other plant-derived products, a steep increase in crop productivity is a scientifically and technically challenging imperative. The CropBooster-P project, a response to the H2020 call 'Future proofing our plants', is developing a roadmap for plant research to improve crops critical for the future of European agriculture by increasing crop yield, nutritional quality, value for non-food applications and sustainability. However, if we want to efficiently improve crop production in Europe and prioritize methods for crop trait improvement in the coming years, we need to take into account future socio-economic, technological and global developments, including numerous policy and socio-economic challenges and constraints. Based on a wide range of possible global trends and key uncertainties, we developed four extreme future learning scenarios that depict complementary future developments. Here, we elaborate on how the scenarios could inform and direct future plant research, and we aim to highlight the crop improvement approaches that could be the most promising or appropriate within each of these four future world scenarios. Moreover, we discuss some key plant technology options that would need to be developed further to meet the needs of multiple future learning scenarios, such as improving methods for breeding and genetic engineering. In addition, other diverse platforms of food production may offer unrealized potential, such as underutilized terrestrial and aquatic species as alternative sources of nutrition and biomass production. We demonstrate that although several methods or traits could facilitate a more efficient crop production system in some of the scenarios, others may offer great potential in all four of the future learning scenarios. Altogether, this indicates that depending on which future we are heading toward, distinct plant research fields should be given priority if we are to meet our food, feed and non-food biomass production needs in the coming decades.

ABSTRACT In this study, we found a single quantitative trait locus for photosystem II efficiency (Φ PSII ) in the Arabidopsis Ler-0 x Col-0 recombinant inbred line population. This locus on chromosome 5 is caused by genetic variation in a cluster of tandemly repeated SQUALENE EPOXIDASE - LIKE ( SQE-like ) genes, with unknown function. We show the QTL is caused by variation in the SQE5 , SQE6 and SQE7 genes affecting Φ PSII in a dose-dependent manner, due to a combination of functional copies. Col-0 carries only one functional copy, SQE5 , while Ler-0 carries functional copies of SQE6 and SQE 7 . Overexpression of a functional copy of SQE6 enhances Φ PSII to exceed that of the Ler-0 parent in Arabidopsis, but does not affect Φ PSII in tobacco. Phylogenetic analysis of the SQE and SQE-likes in 135 plant species revealed that the SQE -likes are evolutionary confined to two sister families, the Cleomaceae and Brassicaceae, and diversified independently. The tandem cluster of four SQE-like genes in Arabidopsis is likely the result of two recent gene duplication events, one generating SQE5 from SQE4 , the next one generating SQE6 and SQE7 from SQE5 . The involvement of SQE-like genes in photosynthesis will open up new avenues to determine the function of these novel genes.

Photosynthesis is the only yield-related trait that has not yet been substantially improved by plant breeding. The limited results of previous attempts to increase yield via improvement of photosynthetic pathways suggest that more knowledge is still needed to achieve this goal. To learn more about the genetic and physiological basis of high photosynthetic light-use efficiency (LUE) at high irradiance, we study Hirschfeldia incana . Here, we compare the transcriptomic response to high light of H. incana with that of three other members of the Brassicaceae, Arabidopsis thaliana, Brassica rapa , and Brassica nigra , which have a lower photosynthetic LUE. First, we built a high-light, high-uniformity growing environment in a climate-controlled room. Plants grown in this system developed normally and showed no signs of stress during the whole growth period. Then we compared gene expression in low and high-light conditions across the four species, utilizing a panproteome to group homologous proteins efficiently. As expected, all species actively regulate genes related to the photosynthetic process. An in-depth analysis on the expression of genes involved in three key photosynthetic pathways revealed a general trend of lower gene expression in high-light conditions. However, H. incana distinguishes itself from the other species through higher expression of certain genes in these pathways, either through constitutive higher expression, as for LHCB8 , ordinary differential expression, as for PSBE , or cumulative higher expression obtained by simultaneous expression of multiple gene copies, as seen for LHCA6 . These differentially expressed genes in photosynthetic path-ways are interesting leads to further investigate the exact relationship between gene expression, protein abundance and turnover, and ultimately the LUE phenotype. In addition, we can also exclude thousands of genes from “explaining” the phenotype, because they do not show differential expression between both light conditions. Finally, we deliver a transcriptomic resource of plant species fully grown under, rather than briefly exposed to, a very high irradiance, supporting efforts to develop highly efficient photosynthesis in crop plants.