Cross-species transcriptomics reveals differential regulation of essential photosynthesis genes in Hirschfeldia incana.

Photosynthesis is the only yield-related trait not yet substantially improved by plant breeding. Previously, we have established Hirschfeldia 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, three 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 three key photosynthetic pathways showed a general trend of lower gene expression under high-light conditions for all four 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, Hirschfeldia 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.

Perspectives on improving photosynthesis to increase crop yield.

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 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.

An open-source controller to build a dynamic light intensity setup.

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.

Improving crop yield potential: Underlying biological processes and future prospects.

The growing world population and global increases in the standard of living both result in an increasing demand for food, feed and other plant-derived products. In the coming years, plant-based research will be among the major drivers ensuring food security and the expansion of the bio-based economy. Crop productivity is determined by several factors, including the available physical and agricultural resources, crop management, and the resource use efficiency, quality and intrinsic yield potential of the chosen crop. This review focuses on intrinsic yield potential, since understanding its determinants and their biological basis will allow to maximize the plant's potential in food and energy production. Yield potential is determined by a variety of complex traits that integrate strictly regulated processes and their underlying gene regulatory networks. Due to this inherent complexity, numerous potential targets have been identified that could be exploited to increase crop yield. These encompass diverse metabolic and physical processes at the cellular, organ and canopy level. We present an overview of some of the distinct biological processes considered to be crucial for yield determination that could further be exploited to improve future crop productivity.

The effects of different daily irradiance profiles on Arabidopsis growth, with special attention to the role of PsbS.

In nature, light is never constant, while in the controlled environments used for vertical farming, in vitro propagation, or plant production for scientific research, light intensity is often kept constant during the photoperiod. To investigate the effects on plant growth of varying irradiance during the photoperiod, we grew Arabidopsis thaliana under three irradiance profiles: a square-wave profile, a parabolic profile with gradually increasing and subsequently decreasing irradiance, and a regime comprised of rapid fluctuations in irradiance. The daily integral of irradiance was the same for all three treatments. Leaf area, plant growth rate, and biomass at time of harvest were compared. Plants grown under the parabolic profile had the highest growth rate and biomass. This could be explained by a higher average light-use efficiency for carbon dioxide fixation. Furthermore, we compared the growth of wild type plants with that of the PsbS-deficient mutant npq4. PsbS triggers the fast non-photochemical quenching process (qE) that protects PSII from photodamage during sudden increases in irradiance. Based mainly on field and greenhouse experiments, the current consensus is that npq4 mutants grow more slowly in fluctuating light. However, our data show that this is not the case for several forms of fluctuating light conditions under otherwise identical controlled-climate room conditions.

The genome sequence of Hirschfeldia incana, a new Brassicaceae model to improve photosynthetic light-use efficiency.

Photosynthesis is a key process in sustaining plant and human life. Improving the photosynthetic capacity of agricultural crops is an attractive means to increase their yields. While the core mechanisms of photosynthesis are highly conserved in C3 plants, these mechanisms are very flexible, allowing considerable diversity in photosynthetic properties. Among this diversity is the maintenance of high photosynthetic light-use efficiency at high irradiance as identified in a small number of exceptional C3 species. Hirschfeldia incana, a member of the Brassicaceae family, is such an exceptional species, and because it is easy to grow, it is an excellent model for studying the genetic and physiological basis of this trait. Here, we present a reference genome of H. incana and confirm its high photosynthetic light-use efficiency. While H. incana has the highest photosynthetic rates found so far in the Brassicaceae, the light-saturated assimilation rates of closely related Brassica rapa and Brassica nigra are also high. The H. incana genome has extensively diversified from that of B. rapa and B. nigra through large chromosomal rearrangements, species-specific transposon activity, and differential retention of duplicated genes. Duplicated genes in H. incana, B. rapa, and B. nigra that are involved in photosynthesis and/or photoprotection show a positive correlation between copy number and gene expression, providing leads into the mechanisms underlying the high photosynthetic efficiency of these species. Our work demonstrates that the H. incana genome serves as a valuable resource for studying the evolution of high photosynthetic light-use efficiency and enhancing photosynthetic rates in crop species.

Genetics as a key to improving crop photosynthesis.

Since the basic biochemical mechanisms of photosynthesis are remarkably conserved among plant species, genetic modification approaches have so far been the main route to improve the photosynthetic performance of crops. Yet, phenotypic variation observed in wild species and between varieties of crop species implies there is standing natural genetic variation for photosynthesis, offering a largely unexplored resource to use for breeding crops with improved photosynthesis and higher yields. The reason this has not yet been explored is that the variation probably involves thousands of genes, each contributing only a little to photosynthesis, making them hard to identify without proper phenotyping and genetic tools. This is changing, though, and increasingly studies report on quantitative trait loci for photosynthetic phenotypes. So far, hardly any of these quantitative trait loci have been used in marker assisted breeding or genomic selection approaches to improve crop photosynthesis and yield, and hardly ever have the underlying causal genes been identified. We propose to take the genetics of photosynthesis to a higher level, and identify the genes and alleles nature has used for millions of years to tune photosynthesis to be in line with local environmental conditions. We will need to determine the physiological function of the genes and alleles, and design novel strategies to use this knowledge to improve crop photosynthesis through conventional plant breeding, based on readily available crop plant germplasm. In this work, we present and discuss the genetic methods needed to reveal natural genetic variation, and elaborate on how to apply this to improve crop photosynthesis.

Designing the Crops for the Future; The CropBooster Program.

The realization of the full objectives of international policies targeting global food security and climate change mitigation, including the United Nation's Sustainable Development Goals, the Paris Climate Agreement COP21 and the European Green Deal, requires that we (i) sustainably increase the yield, nutritional quality and biodiversity of major crop species, (ii) select climate-ready crops that are adapted to future weather dynamic and (iii) increase the resource use efficiency of crops for sustainably preserving natural resources. Ultimately, the grand challenge to be met by agriculture is to sustainably provide access to sufficient, nutritious and diverse food to a worldwide growing population, and to support the circular bio-based economy. Future-proofing our crops is an urgent issue and a challenging goal, involving a diversity of crop species in differing agricultural regimes and under multiple environmental drivers, providing versatile crop-breeding solutions within wider socio-economic-ecological systems. This goal can only be realized by a large-scale, international research cooperation. We call for international action and propose a pan-European research initiative, the CropBooster Program, to mobilize the European plant research community and interconnect it with the interdisciplinary expertise necessary to face the challenge.

High Stomatal Conductance in the Tomato Flacca Mutant Allows for Faster Photosynthetic Induction.

Due to their slow movement and closure upon shade, partially closed stomata can be a substantial limitation to photosynthesis in variable light intensities. The abscisic acid deficient flacca mutant in tomato (Solanum lycopersicum) displays very high stomatal conductance (gs ). We aimed to determine to what extent this substantially increased gs affects the rate of photosynthetic induction. Steady-state and dynamic photosynthesis characteristics were measured in flacca and wildtype leaves, by the use of simultaneous gas exchange and chlorophyll fluorometry. The steady-state response of photosynthesis to CO2, maximum quantum efficiency of photosystem II photochemistry (Fv/Fm ), as well as mesophyll conductance to CO2 diffusion were not significantly different between genotypes, suggesting similar photosynthetic biochemistry, photoprotective capacity, and internal CO2 permeability. When leaves adapted to shade (50 µmol m-2 s-1) at 400 µbar CO2 partial pressure and high humidity (7 mbar leaf-to-air vapour pressure deficit, VPD) were exposed to high irradiance (1500 µmol m-2 s-1), photosynthetic induction was faster in flacca compared to wildtype leaves, and this was attributable to high initial gs in flacca (~0.6 mol m-2 s-1): in flacca, the times to reach 50 (t50 ) and 90% (t90 ) of full photosynthetic induction were 91 and 46% of wildtype values, respectively. Low humidity (15 mbar VPD) reduced gs and slowed down photosynthetic induction in the wildtype, while no change was observed in flacca; under low humidity, t50 was 63% and t90 was 36% of wildtype levels in flacca. Photosynthetic induction in low CO2 partial pressure (200 µbar) increased gs in the wildtype (but not in flacca), and revealed no differences in the rate of photosynthetic induction between genotypes. Effects of higher gs in flacca were also visible in transients of photosystem II operating efficiency and non-photochemical quenching. Our results show that at ambient CO2 partial pressure, wildtype gs is a substantial limitation to the rate of photosynthetic induction, which flacca overcomes by keeping its stomata open at all times, and it does so at the cost of reduced water use efficiency.

Natural variation of photosynthetic efficiency in Arabidopsis thaliana accessions under low temperature conditions.

Low, but non-freezing, temperatures have negative effects on plant growth and development. Despite some molecular signalling pathways being known, the mechanisms causing different responses among genotypes are still poorly understood. Photosynthesis is one of the processes that are affected by low temperatures. Using an automated phenotyping platform for chlorophyll fluorescence imaging the steady state quantum yield of photosystem II (PSII) electron transport (ΦPSII ) was measured and used to quantify the effect of moderately low temperature on a population of Arabidopsis thaliana natural accessions. Observations were made over the course of several weeks in standard and low temperature conditions and a strong decrease in ΦPSII upon the cold treatment was found. A genome wide association study identified several quantitative trait loci (QTLs) that are associated with changes in ΦPSII in low temperature. One candidate for a cold specific QTL was validated with a mutant analysis to be one of the genes that is likely involved in the PSII response to the cold treatment. The gene encodes the PSII associated protein PSB27 which has already been implicated in the adaptation to fluctuating light.

Reciprocal cybrids reveal how organellar genomes affect plant phenotypes.

Assessment of the impact of variation in chloroplast and mitochondrial DNA (collectively termed the plasmotype) on plant phenotypes is challenging due to the difficulty in separating their effect from nuclear-derived variation (the nucleotype). Haploid-inducer lines can be used as efficient plasmotype donors to generate new plasmotype-nucleotype combinations (cybrids)1. We generated a panel comprising all possible cybrids of seven Arabidopsis thaliana accessions and extensively phenotyped these lines for 1,859 phenotypes under both stable and fluctuating conditions. We show that natural variation in the plasmotype results in both additive and epistatic effects across all phenotypic categories. Plasmotypes that induce more additive phenotypic changes also cause more epistatic effects, suggesting a possible common basis for both additive and epistatic effects. On average, epistatic interactions explained twice as much of the variance in phenotypes as additive plasmotype effects. The impact of plasmotypic variation was also more pronounced under fluctuating and stressful environmental conditions. Thus, the phenotypic impact of variation in plasmotypes is the outcome of multi-level nucleotype-plasmotype-environment interactions and, as such, the plasmotype is likely to serve as a reservoir of variation that is predominantly exposed under certain conditions. The production of cybrids using haploid inducers is a rapid and precise method for assessment of the phenotypic effects of natural variation in organellar genomes. It will facilitate efficient screening of unique nucleotype-plasmotype combinations to both improve our understanding of natural variation in these combinations and identify favourable combinations to enhance plant performance.

Demonstration of a relationship between state transitions and photosynthetic efficiency in a higher plant.

A consequence of the series configuration of PSI and PSII is that imbalanced excitation of the photosystems leads to a reduction in linear electron transport and a drop in photosynthetic efficiency. Achieving balanced excitation is complicated by the distinct nature of the photosystems, which differ in composition, absorption spectra, and intrinsic efficiency, and by a spectrally variable natural environment. The existence of long- and short-term mechanisms that tune the photosynthetic apparatus and redistribute excitation energy between the photosystems highlights the importance of maintaining balanced excitation. In the short term, state transitions help restore balance through adjustments which, though not fully characterised, are observable using fluorescence techniques. Upon initiation of a state transition in algae and cyanobacteria, increases in photosynthetic efficiency are observable. However, while higher plants show fluorescence signatures associated with state transitions, no correlation between a state transition and photosynthetic efficiency has been demonstrated. In the present study, state 1 and state 2 were alternately induced in tomato leaves by illuminating leaves produced under artificial sun and shade spectra with a sequence of irradiances extreme in terms of PSI or PSII overexcitation. Light-use efficiency increased in both leaf types during transition from one state to the other with remarkably similar kinetics to that of F'm/Fm, F'o/Fo, and, during the PSII-overexciting irradiance, ΦPSII and qP. We have provided compelling evidence for the first time of a correlation between photosynthetic efficiency and state transitions in a higher plant. The importance of this relationship in natural ecophysiological contexts remains to be elucidated.

High-Altitude Wild Species Solanum arcanum LA385-A Potential Source for Improvement of Plant Growth and Photosynthetic Performance at Suboptimal Temperatures.

Plant growth, development, and yield of current tomato cultivars are directly affected by low temperatures. Although wild tomato species have been suggested as a potential source for low temperature tolerance, very little is known about their behavior during the reproductive phase. Here, we investigated the impact of suboptimal temperatures (SOT, 16/14°C), as compared to control temperatures (CT, 22/20°C), on plant growth, photosynthetic capacity, and carbohydrate metabolism. Under these conditions, two genotypes were analyzed: a Solanum lycopersicum cultivar Moneymaker and a high-altitude wild species Solanum arcanum LA385, from flowering onset until a later stage of fruit development. Total dry matter production in cv. Moneymaker was reduced up to 30% at SOT, whereas it was hardly affected in wild accession LA385. Specific leaf area, total leaf area, and number of fruits were also decreased at SOT in cv. Moneymaker. In contrast, wild accession LA385 showed an acclimation to SOT, in which ΦPSII and net CO2 assimilation rates were less affected; a similar specific leaf area; higher total leaf area; and higher number of fruits compared to those at CT. In addition, LA385 appeared to have a more distinct sucrose metabolism than cv. Moneymaker at both temperatures, in which it had higher contents of sucrose-6-phosphate, sucrose, and ratio of sucrose: starch in leaves and higher ratio of sucrose: hexose in fruits. Overall, our findings indicate that wild accession LA385 is able to acclimate well to SOT during the reproductive phase, whereas growth and development of cv. Moneymaker is reduced at SOT.

PH-dependent cell-cell interactions in the green alga Chara.

Characean internodal cells develop alternating patterns of acid and alkaline zones along their surface in order to facilitate uptake of carbon required for photosynthesis. In this study, we used a pH-indicating membrane dye, 4-heptadecylumbiliferone, to study the kinetics of alkaline band formation and decomposition. The differences in growth/decay kinetics suggested that growth occurred as an active, autocatalytic process, whereas decomposition was due to diffusion. We further investigated mutual interactions between internodal cells and found that their alignment parallel to each other induced matching of the pH banding patterns, which was mirrored by chloroplast activity. In non-aligned cells, the lowered photosynthetic activity was noted upon a rise of the external pH, suggesting that the matching of pH bands was due to a local elevation of membrane conductance by the high pH of the alkaline zones of neighboured cells. Finally, we show that the altered pH banding pattern caused the reorganization of the cortical cytoplasm. Complex plasma membrane elaborations (charasomes) were degraded via endocytosis, and mitochondria were moved away from the cortex when a previously acid region became alkaline and vice versa. Our data show that characean internodal cells react flexibly to environmental cues, including those originating from neighboured cells.

Effects of Continuous or End-of-Day Far-Red Light on Tomato Plant Growth, Morphology, Light Absorption, and Fruit Production.

Shading by sunlit leaves causes a low red (R) to far-red (FR) ratio that results in a low phytochrome stationary state (PSS). A low PSS induces an array of shade avoidance responses that influence plant architecture and development. It has often been suggested that this architectural response is advantageous for plant growth due to its positive effect on light interception. In contrast to sunlight, artificial light sources such as LEDs often lack FR, resulting in a PSS value higher than solar light (∼0.70). The aim of this study was to investigate how PSS values higher than solar radiation influence the growth and development of tomato plants. Additionally, we investigated whether a short period of FR at the end of the day (EOD-FR) could counteract any potentially negative effects caused by a lack of FR during the day. Tomato plants were grown at four PSS levels (0.70, 0.73, 0.80, and 0.88), or with a 15-min end-of-day far-red (EOD-FR) application (PSS 0.10). Photosynthetic Active Radiation (PAR; 150 µmol m-2 s-1) was supplied using red and blue (95/5%) LEDs. In an additional experiment, the same treatments were applied to plants receiving supplementary low-intensity solar light. Increasing PSS above solar PSS resulted in increased plant height. Leaf area and plant dry mass were lower in the treatments completely lacking FR than treatments with FR. EOD-FR-treated plants responded almost similarly to plants grown without FR, except for plant height, which was increased. Simulations with a 3D-model for light absorption revealed that the increase in dry mass was mainly related to an increase in light absorption due to a higher total leaf area. Increased petiole angle and internode length had a negative influence on total light absorption. Additionally, the treatments without FR and the EOD-FR showed strongly reduced fruit production due to reduced fruit growth associated with reduced source strength and delayed flowering. We conclude that growing tomato plants under artificial light without FR during the light period causes a range of inverse shade avoidance responses, which result in reduced plant source strength and reduced fruit production, which cannot be compensated by a simple EOD-FR treatment.

Converging phenomics and genomics to study natural variation in plant photosynthetic efficiency.

In recent years developments in plant phenomic approaches and facilities have gradually caught up with genomic approaches. An opportunity lies ahead to dissect complex, quantitative traits when both genotype and phenotype can be assessed at a high level of detail. This is especially true for the study of natural variation in photosynthetic efficiency, for which forward genetics studies have yielded only a little progress in our understanding of the genetic layout of the trait. High-throughput phenotyping, primarily from chlorophyll fluorescence imaging, should help to dissect the genetics of photosynthesis at the different levels of both plant physiology and development. Specific emphasis should be directed towards understanding the acclimation of the photosynthetic machinery in fluctuating environments, which may be crucial for the identification of genetic variation for relevant traits in food crops. Facilities should preferably be designed to accommodate phenotyping of photosynthesis-related traits in such environments. The use of forward genetics to study the genetic architecture of photosynthesis is likely to lead to the discovery of novel traits and/or genes that may be targeted in breeding or bio-engineering approaches to improve crop photosynthetic efficiency. In the near future, big data approaches will play a pivotal role in data processing and streamlining the phenotype-to-gene identification pipeline.

RAF2 is a RuBisCO assembly factor in Arabidopsis thaliana.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the reaction between gaseous carbon dioxide (CO2 ) and ribulose-1,5-bisphosphate. Although it is one of the most studied enzymes, the assembly mechanisms of the large hexadecameric RuBisCO is still emerging. In bacteria and in the C4 plant Zea mays, a protein with distant homology to pterin-4α-carbinolamine dehydratase (PCD) has recently been shown to be involved in RuBisCO assembly. However, studies of the homologous PCD-like protein (RAF2, RuBisCO assembly factor 2) in the C3 plant Arabidopsis thaliana (A. thaliana) have so far focused on its role in hormone and stress signaling. We investigated whether A. thalianaRAF2 is also involved in RuBisCO assembly. We localized RAF2 to the soluble chloroplast stroma and demonstrated that raf2 A. thaliana mutant plants display a severe pale green phenotype with reduced levels of stromal RuBisCO. We concluded that the RAF2 protein is probably involved in RuBisCO assembly in the C3 plant A. thaliana.

Chlorophyll fluorescence imaging reveals genetic variation and loci for a photosynthetic trait in diploid potato.

Physiology and genetics are tightly interrelated. Understanding the genetic basis of a physiological trait such as the quantum yield of the photosystem II, or photosynthetic responses to environmental changes will benefit the understanding of these processes. By means of chlorophyll fluorescence (CF) imaging, the quantum yield of photosystem II can be determined rapidly, precisely and non-invasively. In this article, the genetic control and variation in the steady-state quantum yield of PSII (ΦPSII ) is analyzed for diploid potato plants. Current progress in potato research and breeding is slow due to high levels of heterozygosity and complexity of tetraploid genetics. Diploid potatoes offer the possibility of overcoming this problem and advance research for one of the globally most important staple foods. With the help of a diploid genetic mapping population two genetic loci that were strongly associated with differences in ΦPSII were identified. This is a proof of principle that genetic analysis for ΦPSII can be done on potato. The effects of three different stress conditions that are important in potato cultivation were also tested: salt stress, low temperature and deficiency in the macronutrient phosphate. For the last two stresses, significant decreases in photosynthetic activity could be shown, revealing potential for stress detection with CF based tools. In general, our findings show the potential of high-throughput phenotyping for physiological research and breeding in potato.

In Silico Analysis of the Regulation of the Photosynthetic Electron Transport Chain in C3 Plants.

We present a new simulation model of the reactions in the photosynthetic electron transport chain of C3 species. We show that including recent insights about the regulation of the thylakoid proton motive force, ATP/NADPH balancing mechanisms (cyclic and noncyclic alternative electron transport), and regulation of Rubisco activity leads to emergent behaviors that may affect the operation and regulation of photosynthesis under different dynamic environmental conditions. The model was parameterized with experimental results in the literature, with a focus on Arabidopsis (Arabidopsis thaliana). A dataset was constructed from multiple sources, including measurements of steady-state and dynamic gas exchange, chlorophyll fluorescence, and absorbance spectroscopy under different light intensities and CO2, to test predictions of the model under different experimental conditions. Simulations suggested that there are strong interactions between cyclic and noncyclic alternative electron transport and that an excess capacity for alternative electron transport is required to ensure adequate redox state and lumen pH. Furthermore, the model predicted that, under specific conditions, reduction of ferredoxin by plastoquinol is possible after a rapid increase in light intensity. Further analysis also revealed that the relationship between ATP synthesis and proton motive force was highly regulated by the concentrations of ATP, ADP, and inorganic phosphate, and this facilitated an increase in nonphotochemical quenching and proton motive force under conditions where metabolism was limiting, such as low CO2, high light intensity, or combined high CO2 and high light intensity. The model may be used as an in silico platform for future research on the regulation of photosynthetic electron transport.