The photoprotective protein PsbS exerts control over CO(2) assimilation rate in fluctuating light in rice

Up-regulation of non-photochemical quenching improves water use efficiency and reduces whole-plant water consumption under drought in Nicotiana tabacum

Water supply limitations will likely impose increasing restrictions on future crop production, underlining a need for crops that use less water per mass of yield. Water use efficiency (WUE) therefore becomes a key consideration in developing resilient and productive crops. In this study, we hypothesized that it is possible to improve WUE under drought conditions via modulation of chloroplast signals for stomatal opening by up-regulation of non-photochemical quenching (NPQ). Nicotiana tabacum plants with strong overexpression of the PsbS gene encoding PHOTOSYSTEM II SUBUNIT S, a key protein in NPQ, were grown under differing levels of drought. The PsbS-overexpressing lines lost 11% less water per unit CO2 fixed under drought and this did not have a significant effect on plant size. Depending on growth conditions, the PsbS-overexpressing lines consumed from 4-30% less water at the whole-plant level than the corresponding wild type. Leaf water and chlorophyll contents showed a positive relation with the level of NPQ. This study therefore provides proof of concept that up-regulation of NPQ can increase WUE, and as such is an important step towards future engineering of crops with improved performance under drought.

Multiplexed CRISPR-Cas9 mutagenesis of rice PSBS1 noncoding sequences for transgene-free overexpression

Understanding CRISPR-Cas9's capacity to produce native overexpression (OX) alleles would accelerate agronomic gains achievable by gene editing. To generate OX alleles with increased RNA and protein abundance, we leveraged multiplexed CRISPR-Cas9 mutagenesis of noncoding sequences upstream of the rice PSBS1 gene. We isolated 120 gene-edited alleles with varying non-photochemical quenching (NPQ) capacity in vivo-from knockout to overexpression-using a high-throughput screening pipeline. Overexpression increased OsPsbS1 protein abundance two- to threefold, matching fold changes obtained by transgenesis. Increased PsbS protein abundance enhanced NPQ capacity and water-use efficiency. Across our resolved genetic variation, we identify the role of 5'UTR indels and inversions in driving knockout/knockdown and overexpression phenotypes, respectively. Complex structural variants, such as the 252-kb duplication/inversion generated here, evidence the potential of CRISPR-Cas9 to facilitate significant genomic changes with negligible off-target transcriptomic perturbations. Our results may inform future gene-editing strategies for hypermorphic alleles and have advanced the pursuit of gene-edited, non-transgenic rice plants with accelerated relaxation of photoprotection.

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.

Photoacclimation and entrainment of photosynthesis by fluctuating light varies according to genotype in Arabidopsis thaliana

Acclimation of photosynthesis to light intensity (photoacclimation) takes days to achieve and so naturally fluctuating light presents a potential challenge where leaves may be exposed to light conditions that are beyond their window of acclimation. Experiments generally have focused on unchanging light with a relatively fixed combination of photosynthetic attributes to confer higher efficiency in those conditions. Here a controlled LED experiment and mathematical modelling was used to assess the acclimation potential of contrasting Arabidopsis thaliana genotypes following transfer to a controlled fluctuating light environment, designed to present frequencies and amplitudes more relevant to natural conditions. We hypothesize that acclimation of light harvesting, photosynthetic capacity and dark respiration are controlled independently. Two different ecotypes were selected, Wassilewskija-4 (Ws), Landsberg erecta (Ler) and a GPT2 knock out mutant on the Ws background (gpt2-), based on their differing abilities to undergo dynamic acclimation i.e. at the sub-cellular or chloroplastic scale. Results from gas exchange and chlorophyll content indicate that plants can independently regulate different components that could optimize photosynthesis in both high and low light; targeting light harvesting in low light and photosynthetic capacity in high light. Empirical modelling indicates that the pattern of 'entrainment' of photosynthetic capacity by past light history is genotype-specific. These data show flexibility of photoacclimation and variation useful for plant improvement.

Mass screening of rice mutant populations at low CO2 for identification of lowered photorespiration and respiration rates

INTRODUCTION

Identifying rice (Oryza sativa) germplasm with improved efficiency of primary metabolism is of utmost importance in order to increase yields. One such approach can be attained through screening genetically diverse populations under altered environmental conditions. Growth or treatment under low carbon dioxide (CO₂) concentrations can be used as a means of revealing altered leaf photorespiration, respiration and other metabolic variants.

METHODS

We developed a pipeline for very high throughput treatment of gamma- and ethyl methanesulfonate- (EMS) induced mutant populations of IR64 rice seedlings at very low CO₂ for 7 days. 1050 seedlings per batch at 5^th leaf stage were exposed to 60 ppm CO₂ for the first day and 30 ppm for the remaining three days. Following this, putative candidates were identified by measuring chlorophyll depletion using SPAD. Screening results showed a distinct difference between the mutants and the WTs.

RESULTS AND DISCUSSION

The mean chlorophyll loss in WTs ranged from 65% to 11% respectively, whereas in the mutant lines chlorophyll loss ranged from 0 to 100%, suggesting considerable phenotypic variation. Rice mutants with a reduced chlorophyll reduction (<10%) were identified as 'Chlorophyll retention mutants' (CRMs) under low CO₂ stress. In total, 1909 mutant lines (14,000 seedlings) were screened for chlorophyll content under 30 ppm CO_2, with 26 lines selected for detailed screening. These 26 putative candidates were self-seeded to produce an M₅ generation, used to determine the genetic control of the altered response to low CO_2. Gas exchange of light and CO₂ response revealed that there were significant variations among photosynthetic properties in two selected rice mutants. The CO₂ compensation points in the absence of photorespiration and leaf respiration rates were lower than the WTs and anatomical analyses showed that CRM 29 had improved mesophyll cell area. We propose that this approach is useful for generating new material for breeding rice with improved primary metabolism.

Heat-induced proteomic changes in anthers of contrasting rice genotypes under variable stress regimes

Heat stress drastically affects anther tissues resulting in poor plant fertility, necessitating an urgent need to determine the key proteome regulation associated with mature anther in response to heat stress. We identified several genotype - specific protein alterations in rice anthers of Moroberekan (Japonica, heat sensitive), IR64 (Indica, moderately heat tolerant), and Nagina22 (Aus, heat tolerant) in the short-term (ST_HS; one cycle of 42°C, 4 hours before anthesis) and long-term (LT_HS; 6 cycles of 38°C, 6 hours before anthesis) heat stress. The proteins upregulated in long-term heat stress in Nagina22 were enriched in biological processes related to unfolded protein binding and carboxylic acid metabolism, including amino acid metabolism. In short-term heat stress, Nagina22 anthers were enriched in proteins associated with vitamin E biosynthesis and GTPase activator activity. In contrast, downregulated proteins were related to ribosomal proteins. The expression of different Hsp20 and DnaJ was genotype specific. Overall, the heat response in Nagina22 was associated with its capacity for adequate metabolic control and cellular homeostasis, which may be critical for its higher reproductive thermotolerance. This study improves our understanding of thermotolerance mechanisms in rice anthers during anthesis and lays a foundation for breeding thermotolerant varieties via molecular breeding.

Increased bundle-sheath leakiness of CO2 during photosynthetic induction shows a lack of coordination between the C4 and C3 cycles

Use of a complete dynamic model of NADP-malic enzyme C₄ photosynthesis indicated that, during transitions from dark or shade to high light, induction of the C₄ pathway was more rapid than that of C₃ , resulting in a predicted transient increase in bundle-sheath CO₂ leakiness (ϕ). Previously, ϕ has been measured at steady state; here we developed a new method, coupling a tunable diode laser absorption spectroscope with a gas-exchange system to track ϕ in sorghum and maize through the nonsteady-state condition of photosynthetic induction. In both species, ϕ showed a transient increase to > 0.35 before declining to a steady state of 0.2 by 1500 s after illumination. Average ϕ was 60% higher than at steady state over the first 600 s of induction and 30% higher over the first 1500 s. The transient increase in ϕ, which was consistent with model prediction, indicated that capacity to assimilate CO₂ into the C₃ cycle in the bundle sheath failed to keep pace with the rate of dicarboxylate delivery by the C₄ cycle. Because nonsteady-state light conditions are the norm in field canopies, the results suggest that ϕ in these major crops in the field is significantly higher and energy conversion efficiency lower than previous measured values under steady-state conditions.

Chloroplastic photoprotective strategies differ between bundle sheath and mesophyll cells in maize (Zea mays L.) Under drought

Bundle sheath cells play a crucial role in photosynthesis in C4 plants, but the structure and function of photosystem II (PSII) in these cells is still controversial. Photoprotective roles of bundle sheath chloroplasts at the occurrence of environmental stresses have not been investigated so far. Non-photochemical quenching (NPQ) of chlorophyll a fluorescence is the photoprotective mechanism that responds to a changing energy balance in chloroplasts. In the present study, we found a much higher NPQ in bundle sheath chloroplasts than in mesophyll chloroplasts under a drought stress. This change was accompanied by a more rapid dephosphorylation of light-harvesting complex II (LHCII) subunits and a greater increase in PSII subunit S (PsbS) protein abundance than in mesophyll cell chloroplasts. Histochemical staining of reactive oxygen species (ROS) suggested that the high NPQ may be one of the main reasons for the lower accumulation of ROS in bundle sheath chloroplasts. This may maintain the stable functioning of bundle sheath cells under drought condition. These results indicate that the superior capacity for dissipation of excitation energy in bundle sheath chloroplasts may be an environmental adaptation unique to C4 plants.

Hydrogen Peroxide Variation Patterns as Abiotic Stress Responses of Egeria densa

In vegetation management, understanding the condition of submerged plants is usually based on long-term growth monitoring. Reactive oxygen species (ROS) accumulate in organelles under environmental stress and are highly likely to be indicators of a plant's condition. However, this depends on the period of exposure to environmental stress, as environmental conditions are always changing in nature. Hydrogen peroxide (H2O2) is the most common ROS in organelles. The responses of submerged macrophytes, Egeria densa, to high light and iron (Fe) stressors were investigated by both laboratory experiments and natural river observation. Plants were incubated with combinations of 30-200 μmol m-2 s-1 of photosynthetically active radiation (PAR) intensity and 0-10 mg L-1 Fe concentration in the media. We have measured H2O2, photosynthetic pigment concentrations, chlorophyll a (Chl-a), chlorophyll b (Chl-b), carotenoid (CAR), Indole-3-acetic acid (IAA) concentrations of leaf tissues, the antioxidant activity of catalase (CAT), ascorbic peroxidase (APX), peroxidase (POD), the maximal quantum yield of PSII (Fv Fm -1), and the shoot growth rate (SGR). The H2O2 concentration gradually increased with Fe concentration in the media, except at very low concentrations and at an increased PAR intensity. However, with extremely high PAR or Fe concentrations, first the chlorophyll contents and then the H2O2 concentration prominently declined, followed by SGR, the maximal quantum yield of PSII (Fv Fm -1), and antioxidant activities. With an increasing Fe concentration in the substrate, the CAT and APX antioxidant levels decreased, which led to an increase in H2O2 accumulation in the plant tissues. Moreover, increased POD activity was proportionate to H2O2 accumulation, suggesting the low-Fe independent nature of POD. Diurnally, H2O2 concentration varies following the PAR variation. However, the CAT and APX antioxidant activities were delayed, which increased the H2O2 concentration level in the afternoon compared with the level in morning for the same PAR intensities. Similar trends were also obtained for the natural river samples where relatively low light intensity was preferable for growth. Together with our previous findings on macrophyte stress responses, these results indicate that H2O2 concentration is a good indicator of environmental stressors and could be used instead of long-term growth monitoring in macrophyte management.

A Comparison of Photoprotective Mechanism in Different Light-Demanding Plants Under Dynamic Light Conditions

Light intensity is highly heterogeneous in nature, and plants have evolved a series of strategies to acclimate to dynamic light due to their immobile lifestyles. However, it is still unknown whether there are differences in photoprotective mechanisms among different light-demanding plants in response to dynamic light, and thus the role of non-photochemical quenching (NPQ), electron transport, and light energy allocation of photosystems in photoprotection needs to be further understood in different light-demanding plants. The activities of photosystem II (PSII) and photosystem I (PSI) in shade-tolerant species Panax notoginseng, intermediate species Polygonatum kingianum, and sun-demanding species Erigeron breviscapus were comparatively measured to elucidate photoprotection mechanisms in different light-demanding plants under dynamic light. The results showed that the NPQ and PSII maximum efficiency (F v'/F m') of E. breviscapus were higher than the other two species under dynamic high light. Meanwhile, cyclic electron flow (CEF) of sun plants is larger under transient high light conditions since the slope of post-illumination, P700 dark reduction rate, and plastoquinone (PQ) pool were greater. NPQ was more active and CEF was initiated more readily in shade plants than the two other species under transient light. Moreover, sun plants processed higher quantum yield of PSII photochemistry (ΦPSII), quantum yield of photochemical energy conversion [Y(I)], and quantum yield of non-photochemical energy dissipation due to acceptor side limitation (Y(NA), while the constitutive thermal dissipation and fluorescence (Φf,d) and quantum yield of non-photochemical energy dissipation due to donor side limitation [Y(ND)] of PSI were higher in shade plants. These results suggest that sun plants had higher NPQ and CEF for photoprotection under transient high light and mainly allocated light energy through ΦPSII and ΦNPQ, while shade plants had a higher Φf,d and a larger heat dissipation efficiency of PSI donor. Overall, it has been demonstrated that the photochemical efficiency and photoprotective capacity are greater in sun plants under transient dynamic light, while shade plants are more sensitive to transient dynamic light.

Low Light Increases the Abundance of Light Reaction Proteins: Proteomics Analysis of Maize (Zea mays L.) Grown at High Planting Density

Maize (Zea mays L.) is usually planted at high density, so most of its leaves grow in low light. Certain morphological and physiological traits improve leaf photosynthetic capacity under low light, but how light absorption, transmission, and transport respond at the proteomic level remains unclear. Here, we used tandem mass tag (TMT) quantitative proteomics to investigate maize photosynthesis-related proteins under low light due to dense planting, finding increased levels of proteins related to photosystem II (PSII), PSI, and cytochrome b₆f. These increases likely promote intersystem electron transport and increased PSI end electron acceptor abundance. OJIP transient curves revealed increases in some fluorescence parameters under low light: quantum yield for electron transport (φE_o), probability that an electron moves beyond the primary acceptor Q_A^- (ψ_o), efficiency/probability of electron transfer from intersystem electron carriers to reduction end electron acceptors at the PSI acceptor side (δR_o), quantum yield for reduction of end electron acceptors at the PSI acceptor side (φR_o), and overall performance up to the PSI end electron acceptors (PI_total). Thus, densely planted maize shows elevated light utilization through increased electron transport efficiency, which promotes coordination between PSII and PSI, as reflected by higher apparent quantum efficiency (AQE), lower light compensation point (LCP), and lower dark respiration rate (R_d).

Short-term warming does not affect intrinsic thermotolerance but induces strong sustaining photoprotection in tropical evergreen citrus genotypes

Consequences of warming and postwarming events on photosynthetic thermotolerance (P_T ) and photoprotective responses in tropical evergreen species remain elusive. We chose Citrus to answer some of the emerging questions related to tropical evergreen species' P_T behaviour including (i) how wide is the genotypic variation in P_T ? (ii) how does P_T respond to short-term warming and (iii) how do photosynthesis and photoprotective functions respond over short-term warming and postwarming events? A study on 21 genotypes revealed significant genotypic differences in P_T , though these were not large. We selected five genotypes with divergent P_T and simulated warming events: T_max 26/20°C (day-time highest maximum/night-time lowest maximum) (Week 1) < T_max 33/30°C (Week 2) < T_max 36/32°C (Week 3) followed by T_max 26/16°C (Week 4, recovery). The P_T of all genotypes remained unaltered despite strong leaf megathermy (leaf temperature > air temperature) during warming events. Though moderate warming showed genotype-specific stimulation in photosynthesis, higher warming unequivocally led to severe loss in net photosynthesis and induced higher nonphotochemical quenching. Even after a week of postwarming, photoprotective mechanisms strongly persisted. Our study points towards a conservative P_T in evergreen citrus genotypes and their need for sustaining higher photoprotection during warming as well as postwarming recovery conditions.

The Responses of Light Reaction of Photosynthesis to Dynamic Sunflecks in a Typically Shade-Tolerant Species Panax notoginseng

Light is highly heterogeneous in natural conditions, and plants need to evolve a series of strategies to acclimate the dynamic light since it is immobile. The present study aimed to elucidate the response of light reaction of photosynthesis to dynamic sunflecks in a shade-tolerant species Panax notoginseng and to examine the regulatory mechanisms involved in an adaptation to the simulated sunflecks. When P. notoginseng was exposed to the simulated sunflecks, non-photochemical quenching (NPQ) increased rapidly to the maximum value. Moreover, in response to the simulated sunflecks, there was a rapid increase in light-dependent heat dissipation quantum efficiency of photosystem II (PSII) (Φ_NPQ), while the maximum quantum yield of PSII under light (F _v'/F _m') declined. The relatively high fluorescence and constitutive heat dissipation quantum efficiency of PSII (Φ_f,d) in the plants exposed to transient high light (400, 800, and 1,600 μmol m^-2 s^-1) was accompanied by the low effective photochemical quantum yield of PSII (Φ_PSII) after the dark recovery for 15 min, whereas the plants exposed to transient low light (50 μmol m^-2 s^-1) has been shown to lead to significant elevation in Φ_PSII after darkness recovery. Furthermore, PSII fluorescence and constitutive heat dissipation electron transfer rate (J _f,d) was increased with the intensity of the simulated sunflecks, the residual absorbed energy used for the non-net carboxylative processes (J _NC) was decreased when the response of electron transfer rate of NPQ pathway of PSII (J _NPQ) to transient low light is restricted. In addition, the acceptor-side limitation of PSI [Y(NA)] was increased, while the donor-side limitation of photosystems I (PSI) [Y(ND)] was decreased at transient high light conditions accompanied with active cyclic electron flow (CEF). Meanwhile, when the leaves were exposed to transient high light, the xanthophyll cycle (V cycle) was activated and subsequently, the J _NPQ began to increase. The de-epoxidation state [(Z + A)/(V + A + Z)] was strongly correlated with NPQ in response to the sunflecks. In the present study, a rapid engagement of lutein epoxide (Lx) after the low intensity of sunfleck together with the lower NPQ contributed to an elevation in the maximum photochemical quantum efficiency of PSII under the light. The analysis based on the correlation between the CEF and electron flow devoted to Ribulose-1, 5-bisphosphate (RuBP) oxygenation (J _O) indicated that at a high light intensity of sunflecks, the electron flow largely devoted to RuBP oxygenation would contribute to the operation of the CEF. Overall, photorespiration plays an important role in regulating the CEF of the shade-tolerant species, such as P. notoginseng in response to transient high light, whereas active Lx cycle together with the decelerated NPQ may be an effective mechanism of elevating the maximum photochemical quantum efficiency of PSII under light exposure to transient low light.

A Systemic View of Carbohydrate Metabolism in Rice to Facilitate Productivity

Carbohydrate metabolism is an important biochemical process related to developmental growth and yield-related traits. Due to global climate change and rapid population growth, increasing rice yield has become vital. To understand whole carbohydrate metabolism pathways and find related clues for enhancing yield, genes in whole carbohydrate metabolism pathways were systemically dissected using meta-transcriptome data. This study identified 866 carbohydrate genes from the MapMan toolkit and the Kyoto Encyclopedia of Genes and Genomes database split into 11 clusters of different anatomical expression profiles. Analysis of functionally characterized carbohydrate genes revealed that source activity and eating quality are the most well-known functions, and they each have a strong correlation with tissue-preferred clusters. To verify the transcriptomic dissection, three pollen-preferred cluster genes were used and found downregulated in the gori mutant. Finally, we summarized carbohydrate metabolism as a conceptual model in gene clusters associated with morphological traits. This systemic analysis not only provided new insights to improve rice yield but also proposed novel tissue-preferred carbohydrate genes for future research.

Towards a dynamic photosynthesis model to guide yield improvement in C4 crops

The most productive C4 food and biofuel crops, such as Saccharum officinarum (sugarcane), Sorghum bicolor (sorghum) and Zea mays (maize), all use NADP-ME-type C4 photosynthesis. Despite high productivities, these crops fall well short of the theoretical maximum solar conversion efficiency of 6%. Understanding the basis of these inefficiencies is key for bioengineering and breeding strategies to increase the sustainable productivity of these major C4 crops. Photosynthesis is studied predominantly at steady state in saturating light. In field stands of these crops light is continually changing, and often with rapid fluctuations. Although light may change in a second, the adjustment of photosynthesis may take many minutes, leading to inefficiencies. We measured the rates of CO₂ uptake and stomatal conductance of maize, sorghum and sugarcane under fluctuating light regimes. The gas exchange results were combined with a new dynamic photosynthesis model to infer the limiting factors under non-steady-state conditions. The dynamic photosynthesis model was developed from an existing C4 metabolic model for maize and extended to include: (i) post-translational regulation of key photosynthetic enzymes and their temperature responses; (ii) dynamic stomatal conductance; and (iii) leaf energy balance. Testing the model outputs against measured rates of leaf CO₂ uptake and stomatal conductance in the three C4 crops indicated that Rubisco activase, the pyruvate phosphate dikinase regulatory protein and stomatal conductance are the major limitations to the efficiency of NADP-ME-type C4 photosynthesis during dark-to-high light transitions. We propose that the level of influence of these limiting factors make them targets for bioengineering the improved photosynthetic efficiency of these key crops.

The coordination of OsbZIP72 and OsMYBS2 with reverse roles regulates the transcription of OsPsbS1 in rice

Nonphotochemical quenching (NPQ), an intricate photoprotective process, plays fundamental roles in maintaining plant fitness. The PsbS protein is essential for the rapid induction of NPQ, and acts in a dose-dependent manner in leaves. However, little information is known on the transcriptional control of PsbS in land plants. Here we demonstrated that the expression of OsPsbS1 is directly upregulated by OsbZIP72 while repressed by OsMYBS2 in rice. We identified a new cis-element GACAGGTG in japonica OsPsbS1 promoter, to which OsbZIP72 could strongly bind and activate the expression of OsPsbS1. The new cis-element CTAATC confers specific binding for OsMYBS2 in japonica OsPsbS1 promoter. OsbZIP72 can be activated by SAPK1, and acts depending on the abscisic acid (ABA) signalling pathway. GF14A protein affects the repression activity of OsMYBS2 by regulating its nucleocytoplasmic shuttling, and Ser53 is necessary for OsMYBS2 to be retained in the cytoplasm. The inducibility of OsPsbS1 transcription under high light conditions in OsbZIP72 knockout lines was greatly impaired, while the repression of OsPsbS1 transcription under a low light environment in OsMYBS2 knockout lines was significantly alleviated. These results reveal cross-talk among NPQ processes, the ABA signalling pathway and abiotic stress signalling. The elaborate mechanisms may help enhance photoprotection and improve photosynthesis in rice.

Variation in key leaf photosynthetic traits across wheat wild relatives is accession dependent not species dependent

The wild relatives of modern wheat represent an underutilized source of genetic and phenotypic diversity and are of interest in breeding owing to their wide adaptation to diverse environments. Leaf photosynthetic traits underpin the rate of production of biomass and yield and have not been systematically explored in the wheat relatives. This paper identifies and quantifies the phenotypic variation in photosynthetic, stomatal, and morphological traits in up to 88 wheat wild relative accessions across five genera. Both steady-state measurements and dynamic responses to step changes in light intensity are assessed. A 2.3-fold variation for flag leaf light and CO₂ -saturated rates of photosynthesis A_max was observed. Many accessions showing higher and more variable A_max , maximum rates of carboxylation, electron transport, and Rubisco activity when compared with modern genotypes. Variation in dynamic traits was also significant; with distinct genus-specific trends in rates of induction of nonphotochemical quenching and rate of stomatal opening. We conclude that utilization of wild relatives for improvement of photosynthesis is supported by the existence of a high degree of natural variation in key traits and should consider not only genus-level properties but variation between individual accessions.

Comparative study on cytogenetics and transcriptome between diploid and autotetraploid rice hybrids harboring double neutral genes

Double pollen fertility neutral genes, San and Sbn, can control pollen sterility in intersubspecific (indica × japonica) rice hybrids, which has excellent potential to increase rice yield. Previous studies showed that polyploidy could increase the interaction of three pollen sterility loci, i.e. Sa, Sb and Sc, which cause pollen sterility in autotetraploid rice hybrids, and hybrid fertility could be improved by double neutral genes, San and Sbn, in autotetraploid rice hybrids. We compared cytological and transcriptome data between autotetraploid and diploid rice hybrid during meiosis and single microspore stages to understand the molecular mechanism of neutral genes for overcoming pollen sterility in autotetraploid rice hybrids, which harbored double neutral genes. Cytological results revealed that the double neutral genes resulted in higher pollen fertility (76.74%) and lower chromosomal abnormalities in autotetraploid hybrid than in parents during metaphase I, metaphase II, anaphase I and anaphase II. Moreover, autotetraploid rice hybrid displayed stronger heterosis than a diploid hybrid. Compared with diploid rice hybrid, a total of 904 and 68 differently expressed genes (DEGs) were identified explicitly in autotetraploid hybrid at meiosis and single microspore stages, respectively. Of these, 133 and 41 genes were detected in higher-parent dominance and transgressive up-regulation dominance, respectively, which were considered autotetraploid potential heterosis genes, including a meiosis-related gene (Os01g0917500, MSP1) and two meiosis specific-genes (Os07g0624900 and Os04g0208600). Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genomes pathway (KEGG) analysis revealed that DEGs significantly enriched in amino acid metabolism and photosynthesis metabolism. These results indicated that meiosis-specific and meiosis-related genes, and amino acids and photosynthesis metabolism-related genes contribute to higher yield and pollen fertility in autotetraploid rice hybrid. This study provides a theoretical basis for molecular mechanisms of heterosis in autotetraploid rice harboring double neutral genes for pollen fertility.

Red and blue light differentially impact retrograde signalling and photoprotection in rice

Chloroplast-to-nucleus retrograde signalling (RS) is known to impact plant growth and development. In Arabidopsis, we and others have shown that RS affects seedling establishment by inhibiting deetiolation. In the presence of lincomycin, a chloroplast protein synthesis inhibitor that triggers RS, Arabidopsis light-grown seedlings display partial skotomorphogenesis with undeveloped plastids and closed cotyledons. By contrast, RS in monocotyledonous has been much less studied. Here, we show that emerging rice seedlings exposed to lincomycin do not accumulate chlorophyll but otherwise remain remarkably unaffected. However, by using high red (R) and blue (B) monochromatic lights in combination with lincomycin, we have uncovered a RS inhibition of length and a reduction in the B light-induced declination of the second leaf. Furthermore, we present data showing that seedlings grown in high B and R light display different non-photochemical quenching capacity. Our findings support the view that excess B and R light impact seedling photomorphogenesis differently to photoprotect and optimize the response to high-light stress. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.

Dynamic non-photochemical quenching in plants: from molecular mechanism to productivity

Photoprotection refers to a set of well defined plant processes that help to prevent the deleterious effects of high and excess light on plant cells, especially within the chloroplast. Molecular components of chloroplast photoprotection are closely aligned with those of photosynthesis and together they influence productivity. Proof of principle now exists that major photoprotective processes such as non-photochemical quenching (NPQ) directly determine whole canopy photosynthesis, biomass and yield via prevention of photoinhibition and a momentary downregulation of photosynthetic quantum yield. However, this phenomenon has neither been quantified nor well characterized across different environments. Here we address this problem by assessing the existing literature with a different approach to that taken previously, beginning with our understanding of the molecular mechanism of NPQ and its regulation within dynamic environments. We then move to the leaf and the plant level, building an understanding of the circumstances (when and where) NPQ limits photosynthesis and linking to our understanding of how this might take place on a molecular and metabolic level. We argue that such approaches are needed to fine tune the relevant features necessary for improving dynamic NPQ in important crop species.

Red/blue light ratio strongly affects steady-state photosynthesis, but hardly affects photosynthetic induction in tomato (Solanum lycopersicum)

Plants are often subjected to rapidly alternating light intensity and quality. While both short- and long-term changes in red and blue light affect leaf photosynthesis, their impact on dynamic photosynthesis is not well documented. It was tested how dynamic and steady-state photosynthetic traits were affected by red/blue ratios, either during growth or during measurements, in tomato leaves. Four red/blue ratios were used: monochromatic red (R₁₀₀ ), monochromatic blue (B₁₀₀ ), a red/blue light ratio of 9:1 (R₉₀ B₁₀ ) and a red/blue light ratio of 7:3 (R₇₀ B₃₀ ). R₁₀₀ grown leaves showed decreased photosynthetic capacity (maximum rates of light-saturated photosynthesis, carboxylation, electron transport and triose phosphate use), leaf thickness and nitrogen concentrations. Acclimation to various red/blue ratios had limited effects on photosynthetic induction in dark-adapted leaves. B₁₀₀ -grown leaves had a approximately 15% larger initial NPQ transient than the other treatments, which may be beneficial for photoprotection under fluctuating light. B₁₀₀ -grown leaves also showed faster stomatal closure when exposed to low light intensity, which likely resulted from smaller stomata and higher stomatal density. When measured under different red/blue ratios, stomatal opening rate and photosynthetic induction rate were hardly accelerated by increased fractions of blue light in both growth chamber-grown leaves and greenhouse-grown leaves. However, steady-state photosynthesis rate 30 min after photosynthetic induction was strongly reduced in leaves exposed to B₁₀₀ during the measurement. We conclude that varying red/blue light ratios during growth and measurement strongly affects steady-state photosynthesis, but has limited effects on photosynthetic induction rate.

Rice plants overexpressing OsEPF1 show reduced stomatal density and increased root cortical aerenchyma formation

Stomata are adjustable pores in the aerial epidermis of plants. The role of stomata is usually described in terms of the trade-off between CO₂ uptake and water loss. Little consideration has been given to their interaction with below-ground development or diffusion of other gases. We overexpressed the rice EPIDERMAL PATTERNING FACTOR1 (OsEPF1) to produce rice plants with reduced stomatal densities, resulting in lowered leaf stomatal conductance and enhanced water use efficiency. Surprisingly, we found that root cortical aerenchyma (RCA) is formed constitutively in OsEPF1OE lines regardless of tissue age and position. Aerenchyma is tissue containing air-spaces that can develop in the plant root during stressful conditions, e.g. oxygen deficiency when it functions to increase O₂ diffusion from shoot to root. The relationship with stomata is unknown. We conclude that RCA development and stomatal development are linked by two possible mechanisms: first that reduced stomatal conductance inhibits the diffusion of oxygen to the root, creating an oxygen deficit and stimulating the formation of RCA, second that an unknown EPF signalling pathway may be involved. Our observations have fundamental implications for the understanding of whole plant gas diffusion and root-to-shoot signalling events.

Strategies and tools to improve crop productivity by targeting photosynthesis

Crop productivity needs to substantially increase to meet global food and feed demand for a rapidly growing world population. Agricultural technology developers are pursuing a variety of approaches based on both traditional technologies such as genetic improvement, pest control and mechanization as well as new technologies such as genomics, gene manipulation and environmental modelling to develop crops that are capable of meeting growing demand. Photosynthesis is a key biochemical process that, many suggest, is not yet optimized for industrial agriculture or the modern global environment. We are interested in identifying control points in maize photoassimilation that are amenable to gene manipulation to improve overall productivity. Our approach encompasses: developing and using novel gene discovery techniques, translating our discoveries into traits and evaluating each trait in a stepwise manner that reflects a modern production environment. Our aim is to provide step change advancement in overall crop productivity and deliver this new technology into the hands of growers.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'.

Enhanced thylakoid photoprotection can increase yield and canopy radiation use efficiency in rice

High sunlight can raise plant growth rates but can potentially cause cellular damage. The likelihood of deleterious effects is lowered by a sophisticated set of photoprotective mechanisms, one of the most important being the controlled dissipation of energy from chlorophyll within photosystem II (PSII) measured as non-photochemical quenching (NPQ). Although ubiquitous, the role of NPQ in plant productivity remains uncertain because it momentarily reduces the quantum efficiency of photosynthesis. Here we used plants overexpressing the gene encoding a central regulator of NPQ, the protein PsbS, within a major crop species (rice)  to assess the effect of photoprotection at the whole canopy scale. We accounted for canopy light interception, to our knowledge for the first time in this context. We show that in comparison to wild-type plants, psbS overexpressors increased canopy radiation use efficiency and grain yield in fluctuating light, demonstrating that photoprotective mechanisms should be altered to improve rice crop productivity.

Photosystem II Subunit S overexpression increases the efficiency of water use in a field-grown crop

Insufficient water availability for crop production is a mounting barrier to achieving the 70% increase in food production that will be needed by 2050. One solution is to develop crops that require less water per unit mass of production. Water vapor transpires from leaves through stomata, which also facilitate the influx of CO2 during photosynthetic assimilation. Here, we hypothesize that Photosystem II Subunit S (PsbS) expression affects a chloroplast-derived signal for stomatal opening in response to light, which can be used to improve water-use efficiency. Transgenic tobacco plants with a range of PsbS expression, from undetectable to 3.7 times wild-type are generated. Plants with increased PsbS expression show less stomatal opening in response to light, resulting in a 25% reduction in water loss per CO2 assimilated under field conditions. Since the role of PsbS is universal across higher plants, this manipulation should be effective across all crops.

The 4-Dimensional Plant: Effects of Wind-Induced Canopy Movement on Light Fluctuations and Photosynthesis

Physical perturbation of a plant canopy brought about by wind is a ubiquitous phenomenon and yet its biological importance has often been overlooked. This is partly due to the complexity of the issue at hand: wind-induced movement (or mechanical excitation) is a stochastic process which is difficult to measure and quantify; plant motion is dependent upon canopy architectural features which, until recently, were difficult to accurately represent and model in 3-dimensions; light patterning throughout a canopy is difficult to compute at high-resolutions, especially when confounded by other environmental variables. Recent studies have reinforced the expectation that canopy architecture is a strong determinant of productivity and yield; however, links between the architectural properties of the plant and its mechanical properties, particularly its response to wind, are relatively unknown. As a result, biologically relevant data relating canopy architecture, light- dynamics, and short-scale photosynthetic responses in the canopy setting are scarce. Here, we hypothesize that wind-induced movement will have large consequences for the photosynthetic productivity of our crops due to its influence on light patterning. To address this issue, in this study we combined high resolution 3D reconstructions of a plant canopy with a simple representation of canopy perturbation as a result of wind using solid body rotation in order to explore the potential effects on light patterning, interception, and photosynthetic productivity. We looked at two different scenarios: firstly a constant distortion where a rice canopy was subject to a permanent distortion throughout the whole day; and secondly, a dynamic distortion, where the canopy was distorted in incremental steps between two extremes at set time points in the day. We find that mechanical canopy excitation substantially alters light dynamics; light distribution and modeled canopy carbon gain. We then discuss methods required for accurate modeling of mechanical canopy excitation (here coined the 4-dimensional plant) and some associated biological and applied implications of such techniques. We hypothesize that biomechanical plant properties are a specific adaptation to achieve wind-induced photosynthetic enhancement and we outline how traits facilitating canopy excitation could be used as a route for improving crop yield.

Nitrogen can improve the rapid response of photosynthesis to changing irradiance in rice (Oryza sativa L.) plants

To identify the effect of nitrogen (N) nutrition on the dynamic photosynthesis of rice plants, a pot experiment was conducted under two N conditions. The leaf N and chlorophyll levels, as well as steady–state photosynthesis, were significantly increased under high N. After the transition from saturating to low light levels, decreases in the induction state (IS%) of leaf photosynthesis (A) and stomatal conductance (g_s) were more severe under low than under high N supply. After the transition from low to flecked irradiance, the times to 90% of maximum A (T_90%A) were significantly longer under low than under high N supply. Under flecked irradiance, the maximum A under saturating light (A_max–fleck) and the steady–state A under low light (A_min–fleck) were both lower than those under uniform irradiance (A_sat and A_initial). Under high N supply, A_max–fleck was 14.12% lower than A_sat, while it was 22.80% lower under low N supply. The higher IS%, shorter T_90%A, and the lower depression of A_max–fleck from A_sat under high N supply led to a less carbon loss compared with under a low N supply. Therefore, we concluded that N can improve the rapid response of photosynthesis to changing irradiance.

Metabolic and diffusional limitations of photosynthesis in fluctuating irradiance in Arabidopsis thaliana

A better understanding of the metabolic and diffusional limitations of photosynthesis in fluctuating irradiance can help identify targets for improving crop yields. We used different genotypes of Arabidopsis thaliana to characterise the importance of Rubisco activase (Rca), stomatal conductance (g_s), non-photochemical quenching of chlorophyll fluorescence (NPQ) and sucrose phosphate synthase (SPS) on photosynthesis in fluctuating irradiance. Leaf gas exchange and chlorophyll fluorescence were measured in leaves exposed to stepwise increases and decreases in irradiance. rwt43, which has a constitutively active Rubisco enzyme in different irradiance intensities (except in darkness), showed faster increases than the wildtype, Colombia-0, in photosynthesis rates after step increases in irradiance. rca-2, having decreased Rca concentration, showed lower rates of increase. In aba2-1, high g_s increased the rate of change after stepwise irradiance increases, while in C24, low g_s tended to decrease it. Differences in rates of change between Colombia-0 and plants with low levels of NPQ (npq1-2, npq4-1) or SPS (spsa1) were negligible. In Colombia-0, the regulation of Rubisco activation and of g_s were therefore limiting for photosynthesis in fluctuating irradiance, while levels of NPQ or SPS were not. This suggests Rca and g_s as targets for improvement of photosynthesis of plants in fluctuating irradiance.

A physiological role of cyclic electron transport around photosystem I in sustaining photosynthesis under fluctuating light in rice

Plants experience a highly variable light environment over the course of the day. To reveal the molecular mechanisms of their photosynthetic response to fluctuating light, we examined the role of two cyclic electron flows around photosystem I (CEF-PSI)--one depending on PROTON GRADIENT REGULATION 5 (PGR5) and one on NADH dehydrogenase-like complex (NDH)--in photosynthetic regulation under fluctuating light in rice (Oryza sativa L.). The impairment of PGR5-dependent CEF-PSI suppressed the photosynthetic response immediately after sudden irradiation, whereas the impairment of NDH-dependent CEF-PSI did not. However, the impairment of either PGR5-dependent or NDH-dependent CEF-PSl reduced the photosynthetic rate under fluctuating light, leading to photoinhibition at PSI and consequently a reduction in plant biomass. The results highlight that (1) PGR5-dependent CEF-PSI is a key regulator of rapid photosynthetic responses to high light intensity under fluctuating light conditions after constant high light; and (2) both PGR5-dependent and NDH-dependent CEF-PSI have physiological roles in sustaining photosynthesis and plant growth in rice under repeated light fluctuations. The highly responsive regulatory system managed by CEF-PSI appears able to optimize photosynthesis and plant growth under naturally fluctuating light conditions.

The role of putrescine in the regulation of proteins and fatty acids of thylakoid membranes under salt stress

Polyamines can alleviate the inhibitory effects of salinity on plant growth by regulating photosynthetic efficiency. However, little information is available to explain the specific mechanisms underlying the contribution of polyamines to salt tolerance of the photosynthetic apparatus. Here, we investigated the role of putrescine (Put) on the photosynthetic apparatus of cucumber seedlings under salt stress. We found that NaCl stress resulted in severe ion toxicity and oxidative stress in cucumber chloroplasts. In addition, salinity caused a significant increase in the saturated fatty acid contents of thylakoid membranes. Put altered unsaturated fatty acid content, thereby alleviating the disintegration of thylakoid grana lamellae and reducing the number of plastoglobuli in thylakoid membranes. BN-PAGE revealed Put up-regulated the expression of ATP synthase, CP47, D1, Qb, and psbA proteins and down-regulated CP24, D2, and LHCII type III in NaCl-stressed thylakoid membranes. qRT-PCR analysis of gene expression was used to compare transcript and protein accumulation among 10 candidate proteins. For five of these proteins, induced transcript accumulation was consistent with the pattern of induced protein accumulation. Our results suggest that Put regulates protein expression at transcriptional and translational levels by increasing endogenous polyamines levels in thylakoid membranes, which may stabilise photosynthetic apparatus under salt stress.

Optimization of light harvesting and photoprotection: molecular mechanisms and physiological consequences

The distinctive lateral organization of the protein complexes in the thylakoid membrane investigated by Jan Anderson and co-workers is dependent on the balance of various attractive and repulsive forces. Modulation of these forces allows critical physiological regulation of photosynthesis that provides efficient light-harvesting in limiting light but dissipation of excess potentially damaging radiation in saturating light. The light-harvesting complexes (LHCII) are central to this regulation, which is achieved by phosphorylation of stromal residues, protonation on the lumen surface and de-epoxidation of bound violaxanthin. The functional flexibility of LHCII derives from a remarkable pigment composition and configuration that not only allow efficient absorption of light and efficient energy transfer either to photosystem II or photosystem I core complexes, but through subtle configurational changes can also exhibit highly efficient dissipative reactions involving chlorophyll-xanthophyll and/or chlorophyll-chlorophyll interactions. These changes in function are determined at a macroscopic level by alterations in protein-protein interactions in the thylakoid membrane. The capacity and dynamics of this regulation are tuned to different physiological scenarios by the exact protein and pigment content of the light-harvesting system. Here, the molecular mechanisms involved will be reviewed, and the optimization of the light-harvesting system in different environmental conditions described.