Improvement of photosynthesis in rice (Oryza sativa L.) by inserting the C4 pathway

C4 cereal and biofuel crop microbiomes

Microbiomes provide multiple life-support functions for plants, including nutrient acquisition and tolerance to abiotic and biotic stresses. Considering the importance of C4 cereal and biofuel crops for food security under climate change conditions, more attention has been given recently to C4 plant microbiome assembly and functions. Here, we review the current status of C4 cereal and biofuel crop microbiome research with a focus on beneficial microbial traits for crop growth and health. We highlight the importance of environmental factors and plant genetics in C4 crop microbiome assembly and pinpoint current knowledge gaps. Finally, we discuss the potential of foxtail millet as a C4 model species and outline future perspectives of C4 plant microbiome research.

Overexpression of Setaria italica phosphoenolpyruvate carboxylase gene in rice positively impacts photosynthesis and agronomic traits

C₄ plants have the inherent capacity to concentrate atmospheric CO₂ in the vicinity of RuBisCo, thereby increasing carboxylation, and inhibiting photorespiration. Carbonic anhydrase (CA), the first enzyme of C₄ photosynthesis, converts atmospheric CO₂ to HCO₃^-, which is utilized by PEPC to produce C₄ acids. Bioengineering of C₄ traits into C₃ crops is an attractive strategy to increase photosynthesis and water use efficiency. In the present study, we isolated the PEPC gene from the C₄ plant Setaria italica and transferred it to C₃ rice. Overexpression of SiPEPC resulted in a 2-6-fold increment in PEPC enzyme activity in transgenic lines with respect to non-transformed control. Photosynthetic efficiency was enhanced in transformed plants, which was associated with increased ФPSII, ETR, lower NPQ, and higher chlorophyll accumulation. Water use efficiency was increased by 16-22% in PEPC transgenic rice lines. Increased PEPC activity enhanced quantum yield and carboxylation efficiency of PEPC transgenic lines. Transgenic plants exhibited higher light saturation photosynthesis rate and lower CO₂ compensation point, as compared to non-transformed control. An increase in net photosynthesis increased the yield by (23-28.9%) and biomass by (24.1-29%) in transgenic PEPC lines. Altogether, our findings indicate that overexpression of C_4-specific SiPEPC enzyme is able to enhance photosynthesis and related parameters in transgenic rice.

Role of C4 photosynthetic enzyme isoforms in C3 plants and their potential applications in improving agronomic traits in crops

As compared to C3, C4 plants have higher photosynthetic rates and better tolerance to high temperature and drought. These traits are highly beneficial in the current scenario of global warming. Interestingly, all the genes of the C4 photosynthetic pathway are present in C3 plants, although they are involved in diverse non-photosynthetic functions. Non-photosynthetic isoforms of carbonic anhydrase (CA), phosphoenolpyruvate carboxylase (PEPC), malate dehydrogenase (MDH), the decarboxylating enzymes NAD/NADP-malic enzyme (NAD/NADP-ME), and phosphoenolpyruvate carboxykinase (PEPCK), and finally pyruvate orthophosphate dikinase (PPDK) catalyze reactions that are essential for major plant metabolism pathways, such as the tricarboxylic acid (TCA) cycle, maintenance of cellular pH, uptake of nutrients and their assimilation. Consistent with this view differential expression pattern of these non-photosynthetic C3 isoforms has been observed in different tissues across the plant developmental stages, such as germination, grain filling, and leaf senescence. Also abundance of these C3 isoforms is increased considerably in response to environmental fluctuations particularly during abiotic stress. Here we review the vital roles played by C3 isoforms of C4 enzymes and the probable mechanisms by which they help plants in acclimation to adverse growth conditions. Further, their potential applications to increase the agronomic trait value of C3 crops is discussed.

Progress and prospects of C4 trait engineering in plants

Incorporating C₄ photosynthetic traits into C₃ crops is a rational approach for sustaining future demands for crop productivity. Using classical plant breeding, engineering this complex trait is unlikely to achieve its target. Therefore, it is critical and timely to implement novel biotechnological crop improvement strategies to accomplish this goal. However, a fundamental understanding of C₃ , C₄ , and C₃ -C₄ intermediate metabolism is crucial for the targeted use of biotechnological tools. This review assesses recent progress towards engineering C₄ photosynthetic traits in C₃ crops. We also discuss lessons learned from successes and failures of recent genetic engineering attempts in C₃ crops, highlighting the pros and cons of using rice as a model plant for short-, medium- and long-term goals of genetic engineering. This review provides an integrated approach towards engineering improved photosynthetic efficiency in C₃ crops for sustaining food, fibre and fuel production around the globe.

Mutation of OsPIN1b by CRISPR/Cas9 Reveals a Role for Auxin Transport in Modulating Rice Architecture and Root Gravitropism

The distribution and content of auxin within plant tissues affect a variety of important growth and developmental processes. Polar auxin transport (PAT), mainly mediated by auxin influx and efflux transporters, plays a vital role in determining auxin maxima and gradients in plants. The auxin efflux carrier PIN-FORMED (PIN) family is one of the major protein families involved in PAT. Rice (Oryza sativa L.) genome possesses 12 OsPIN genes. However, the detailed functions of OsPIN genes involved in regulating the rice architecture and gravity response are less well understood. In the present study, OsPIN1b was disrupted by CRISPR/Cas9 technology, and its roles in modulating rice architecture and root gravitropism were investigated. Tissue-specific analysis showed that OsPIN1b was mainly expressed in roots, stems and sheaths at the seedling stage, and the transcript abundance was progressively decreased during the seedling stages. Expression of OsPIN1b could be quickly and greatly induced by NAA, indicating that OsPIN1b played a vital role in PAT. IAA homeostasis was disturbed in ospin1b mutants, as evidenced by the changed sensitivity of shoot and root to NAA and NPA treatment, respectively. Mutation of OsPIN1b resulted in pleiotropic phenotypes, including decreased growth of shoots and primary roots, reduced adventitious root number in rice seedlings, as well as shorter and narrower leaves, increased leaf angle, more tiller number and decreased plant height and panicle length at the late developmental stage. Moreover, ospin1b mutants displayed a curly root phenotype cultured with tap water regardless of lighting conditions, while nutrient solution culture could partially rescue the curly root phenotype in light and almost completely abolish this phenotype in darkness, indicating the involvement of the integration of light and nutrient signals in root gravitropism regulation. Additionally, amyloplast sedimentation was impaired in the peripheral tiers of the ospin1b root cap columella cell, while it was not the main contributor to the abnormal root gravitropism. These data suggest that OsPIN1b not only plays a vital role in regulating rice architecture but also functions in regulating root gravitropism by the integration of light and nutrient signals.

Meeting in the Middle: Lessons and Opportunities from Studying C3-C4 Intermediates

The discovery of C₃-C₄ intermediate species nearly 50 years ago opened up a new avenue for studying the evolution of photosynthetic pathways. Intermediate species exhibit anatomical, biochemical, and physiological traits that range from C₃ to C₄. A key feature of C₃-C₄ intermediates that utilize C₂ photosynthesis is the improvement in photosynthetic efficiency compared with C₃ species. Although the recruitment of some core enzymes is shared across lineages, there is significant variability in gene expression patterns, consistent with models that suggest numerous evolutionary paths from C₃ to C₄ photosynthesis. Despite the many evolutionary trajectories, the recruitment of glycine decarboxylase for C₂ photosynthesis is likely required. As technologies enable high-throughput genotyping and phenotyping, the discovery of new C₃-C₄ intermediates species will enrich comparisons between evolutionary lineages. The investigation of C₃-C₄ intermediate species will enhance our understanding of photosynthetic mechanisms and evolutionary processes and will potentially aid in crop improvement.

Assessment of the Photosynthetic Apparatus Functions by Chlorophyll Fluorescence and P700 Absorbance in C3 and C4 Plants under Physiological Conditions and under Salt Stress

Functions of the photosynthetic apparatus of C3 (Pisum sativum L.) and C4 (Zea mays L.) plants under physiological conditions and after treatment with different NaCl concentrations (0-200 mM) were investigated using chlorophyll a fluorescence (pulse-amplitude-modulated (PAM) and JIP test) and P700 photooxidation measurement. Data revealed lower density of the photosynthetic structures (RC/CSo), larger relative size of the plastoquinone (PQ) pool (N) and higher electron transport capacity and photosynthetic rate (parameter RFd) in C4 than in C3 plants. Furthermore, the differences were observed between the two studied species in the parameters characterizing the possibility of reduction in the photosystem (PSI) end acceptors (REo/RC, REo/CSo and δRo). Data revealed that NaCl treatment caused a decrease in the density of the photosynthetic structures and relative size of the PQ pool as well as decrease in the electron transport to the PSI end electron acceptors and the probability of their reduction as well as an increase in the thermal dissipation. The effects were stronger in pea than in maize. The enhanced energy losses after high salt treatment in maize were mainly from the increase in the regulated energy losses (ΦNPQ), while in pea from the increase in non-regulated energy losses (ΦNO). The reduction in the electron transport from QA to the PSI end electron acceptors influenced PSI activity. Analysis of the P700 photooxidation and its decay kinetics revealed an influence of two PSI populations in pea after treatment with 150 mM and 200 mM NaCl, while in maize the negligible changes were registered only at 200 mM NaCl. The experimental results clearly show less salt tolerance of pea than maize.

Functional-Structural Plant Models Mission in Advancing Crop Science: Opportunities and Prospects

Functional-structural plant models (FSPMs) have been evolving for over 2 decades and their future development, to some extent, depends on the value of potential applications in crop science. To date, stabilizing crop production by identifying valuable traits for novel cultivars adapted to adverse environments is topical in crop science. Thus, this study will examine how FSPMs are able to address new challenges in crop science for sustainable crop production. FSPMs developed to simulate organogenesis, morphogenesis, and physiological activities under various environments and are amenable to downscale to the tissue, cellular, and molecular level or upscale to the whole plant and ecological level. In a modeling framework with independent and interactive modules, advanced algorithms provide morphophysiological details at various scales. FSPMs are shown to be able to: (i) provide crop ideotypes efficiently for optimizing the resource distribution and use for greater productivity and less disease risk, (ii) guide molecular design breeding via linking molecular basis to plant phenotypes as well as enrich crop models with an additional architectural dimension to assist breeding, and (iii) interact with plant phenotyping for molecular breeding in embracing three-dimensional (3D) architectural traits. This study illustrates that FSPMs have great prospects in speeding up precision breeding for specific environments due to the capacity for guiding and integrating ideotypes, phenotyping, molecular design, and linking molecular basis to target phenotypes. Consequently, the promising great applications of FSPMs in crop science will, in turn, accelerate their evolution and vice versa.

Systems-based rice improvement approaches for sustainable food and nutritional security

An integrated research approach to ensure sustainable rice yield increase of a crop grown by 25% of the world's farmers in 10% of cropland is essential for global food security. Rice, being a global staple crop, feeds about 56% of the world population and sustains 40% of the world's poor. At ~ $200 billion, it also accounts for 13% of the annual crop value. With hunger and malnutrition rampant among the poor, rice research for development is unique in global food and nutrition security. A systems-based, sustainable increase in rice quantity and quality is imperative for environmental and biodiversity benefits. Upstream 'discovery' through biotechnology, midstream 'development' through breeding and agronomy, downstream 'dissemination and deployment' must be 'demand-driven' for 'distinct socio-economic transformational impacts'. Local agro-ecology and livelihood nexus must drive the research agenda for targeted benefits. This necessitates sustained long-term investments by government, non-government and private sectors to secure the future food, nutrition, environment, prosperity and equity status.

The potential of resilient carbon dynamics for stabilizing crop reproductive development and productivity during heat stress

Impaired carbon metabolism and reproductive development constrain crop productivity during heat stress. Reproductive development is energy intensive, and its requirement for respiratory substrates rises as associated metabolism increases with temperature. Understanding how these processes are integrated and the extent to which they contribute to the maintenance of yield during and following periods of elevated temperatures is important for developing climate-resilient crops. Recent studies are beginning to demonstrate links between processes underlying carbon dynamics and reproduction during heat stress, consequently a summation of research that has been reported thus far and an evaluation of purported associations are needed to guide and stimulate future research. To this end, we review recent studies relating to source-sink dynamics, non-foliar photosynthesis and net carbon gain as pivotal in understanding how to improve reproductive development and crop productivity during heat stress. Rapid and precise phenotyping during narrow phenological windows will be important for understanding mechanisms underlying these processes, thus we discuss the development of relevant high-throughput phenotyping approaches that will allow for more informed decision-making regarding future crop improvement.

Robustification of GWAS to explore effective SNPs addressing the challenges of hidden population stratification and polygenic effects

Genome-wide association studies (GWAS) play a vital role in identifying important genes those is associated with the phenotypic variations of living organisms. There are several statistical methods for GWAS including the linear mixed model (LMM) which is popular for addressing the challenges of hidden population stratification and polygenic effects. However, most of these methods including LMM are sensitive to phenotypic outliers that may lead the misleading results. To overcome this problem, in this paper, we proposed a way to robustify the LMM approach for reducing the influence of outlying observations using the β-divergence method. The performance of the proposed method was investigated using both synthetic and real data analysis. Simulation results showed that the proposed method performs better than both linear regression model (LRM) and LMM approaches in terms of powers and false discovery rates in presence of phenotypic outliers. On the other hand, the proposed method performed almost similar to LMM approach but much better than LRM approach in absence of outliers. In the case of real data analysis, our proposed method identified 11 SNPs that are significantly associated with the rice flowering time. Among the identified candidate SNPs, some were involved in seed development and flowering time pathways, and some were connected with flower and other developmental processes. These identified candidate SNPs could assist rice breeding programs effectively. Thus, our findings highlighted the importance of robust GWAS in identifying candidate genes.

Improving crop yield and resilience through optimization of photosynthesis: panacea or pipe dream?

Increasing the speed of breeding to enhance crop productivity and adaptation to abiotic stresses is urgently needed. The perception that a second Green Revolution should be implemented is widely established within the scientific community and among stakeholders. In recent decades, different alternatives have been proposed for increasing crop yield through manipulation of leaf photosynthetic efficiency. However, none of these has delivered practical or relevant outputs. Indeed, the actual increases in photosynthetic rates are not expected to translate into yield increases beyond 10-15%. Furthermore, instantaneous rates of leaf photosynthesis are not necessarily the reference target for research. Yield is the result of canopy photosynthesis, understood as the contribution of laminar and non-laminar organs over time, within which concepts such as canopy architecture, stay-green, or non-laminar photosynthesis need to be taken into account. Moreover, retrospective studies show that photosynthetic improvements have been more common at the canopy level. Nevertheless, it is crucial to place canopy photosynthesis in the context of whole-plant functioning, which includes sink-source balance and transport of photoassimilates, and the availability and uptake of nutrients, such as nitrogen in particular. Overcoming this challenge will only be feasible if a multiscale crop focus combined with a multidisciplinary scientific approach is adopted.

Different physiological responses of C3 and C4 plants to nanomaterials

Several studies have previously reported that nanomaterial uptake and toxicity in plants are species dependent. However, the differences between photosynthetic pathways, C3 and C4, following nanomaterial exposure are poorly understood. In the current work, wheat and rice, two C3 pathway species are compared to amaranth and maize, which utilize the C4 photosynthetic mechanism. These plants were cultured in soils which were spiked with CuO, Ag, TiO₂, MWCNT, and FLG nanomaterials. Overall, the C4 plant exhibited higher resilience to NM stress than C3 plants. In particular, significant differences were observed in chlorophyll contents with rice returning a 40.9-54.2% decrease compared to 3.5-15.1% for maize. Fv/Fm levels were significantly reduced by up to 51% in rice whereas no significant reductions were observed in amaranth and maize. Furthermore, NM uptake in the C3 species was greater than that in C4 plants, a trend that was also seen in metal concentration. TEM results showed that CuO NPs altered the chloroplast thylakoid structure in rice leaves and a large number of CuO NPs were observed in the vascular sheath cells. In contrast, there were no significant changes in the chloroplasts in the vascular sheath and no significant CuO NPs were found in maize leaves. This study was the first to systematically characterize the effect of metal and carbon-based nanomaterials in soil on C3 and C4 plants, providing a new perspective for understanding the impact of nanomaterials on plants.

Exploiting differences in the energy budget among C4 subtypes to improve crop productivity

C₄ crops of agricultural importance all belong to the NADP-malic enzyme (ME) subtype, and this subtype has been the template for C₄ introductions into C₃ crops, like rice, to improve their productivity. However, the ATP cost for the C₄ cycle in both NADP-ME and NAD-ME subtypes accounts for > 40% of the total ATP requirement for CO₂ assimilation. These high ATP costs, and the associated need for intense cyclic electron transport and low intrinsic quantum yield ΦCO2 , are major constraints in realizing strong improvements of canopy photosynthesis and crop productivity. Based on mathematical modelling, we propose a C₄ ideotype that utilizes low chloroplastic ATP requirements present in the nondomesticated phosphoenolpyruvate carboxykinase (PEP-CK) subtype. The ideotype is a mixed form of NAD(P)-ME and PEP-CK types, requires no cyclic electron transport under low irradiances, and its theoretical ΦCO2 is c. 25% higher than that of a C₄ crop type. Its cell-type-specific ATP and NADPH requirements can be fulfilled by local energy production. The ideotype is projected to have c. 10% yield advantage over NADP-ME-type crops and > 50% advantage over C₃ counterparts. The ideotype provides a unique (theoretical) case where ΦCO2 could be improved, thereby paving a new avenue for improving photosynthesis in both C₃ and C₄ crops.

Differences in Physiological Responses of Two Oat (Avena nuda L.) Lines to Sodic-Alkalinity in the Vegetative Stage

Sodic-alkalinity is a more seriously limiting factor in agricultural productivity than salinity. Oat (Avena nuda) is a salt-tolerant crop species and is therefore useful in studying the physiological responses of cereals to alkalinity. We evaluated the differential effects of sodic-alkalinity on two naked oat lines, Caoyou1 and Yanke1. Seedlings of the two lines were exposed to 50 mM alkaline salt mixture of NaHCO₃ and Na₂CO₃ (18:1 molar ratio; pH 8.5) for 2 weeks in a soil environment. Sodic-alkalinity exposure led the assimilation of abundant Na⁺ at similar concentrations in the organs of both lines. However, Caoyou1 showed much stronger growth than Yanke1, exhibiting a higher dry weight, total leaf area, and shoot height under sodic-alkalinity. Further analysis showed that Caoyou1 was more sodic-alkalinity tolerance than Yanke1. This was firstly because of differences in the oxidative stress defense mechanisms in leaves of the two lines. Antioxidant enzyme activities were either slightly elevated (catalase (CAT), ascorbate peroxidase (APX), guaiacol peroxidase (GP), glutathione reductase (GR)) or unaltered (superoxide dismutase (SOD)) in Caoyou1 leaves, but some enzyme (SOD, GPOX, GR) activities were significantly reduced in Yanke1. AnAPX1 transcript levels significantly increased in Caoyou1 under sodic-alkalinity conditions compared with Yanke1, indicating its better antioxidant capacity. Secondly, the related parameters of Mg²⁺ concentration, phosphoenolpyruvate carboxylase (PEPC) activity, and AnPEPC transcript levels in the leaves showed significantly higher values in Caoyou1 compared with Yanke1. This demonstrated the effective utilization by Caoyou1 of accumulated HCO₃^- in the irreversible reaction from phosphoenolpyruvate to oxaloacetate to produce inorganic phosphorus, which was elevated in Caoyou1 leaves under alkalinity stress. Overall, the results demonstrated that the greater sodic-alkalinity tolerance of Caoyou1 is the result of: (1) maintained antioxidant enzyme activities; and (2) a higher capacity for the phosphoenolpyruvate to oxaloacetate reactions, as shown by the higher PEPC activity, Mg²⁺ concentration, and total phosphorus concentration in its leaves, despite the lower soil pH.

Ectopic Expression of a Transmembrane Protein KaCyt b6 from a Red Seaweed Kappaphycus alvarezii in Transgenic Tobacco Augmented the Photosynthesis and Growth

Cytochrome b6f complex is a thylakoid membrane-localized protein and catalyses the transfer of electrons from plastoquinol to plastocyanin in photosynthetic electron transport chain. In the present study, Cytochrome b6 (KaCyt b6) gene from Kappaphycus alvarezii (a red seaweed) was overexpressed in tobacco. A 935 base pair (bp) long KaCyt b6 cDNA contained an open reading frame of 648 bp encoding a protein of 215 amino acids with an expected isoelectric point of 8.67 and a molecular mass of 24.37 kDa. The KaCyt b6 gene was overexpressed in tobacco under control of CaMV35S promoter. The transgenic tobacco had higher electron transfer rate and photosynthetic yield over wild-type and vector control tobacco. The KaCyt b6 tobacco also exhibited significantly higher photosynthetic gas exchange (PN) and improved water use efficiency. The transgenic plants had higher ratio of PN and intercellular CO2. The KaCyt b6 transgenic tobacco showed higher estimates of photosystem II quantum yield, higher activity of the water-splitting complex, PSII photochemistry, and photochemical quenching. The basal quantum yield of nonphotochemical processes in PSII was recorded lower in KaCyt b6 tobacco. Transgenic tobacco contained higher contents of carotenoids and total chlorophyll and also had better ratios of chlorophyll a and b, and carotenoids and total chlorophyll contents hence improved photosynthetic efficiency and production of sugar and starch. The KaCyt b6 transgenic plants performed superior under control and greenhouse conditions. To the best of our knowledge through literature survey, this is the first report on characterization of KaCyt b6 gene from K. alvarezii for enhanced photosynthetic efficiency and growth in tobacco.

The bHLH transcription factor PPLS1 regulates the color of pulvinus and leaf sheath in foxtail millet (Setaria italica)

The bHLH transcription factor, PPLS1, interacts with SiMYB85 to control the color of pulvinus and leaf sheath by regulating anthocyanin biosynthesis in foxtail millet (Setaria italica). Foxtail millet (Setaria italica), a self-pollinated crop with numerous small florets, is difficult for cross-pollination. The color of pulvinus and leaf sheath with purple being dominant to green is an indicative character and often used for screening authentic hybrids in foxtail millet crossing. Deciphering molecular mechanism controlling this trait would greatly facilitate genetic improvement of cultivars in foxtail millet. Here, using the F₂ bulk specific-locus amplified fragment sequencing approach, we mapped the putative causal gene for the purple color of pulvinus and leaf sheath (PPLS) trait to a 100 Kb region on chromosome 7. Expression analyses of the 15 genes in this region revealed that Seita.7G195400 (renamed here as PPLS1) was differentially expressed between purple and green cultivars. PPLS1 encodes a bHLH transcription factor and is localized in the nucleus with a transactivation activity. Furthermore, we observed that expression of a MYB transcription factor gene, SiMYB85 (Seita.4G086300) involved in anthocyanin biosynthesis, shows a totally positive association with that of PPLS1. Heterologous co-expression of both PPLS1 and SiMYB85 in tobacco leaves led to elevated anthocyanin accumulation and expression of some anthocyanin-related genes. Furthermore, PPLS1 physically interacts with SiMYB85. Taken together, our results suggest that PPLS1 interacts with SiMYB85 to control the color of pulvinus and leaf sheath by regulating anthocyanin biosynthesis in foxtail millet.

Key-Marker Volatile Compounds in Aromatic Rice (Oryza sativa) Grains: An HS-SPME Extraction Method Combined with GC×GC-TOFMS

The aroma of rice essentially contributes to the quality of rice grains. For some varieties, their aroma properties really drive consumer preferences. In this paper, using a dynamic headspace solid-phase microextraction (HS-SPME) system coupled to a two-dimensional gas chromatography (GC×GC) using a time-of-flight mass spectrometric detector (TOFMS) and multivariate analysis, the volatile compounds of aromatic and non-aromatic rice grains were contrasted to define some chemical markers. Fifty-one volatile compounds were selected for principal component analysis resulting in eight key-marker volatile compounds (i.e., pentanal, hexanal, 2-pentyl-furan, 2,4-nonadienal, pyridine, 1-octen-3-ol and (E)-2-octenal) as responsible for the differences between aromatic and non-aromatic rice varieties. The factors that are most likely to affect the HS-SPME efficiency for the aforementioned key-marker compounds were evaluated using a 2III5−2 fractional factorial design in conjunction with multi-response optimisation. The method precision values, expressed as % of coefficient of variation (CV), were ranging from 1.91% to 26.90% for repeatability (n = 9) and 7.32% to 37.36% for intermediate precision (n = 3 × 3). Furthermore, the method was successfully applied to evaluate the volatile compounds of rice varieties from some Asian countries.

Comparative Genomic Analysis of Rice with Contrasting Photosynthesis and Grain Production under Salt Stress

Unfavourable environmental conditions, including soil salinity, lead to decreased rice (Oryza sativa L.) productivity, especially at the reproductive stage. In this study, we examined 30 rice varieties, which revealed significant differences in the photosynthetic performance responses under salt stress conditions during the reproductive stage, which ultimately affected yield components after recovery. In rice with a correlation between net photosynthetic rate (P_N) and intercellular CO₂ concentration (C_i) under salt stress, P_N was found to be negatively correlated with filled grain number after recovery. Applying stringent criteria, we identified 130,317 SNPs and 15,396 InDels between two “high-yield rice” varieties and two “low-yield rice” varieties with contrasting photosynthesis and grain yield characteristics. A total of 2089 genes containing high- and moderate-impact SNPs or InDels were evaluated by gene ontology (GO) enrichment analysis, resulting in over-represented terms in the apoptotic process and kinase activity. Among these genes, 262 were highly expressed in reproductive tissues, and most were annotated as receptor-like protein kinases. These findings highlight the importance of variations in signaling components in the genome and these loci can serve as potential genes in rice breeding to produce a variety with salt avoidance that leads to increased yield in saline soil.

Current and possible approaches for improving photosynthetic efficiency

One of the most important tasks laying ahead today's biotechnology is to improve crop productivity with the aim of meeting increased food and energy demands of humankind. Plant productivity depends on many genetic factors, including life cycle, harvest index, stress tolerance and photosynthetic activity. Many approaches were already tested or suggested to improve either. Limitations of photosynthesis have also been uncovered and efforts been taken to increase its efficiency. Examples include decreasing photosynthetic antennae size, increasing the photosynthetically available light spectrum, countering oxygenase activity of Rubisco by implementing C4 photosynthesis to C3 plants and altering source to sink transport of metabolites. A natural and effective photosynthetic adaptation, the sugar alcohol metabolism got however remarkably little attention in the last years, despite being comparably efficient as C4, and can be considered easier to introduce to new species. We also propose root to shoot carbon-dioxide transport as a means to improve photosynthetic performance and drought tolerance at the same time. Different suggestions and successful examples are covered here for improving plant photosynthesis as well as novel perspectives are presented for future research.

Changes in redox regulation during transition from C3 to single cell C4 photosynthesis in Bienertia sinuspersici

Bienertia sinuspersici performs single cell C₄ photosynthesis without Kranz anatomy. Peripheral and central cytoplasmic compartments in a single chlorenchyma cell act as mesophyll cells and bundle sheath cells. Development of this specialized mechanism is gradual during plant development. Young leaves perform C₃ photosynthesis, while mature leaves have complete C₄ cycle. The aim of this work was to investigate changes in redox regulation and antioxidant defence during transition from C₃ to single cell C₄ photosynthesis in B. sinuspersici leaves. First, we confirmed gradual development of C₄ with protein blot and qRT-PCR analysis of C₄ enzymes. After this activities and isoenzymes of superoxide dismutase (SOD), catalase (CAT), peroxidase (POX), ascorbate peroxidase (APX), glutathione reductase (GR), dehydroascorbate reductase (DHAR) and H₂O₂ and TBARS and glutathione pool and redox status (GSH/GSSG) were determined in young, developing and mature leaves during transition from C₃ to single cell C₄ photosynthesis. Activities of SOD, APX and POX decrease, while GR and DHAR were increased. However, most striking results were the changes in isoenzyme patterns of SOD, CAT and GR which were gradual through transition to C₄ photosynthesis.

A transatlantic perspective on 20 emerging issues in biological engineering

Advances in biological engineering are likely to have substantial impacts on global society. To explore these potential impacts we ran a horizon scanning exercise to capture a range of perspectives on the opportunities and risks presented by biological engineering. We first identified 70 potential issues, and then used an iterative process to prioritise 20 issues that we considered to be emerging, to have potential global impact, and to be relatively unknown outside the field of biological engineering. The issues identified may be of interest to researchers, businesses and policy makers in sectors such as health, energy, agriculture and the environment.

Improved short-term drought response of transgenic rice over-expressing maize C4 phosphoenolpyruvate carboxylase via calcium signal cascade

To understand the link between long-term drought tolerance and short-term drought responses in plants, transgenic rice (Oryza sativa L.) plants over-expressing the maize C_4-pepc gene encoding phosphoenolpyruvate carboxylase (PC) and wild-type (WT) rice plants were subjected to PEG 6000 treatments to simulate drought stress. Compared with WT, PC had the higher survival rate and net photosynthetic rate after 16days of drought treatment, and had higher relative water content in leaves after 2h of drought treatment as well, conferring drought tolerance. WT accumulated higher amounts of malondialdehyde, superoxide radicals, and H₂O₂ than PC under the 2-h PEG 6000 treatment, indicating greater damages in WT. Results from pretreatments with a Ca²⁺ chelator and/or antagonist showed that the regulation of the early drought response in PC was Ca²⁺-dependent. The NO and H₂O₂ levels in PC lines were also up-regulated via Ca²⁺ signals, indicating that Ca²⁺ in PC lines also reacted upstream of NO and H₂O₂. 2-h drought treatment increased the transcripts of CPK9 and CPK4 in PC via positive up-regulation of Ca²⁺. The transcripts of NAC6 [NACs (NAM, ATAF1, ATAF2, and CUC2)] and bZIP60 (basic leucine zipper, bZIP) were up-regulated, but those of DREB2B (dehydration-responsive element-binding protein, DREB) were down-regulated, both via Ca²⁺ signals in PC. PEPC activity, expressions of C₄-pepc, and the antioxidant enzyme activities in PC lines were up-regulated via Ca²⁺. These results indicated that Ca²⁺ signals in PC lines can up-regulate the NAC6 and bZIP60 and the downstream targets for early drought responses, conferring drought tolerance for the long term.

Increasing Leaf Vein Density via Mutagenesis in Rice Results in an Enhanced Rate of Photosynthesis, Smaller Cell Sizes and Can Reduce Interveinal Mesophyll Cell Number

Improvements to leaf photosynthetic rates of crops can be achieved by targeted manipulation of individual component processes, such as the activity and properties of RuBisCO or photoprotection. This study shows that simple forward genetic screens of mutant populations can also be used to rapidly generate photosynthesis variants that are useful for breeding. Increasing leaf vein density (concentration of vascular tissue per unit leaf area) has important implications for plant hydraulic properties and assimilate transport. It was an important step to improving photosynthetic rates in the evolution of both C3 and C4 species and is a foundation or prerequisite trait for C4 engineering in crops like rice (Oryza sativa). A previous high throughput screen identified five mutant rice lines (cv. IR64) with increased vein densities and associated narrower leaf widths (Feldman et al., 2014). Here, these high vein density rice variants were analyzed for properties related to photosynthesis. Two lines were identified as having significantly reduced mesophyll to bundle sheath cell number ratios. All five lines had 20% higher light saturated photosynthetic capacity per unit leaf area, higher maximum carboxylation rates, dark respiration rates and electron transport capacities. This was associated with no significant differences in leaf thickness, stomatal conductance or CO2 compensation point between mutants and the wild-type. The enhanced photosynthetic rate in these lines may be a result of increased RuBisCO and electron transport component amount and/or activity and/or enhanced transport of photoassimilates. We conclude that high vein density (associated with altered mesophyll cell length and number) is a trait that may confer increased photosynthetic efficiency without increased transpiration.

Engineering central metabolism - a grand challenge for plant biologists

The goal of increasing crop productivity and nutrient-use efficiency is being addressed by a number of ambitious research projects seeking to re-engineer photosynthetic biochemistry. Many of these projects will require the engineering of substantial changes in fluxes of central metabolism. However, as has been amply demonstrated in simpler systems such as microbes, central metabolism is extremely difficult to rationally engineer. This is because of multiple layers of regulation that operate to maintain metabolic steady state and because of the highly connected nature of central metabolism. In this review we discuss new approaches for metabolic engineering that have the potential to address these problems and dramatically improve the success with which we can rationally engineer central metabolism in plants. In particular, we advocate the adoption of an iterative 'design-build-test-learn' cycle using fast-to-transform model plants as test beds. This approach can be realised by coupling new molecular tools to incorporate multiple transgenes in nuclear and plastid genomes with computational modelling to design the engineering strategy and to understand the metabolic phenotype of the engineered organism. We also envisage that mutagenesis could be used to fine-tune the balance between the endogenous metabolic network and the introduced enzymes. Finally, we emphasise the importance of considering the plant as a whole system and not isolated organs: the greatest increase in crop productivity will be achieved if both source and sink metabolism are engineered.

Viewing oxidative stress through the lens of oxidative signalling rather than damage

Concepts of the roles of reactive oxygen species (ROS) in plants and animals have shifted in recent years from focusing on oxidative damage effects to the current view of ROS as universal signalling metabolites. Rather than having two opposing activities, i.e. damage and signalling, the emerging concept is that all types of oxidative modification/damage are involved in signalling, not least in the induction of repair processes. Examining the multifaceted roles of ROS as crucial cellular signals, we highlight as an example the loss of photosystem II function called photoinhibition, where photoprotection has classically been conflated with oxidative damage.

Combining genetic and evolutionary engineering to establish C4 metabolism in C3 plants

To feed a world population projected to reach 9 billion people by 2050, the productivity of major crops must be increased by at least 50%. One potential route to boost the productivity of cereals is to equip them genetically with the 'supercharged' C₄ type of photosynthesis; however, the necessary genetic modifications are not sufficiently understood for the corresponding genetic engineering programme. In this opinion paper, we discuss a strategy to solve this problem by developing a new paradigm for plant breeding. We propose combining the bioengineering of well-understood traits with subsequent evolutionary engineering, i.e. mutagenesis and artificial selection. An existing mathematical model of C₃-C₄ evolution is used to choose the most promising path towards this goal. Based on biomathematical simulations, we engineer Arabidopsis thaliana plants that express the central carbon-fixing enzyme Rubisco only in bundle sheath cells (Ru-BSC plants), the localization characteristic for C₄ plants. This modification will initially be deleterious, forcing the Ru-BSC plants into a fitness valley from where previously inaccessible adaptive steps towards C₄ photosynthesis become accessible through fitness-enhancing mutations. Mutagenized Ru-BSC plants are then screened for improved photosynthesis, and are expected to respond to imposed artificial selection pressures by evolving towards C₄ anatomy and biochemistry.

Influence of leaf vein density and thickness on hydraulic conductance and photosynthesis in rice (Oryza sativa L.) during water stress

The leaf venation architecture is an ideal, highly structured and efficient irrigation system in plant leaves. Leaf vein density (LVD) and vein thickness are the two major properties of this system. Leaf laminae carry out photosynthesis to harvest the maximum biological yield. It is still unknown whether the LVD and/or leaf vein thickness determines the plant hydraulic conductance (Kplant) and leaf photosynthetic rate (A). To investigate this topic, the current study was conducted with two varieties under three PEG-induced water deficit stress (PEG-IWDS) levels. The results showed that PEG-IWDS significantly decreased A, stomatal conductance (gs), and Kplant in both cultivars, though the IR-64 strain showed more severe decreases than the Hanyou-3 strain. PEG-IWDS significantly decreased the major vein thickness, while it had no significant effect on LVD. A, gs and Kplant were positively correlated with each other, and they were negatively correlated with LVD. A, gs and Kplant were positively correlated with the inter-vein distance and major vein thickness. Therefore, the decreased photosynthesis and hydraulic conductance in rice plants under water deficit conditions are related to the decrease in the major vein thickness.

Accumulation of the components of cyclic electron flow around photosystem I in C4 plants, with respect to the requirements for ATP

By concentrating CO2, C4 photosynthesis can suppress photorespiration and achieve high photosynthetic efficiency, especially under conditions of high light, high temperature, and drought. To concentrate CO2, extra ATP is required, which would also require a change in photosynthetic electron transport in C4 photosynthesis from that in C3 photosynthesis. Several analyses have shown that the accumulation of the components of cyclic electron flow (CEF) around photosystem I, which generates the proton gradient across thylakoid membranes (ΔpH) and functions in ATP production without producing NADPH, is increased in various NAD-malic enzyme and NADP-malic enzyme C4 plants, suggesting that CEF may be enhanced to satisfy the increased need for ATP in C4 photosynthesis. However, in C4 plants, the accumulation patterns of the components of two partially redundant pathways of CEF, NAD(P)H dehydrogenase-like complex and PROTON GRADIENT REGULATION5-PGR5-like1 complex, are not identical, suggesting that these pathways may play different roles in C4 photosynthesis. Accompanying the increase in the amount of NDH, the expression of some genes which encode proteins involved in the assembly of NDH is also increased at the mRNA level in various C4 plants, suggesting that this increase is needed to increase the accumulation of NDH. To better understand the relation between CEF and C4 photosynthesis, a reverse genetic approach to generate C4 transformants with respect to CEF will be necessary.

Carbon isotope discrimination as a diagnostic tool for C4 photosynthesis in C3-C4 intermediate species

The presence and activity of the C4 cycle in C3-C4 intermediate species have proven difficult to analyze, especially when such activity is low. This study proposes a strategy to detect C4 activity and estimate its contribution to overall photosynthesis in intermediate plants, by using tunable diode laser absorption spectroscopy (TDLAS) coupled to gas exchange systems to simultaneously measure the CO2 responses of CO2 assimilation (A) and carbon isotope discrimination (Δ) under low O2 partial pressure. Mathematical models of C3-C4 photosynthesis and Δ are then fitted concurrently to both responses using the same set of constants. This strategy was applied to the intermediate species Flaveria floridana and F. brownii, and to F. pringlei and F. bidentis as C3 and C4 controls, respectively. Our results support the presence of a functional C4 cycle in F. floridana, that can fix 12-21% of carbon. In F. brownii, 75-100% of carbon is fixed via the C4 cycle, and the contribution of mesophyll Rubisco to overall carbon assimilation increases with CO2 partial pressure in both intermediate plants. Combined gas exchange and Δ measurement and modeling is a powerful diagnostic tool for C4 photosynthesis.

Association analysis for disease resistance to Fusarium oxysporum in cape gooseberry (Physalis peruviana L)

BACKGROUND

Vascular wilt caused by Fusarium oxysporum is the most important disease in cape gooseberry (Physalis peruviana L.) in Colombia. The development of resistant cultivars is considered one of the most cost-effective means to reduce the impact of this disease. In order to do so, it is necessary to provide breeders with molecular markers and promising germplasm for introgression of different resistance loci as part of breeding schemes. Here we described an association mapping study in cape gooseberry with the goal to: (i) select promising materials for use in plant breeding and (ii) identify SNPs associated with the cape gooseberry resistance response to the F. oxysporum pathogen under greenhouse conditions, as potential markers for cape gooseberry breeding.

RESULTS

We found a total of 21 accessions with different resistance responses within a diversity panel of 100 cape gooseberry accessions. A total of 60,663 SNPs were also identified within the same panel by means of GBS (Genotyping By Sequencing). Model-based population structure and neighbor-joining analyses showed three populations comprising the cape gooseberry panel. After correction for population structure and kinship, we identified SNPs markers associated with the resistance response against F. oxysporum. The identification of markers was based on common tags using the reference genomes of tomato and potato as well as the root/stem transcriptome of cape gooseberry. By comparing their location with the tomato genome, 16 SNPs were found in genes involved in defense/resistance response to pathogens, likewise when compared with the genome of potato, 12 markers were related.

CONCLUSIONS

The work presented herein provides the first association mapping study in cape gooseberry showing both the identification of promising accessions with resistance response phenotypes and the identification of a set of SNP markers mapped to defense/resistance response genes of reference genomes. Thus, the work also provides new knowledge on candidate genes involved in the P. peruviana - F. oxysporum pathosystem as a foundation for further validation in marker-assisted selection. The results have important implications for conservation and breeding strategies in cape gooseberry.

Analysis of Stress-Responsive Gene Expression in Cultivated and Weedy Rice Differing in Cold Stress Tolerance

Rice (Oryza sativa L.) cultivars show impairment of growth in response to environmental stresses such as cold at the early seedling stage. Locally adapted weedy rice is able to survive under adverse environmental conditions, and can emerge in fields from greater soil depth. Cold-tolerant weedy rice can be a good genetic source for developing cold-tolerant, weed-competitive rice cultivars. An in-depth analysis is presented here of diverse indica and japonica rice genotypes, mostly weedy rice, for cold stress response to provide an understanding of different stress adaptive mechanisms towards improvement of the rice crop performance in the field. We have tested a collection of weedy rice genotypes to: 1) classify the subspecies (ssp.) grouping (japonica or indica) of 21 accessions; 2) evaluate their sensitivity to cold stress; and 3) analyze the expression of stress-responsive genes under cold stress and a combination of cold and depth stress. Seeds were germinated at 25°C at 1.5- and 10-cm sowing depth for 10d. Seedlings were then exposed to cold stress at 10°C for 6, 24 and 96h, and the expression of cold-, anoxia-, and submergence-inducible genes was analyzed. Control plants were seeded at 1.5cm depth and kept at 25°C. The analysis revealed that cold stress signaling in indica genotypes is more complex than that of japonica as it operates via both the CBF-dependent and CBF-independent pathways, implicated through induction of transcription factors including OsNAC2, OsMYB46 and OsF-BOX28. When plants were exposed to cold + sowing depth stress, a complex signaling network was induced that involved cross talk between stresses mediated by CBF-dependent and CBF-independent pathways to circumvent the detrimental effects of stresses. The experiments revealed the importance of the CBF regulon for tolerance to both stresses in japonica and indica ssp. The mechanisms for cold tolerance differed among weedy indica genotypes and also between weedy indica and cultivated japonica ssp. as indicated by the up/downregulation of various stress-responsive pathways identified from gene expression analysis. The cold-stress response is described in relation to the stress signaling pathways, showing complex adaptive mechanisms in different genotypes.

Microsatellite Variations of Elite Setaria Varieties Released during Last Six Decades in China

Crop improvement is a multifaceted micro-evolutionary process, involving changes in breeding approaches, planting configurations and consumption preferences of human beings. Recent research has started to identify the specific genes or genomic regions correlate to improved agronomic traits, however, an apparent blank between the genetic structure of crop elite varieties and their improving histories in diverse modern breeding programs is still in existence. Foxtail millet (Setaria italica) was one of the earliest cereal crops to be domesticated and served as a staple crop for early civilizations in China, where it is still widely grown today. In the present trial, a panel of foxtail millet elite varieties, which were released in the last sixty years in different geographical regions of China, was characterized using microsatellite markers (SSRs). A clear separation of two subpopulations corresponding to the two eco-geographical regions of foxtail millet production in China was identified by the dataset, which also indicated that in more recently released elite varieties, large quantities of accessions have been transferred from spring-sowing to summer-sowing ecotypes, likely as a result of breeding response to planting configurations. An association mapping study was conducted to identify loci controlling traits of major agronomic interest. Furthermore, selective sweeps involved in improvement of foxtail millet were identified as multi-diverse minor effect loci controlling different agronomic traits during the long-term improvement of elite varieties. Our results highlight the effect of transition of planting configuration and breeding preference on genetic evolvement of crop species.

Molecular integrity of chloroplast DNA and mitochondrial DNA in mesophyll and bundle sheath cells of maize

When compared to maize mesophyll cells, the plastid and mitochondrial DNAs in bundle sheath cells are less fragmented, less damaged, and contain fewer DNA polymerase-blocking impediments. Plants that conduct C4 photosynthesis differ from those that employ C3 photosynthesis with respect to leaf anatomy, biochemical pathways, and the proteins and RNA transcripts present in the leaf mesophyll (M) and bundle sheath (BS) cells. Here, we investigate the organellar DNA (orgDNA) from plastids and mitochondria in these two cell types. We use standard qPCR, long PCR, and DNA damage analysis to quantify the amount and quality of orgDNA in isolated M and BS cells of maize. When compared to M cells, BS cells have less orgDNA damage and a higher percentage of unimpeded orgDNA. In addition, the orgDNA is more fragmented in M than BS cells, although orgDNA in BS is subject to more in vitro repair. We suggest that the differences in molecular integrity of orgDNA in these two cells are due to higher levels of reactive oxygen species in M than BS cells.

Photosynthesis at the forefront of a sustainable life

The development of a sustainable bio-based economy has drawn much attention in recent years, and research to find smart solutions to the many inherent challenges has intensified. In nature, perhaps the best example of an authentic sustainable system is oxygenic photosynthesis. The biochemistry of this intricate process is empowered by solar radiation influx and performed by hierarchically organized complexes composed by photoreceptors, inorganic catalysts, and enzymes which define specific niches for optimizing light-to-energy conversion. The success of this process relies on its capability to exploit the almost inexhaustible reservoirs of sunlight, water, and carbon dioxide to transform photonic energy into chemical energy such as stored in adenosine triphosphate. Oxygenic photosynthesis is responsible for most of the oxygen, fossil fuels, and biomass on our planet. So, even after a few billion years of evolution, this process unceasingly supports life on earth, and probably soon also in outer-space, and inspires the development of enabling technologies for a sustainable global economy and ecosystem. The following review covers some of the major milestones reached in photosynthesis research, each reflecting lasting routes of innovation in agriculture, environmental protection, and clean energy production.