Finding the genes to build C4 rice

Beneficial effects of Bacillus mojavensis strain MTC-8 on plant growth, immunity and disease resistance against Magnaporthe oryzae

Rice blast, a prevalent and highly destructive rice disease that significantly impacts rice yield, is caused by the rice blast fungus. In the present study, a strain named MTC-8, identified as Bacillus mojavensis, was demonstrated has strong antagonistic activity against the rice blast fungus, Rhizoctonia solani, Ustilaginoidea virens, and Bipolaria maydis. The potential biocontrol agents were identified using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis and chromatography. Further investigations elucidated the inhibitory mechanism of the isolated compound and demonstrated its ability to suppress spore germination, alter hyphal morphology, disrupt cell membrane integrity, and induce defense-related gene expression in rice. MTC-8 promoted plant growth and may lead to the development of a biocontrol agent that meets agricultural standards. Overall, the Bacillus mojavensis MTC-8 strain exerted beneficial effects on plant growth, immunity and disease resistance against rice blast fungus. In this study, we isolated and purified a bioactive substance from fermentation broth, and the results provide a foundation for the development and application of biopesticides. Elucidation of the inhibitory mechanism against rice blast fungus provides theoretical support for the identification of molecular targets. The successful development of a biocontrol agent lays the groundwork for its practical application in agriculture.

The WIP6 transcription factor TOO MANY LATERALS specifies vein type in C4 and C3 grass leaves

Grass leaves are invariantly strap shaped with an elongated distal blade and a proximal sheath that wraps around the stem. Underpinning this shape is a scaffold of leaf veins, most of which extend in parallel along the proximo-distal leaf axis. Differences between species are apparent both in the vein types that develop and in the distance between veins across the medio-lateral leaf axis. A prominent engineering goal is to increase vein density in leaves of C3 photosynthesizing species to facilitate the introduction of the more efficient C4 pathway. Here, we discover that the WIP6 transcription factor TOO MANY LATERALS (TML) specifies vein rank in both maize (C4) and rice (C3). Loss-of-function tml mutations cause large lateral veins to develop in positions normally occupied by smaller intermediate veins, and TML transcript localization in wild-type leaves is consistent with a role in suppressing lateral vein development in procambial cells that form intermediate veins. Attempts to manipulate TML function in rice were unsuccessful because transgene expression was silenced, suggesting that precise TML expression is essential for shoot viability. This finding may reflect the need to prevent the inappropriate activation of downstream targets or, given that transcriptome analysis revealed altered cytokinin and auxin signaling profiles in maize tml mutants, the need to prevent local or general hormonal imbalances. Importantly, rice tml mutants display an increased occupancy of veins in the leaf, providing a step toward an anatomical chassis for C4 engineering. Collectively, a conserved mechanism of vein rank specification in grass leaves has been revealed.

Photosynthesis and food security: the evolving story of C4 rice

Traditional "Green Revolution" cereal breeding strategies to improve yield are now reaching a plateau in our principal global food crop rice. Photosynthesis has now become a major target of international consortia to increase yield potential. Synthetic biology is being used across multiple large projects to improve photosynthetic efficiency. This review follows the genesis and progress of one of the first of these consortia projects, now in its 13th year; the Bill and Melinda Gates funded C4 Rice Project. This project seeks to install the biochemical and anatomical attributes necessary to support C4 photosynthesis in the C3 crop rice. Here we address the advances made thus far in installing the biochemical pathway and some of the key targets yet to be reached.

Interaction of negative regulator OsWD40-193 with OseEF1A1 inhibits Oryza sativa resistance to Hirschmanniella mucronata infection

Rice is a crucial food crop worldwide, but it is highly susceptible to Hirschmanniella mucronata, a migratory parasitic nematode. No rice variety has been identified that could resist H. mucronata infection. Therefore, it is very important to study the interaction between rice and H. mucronata to breed resistant rice varieties. Here, we demonstrated that protein OsWD40-193 interacted with the extension factor OseEF1A1 and both were negative regulators inhibiting rice resistance to H. mucronata infection. Overexpression of either OsWD40-193 or OseEF1A1 led to enhance susceptibility to H. mucronata, whereas the absence of OsWD40-193 or OseEF1A1 led to resistance. Further transcriptomic analysis showed that OseEF1A1 deletion altered the expression of genes association with salicylic acid, jasmonic acid and abolic acid signaling pathways and increased the accumulation of secondary metabolites to enhance resistance in rice. Our study showed that H. mucronata infection affected the expression of negative regulators in rice and inhibited rice resistance, which was conducive to the infection of nematode. Together, our data showed that H. mucronata affected the expression of negative regulators to facilitate its infection and provided potential target genes to engineering resistance germplasm via gene editing of the negative regulators.

Integrated global analysis in spider flowers illuminates features underlying the evolution and maintenance of C4 photosynthesis

The carbon concentrating mechanism-C4 photosynthesis-represents a classic example of convergent evolution, but how this important trait originated and evolved remains largely enigmatic. The spider flower Gynandropsis gynandra is a valuable leafy vegetable crop and medicinal plant that has also been recognized as a C4 model species. Here we present a high-quality chromosome-scale annotated genome assembly of G. gynandra through a combination of Oxford Nanopore Technology (ONT), HiFi and Hi-C technology. The 17 super-scaffolds cover 98.66% of the estimated genome (997.61 Mb), with a contig N50 of 11.43 Mb and a scaffold N50 of 51.02 Mb. Repetitive elements occupy up to 71.91% of its genome, and over half are long terminal repeat retrotransposons (LTR-RTs) derived from recent bursts, contributing to genome size expansion. Strikingly, LTR-RT explosion also played a critical role in C4 evolution by altering expression features of photosynthesis-associated genes via preferential insertion in promoters. Integrated multiomics analyses of G. gynandra and the ornamental horticulture C3 relative Tarenaya hassleriana reveal that species-specific whole-genome duplication, gene family expansion, recent LTR-RT amplification, and more recent tandem duplication events have all facilitated the evolution of C4 photosynthesis, revealing uniqueness of C4 evolution in the Cleome genus. Moreover, high leaf vein density and heat stress resilience are associated with shifted gene expression patterns. The mode of C3-to-C4 transition found here yields new insights into evolutionary convergence of a complex plant trait. The availability of this reference-grade genomic resource makes G. gynandra an ideal model system facilitating efforts toward C4-aimed crop engineering.

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.

Closer vein spacing by ectopic expression of nucleotide-binding and leucine-rich repeat proteins in rice leaves

Elevated expression of nucleotide-binding and leucine-rich repeat proteins led to closer vein spacing and higher vein density in rice leaves. To feed the growing global population and mitigate the negative effects of climate change, there is a need to improve the photosynthetic capacity and efficiency of major crops such as rice to enhance grain yield potential. Alterations in internal leaf morphology and cellular architecture are needed to underpin some of these improvements. One of the targets is to generate a "Kranz-like" anatomy in leaves that includes decreased interveinal spacing close to that in C₄ plant species. As C₄ photosynthesis has evolved from C₃ photosynthesis independently in multiple lineages, the genes required to facilitate C₄ may already be present in the rice genome. The Taiwan Rice Insertional Mutants (TRIM) population offers the advantage of gain-of-function phenotype trapping, which accelerates the identification of rice gene function. In the present study, we screened the TRIM population to determine the extent to which genetic plasticity can alter vein density (VD) in rice. Close vein spacing mutant 1 (CVS1), identified from a VD screening of approximately 17,000 TRIM lines, conferred heritable high leaf VD. Increased vein number in CVS1 was confirmed to be associated with activated expression of two nucleotide-binding and leucine-rich repeat (NB-LRR) proteins. Overexpression of the two NB-LRR genes individually in rice recapitulates the high VD phenotype, due mainly to reduced interveinal mesophyll cell (M cell) number, length, bulliform cell size and thus interveinal distance. Our studies demonstrate that the trait of high VD in rice can be achieved by elevated expression of NB-LRR proteins limited to no yield penalty.

Proto Kranz-like leaf traits and cellular ionic regulation are associated with salinity tolerance in a halophytic wild rice

Species of wild rice (Oryza spp.) possess a wide range of stress tolerance traits that can be potentially utilized in breeding climate-resilient cultivated rice cultivars (Oryza sativa) thereby aiding global food security. In this study, we conducted a greenhouse trial to evaluate the salinity tolerance of six wild rice species, one cultivated rice cultivar (IR64) and one landrace (Pokkali) using a range of electrophysiological, imaging, and whole-plant physiological techniques. Three wild species (O. latifolia, O. officinalis and O. coarctata) were found to possess superior salinity stress tolerance. The underlying mechanisms, however, were strikingly different. Na+ accumulation in leaves of O. latifolia, O. officinalis and O. coarctata were significantly higher than the tolerant landrace, Pokkali. Na+ accumulation in mesophyll cells was only observed in O. coarctata, suggesting that O. officinalis and O. latifolia avoid Na+ accumulation in mesophyll by allocating Na+ to other parts of the leaf. The finding also suggests that O. coarctata might be able to employ Na+ as osmolyte without affecting its growth. Further study of Na+ allocation in leaves will be helpful to understand the mechanisms of Na+ accumulation in these species. In addition, O. coarctata showed Proto Kranz-like leaf anatomy (enlarged bundle sheath cells and lower numbers of mesophyll cells), and higher expression of C4-related genes (e.g., NADPME, PPDK) and was a clear outlier with respect to salinity tolerance among the studied wild and cultivated Oryza species. The unique phylogenetic relationship of O. coarctata with C4 grasses suggests the potential of this species for breeding rice with high photosynthetic rate under salinity stress in the future.

Ribosome profiling elucidates differential gene expression in bundle sheath and mesophyll cells in maize

The efficiencies offered by C4 photosynthesis have motivated efforts to understand its biochemical, genetic, and developmental basis. Reactions underlying C4 traits in most C4 plants are partitioned between two cell types, bundle sheath (BS), and mesophyll (M) cells. RNA-seq has been used to catalog differential gene expression in BS and M cells in maize (Zea mays) and several other C4 species. However, the contribution of translational control to maintaining the distinct proteomes of BS and M cells has not been addressed. In this study, we used ribosome profiling and RNA-seq to describe translatomes, translational efficiencies, and microRNA abundance in BS- and M-enriched fractions of maize seedling leaves. A conservative interpretation of our data revealed 182 genes exhibiting cell type-dependent differences in translational efficiency, 31 of which encode proteins with core roles in C4 photosynthesis. Our results suggest that non-AUG start codons are used preferentially in upstream open reading frames of BS cells, revealed mRNA sequence motifs that correlate with cell type-dependent translation, and identified potential translational regulators that are differentially expressed. In addition, our data expand the set of genes known to be differentially expressed in BS and M cells, including genes encoding transcription factors and microRNAs. These data add to the resources for understanding the evolutionary and developmental basis of C4 photosynthesis and for its engineering into C3 crops.

What is quantitative plant biology?

Quantitative plant biology is an interdisciplinary field that builds on a long history of biomathematics and biophysics. Today, thanks to high spatiotemporal resolution tools and computational modelling, it sets a new standard in plant science. Acquired data, whether molecular, geometric or mechanical, are quantified, statistically assessed and integrated at multiple scales and across fields. They feed testable predictions that, in turn, guide further experimental tests. Quantitative features such as variability, noise, robustness, delays or feedback loops are included to account for the inner dynamics of plants and their interactions with the environment. Here, we present the main features of this ongoing revolution, through new questions around signalling networks, tissue topology, shape plasticity, biomechanics, bioenergetics, ecology and engineering. In the end, quantitative plant biology allows us to question and better understand our interactions with plants. In turn, this field opens the door to transdisciplinary projects with the society, notably through citizen science.

Formation of Proto-Kranz in C3 Rice Induced by Spike-Stalk Injection Method

Introduction of C4 photosynthetic traits into C3 crops is an important strategy for improving photosynthetic capacity and productivity. Here, we report the research results of a variant line of sorghum-rice (SR) plant with big panicle and high spikelet density by introducing sorghum genome DNA into rice by spike-stalk injection. The whole-genome resequencing showed that a few sorghum genes could be integrated into the rice genome. Gene expression was confirmed for two C4 photosynthetic enzymes containing pyruvate, orthophosphate dikinase and phosphoenolpyruvate carboxykinase. Exogenous sorghum DNA integration induced a series of key traits associated with the C4 pathway called "proto-Kranz" anatomy, including leaf thickness, bundle sheath number and size, and chloroplast size in bundle sheath cells. Significantly, transgenic plants exhibited enhanced photosynthetic capacity resulting from both photosynthetic CO₂-concentrating effect and improved energy balance, which led to an increase in carbohydrate levels and productivity. Furthermore, such rice plant exhibited delayed leaf senescence. In summary, this study provides a proof for the feasibility of inducing the transition from C3 leaf anatomy to proto-Kranz by spike-stalk injection to achieve efficient photosynthesis and increase productivity.

OsARF11 Promotes Growth, Meristem, Seed, and Vein Formation during Rice Plant Development

The plant hormone auxin acts as a mediator providing positional instructions in a range of developmental processes. Studies in Arabidopsis thaliana L. show that auxin acts in large part via activation of Auxin Response Factors (ARFs) that in turn regulate the expression of downstream genes. The rice (Oryza sativa L.) gene OsARF11 is of interest because of its expression in developing rice organs and its high sequence similarity with MONOPTEROS/ARF5, a gene with prominent roles in A. thaliana development. We have assessed the phenotype of homozygous insertion mutants in the OsARF11 gene and found that in relation to wildtype, osarf11 seedlings produced fewer and shorter roots as well as shorter and less wide leaves. Leaves developed fewer veins and larger areoles. Mature osarf11 plants had a reduced root system, fewer branches per panicle, fewer grains per panicle and fewer filled seeds. Mutants had a reduced sensitivity to auxin-mediated callus formation and inhibition of root elongation, and phenylboronic acid (PBA)-mediated inhibition of vein formation. Taken together, our results implicate OsARF11 in auxin-mediated growth of multiple organs and leaf veins. OsARF11 also appears to play a central role in the formation of lateral root, panicle branch, and grain meristems.

Overexpression of the chloroplastic 2-oxoglutarate/malate transporter disturbs carbon and nitrogen homeostasis in rice

The chloroplastic 2-oxaloacetate (OAA)/malate transporter (OMT1 or DiT1) takes part in the malate valve that protects chloroplasts from excessive redox poise through export of malate and import of OAA. Together with the glutamate/malate transporter (DCT1 or DiT2), it connects carbon with nitrogen assimilation, by providing 2-oxoglutarate for the GS/GOGAT (glutamine synthetase/glutamate synthase) reaction and exporting glutamate to the cytoplasm. OMT1 further plays a prominent role in C4 photosynthesis: OAA resulting from phosphoenolpyruvate carboxylation is imported into the chloroplast, reduced to malate by plastidic NADP-malate dehydrogenase, and then exported for transport to bundle sheath cells. Both transport steps are catalyzed by OMT1, at the rate of net carbon assimilation. To engineer C4 photosynthesis into C3 crops, OMT1 must be expressed in high amounts on top of core C4 metabolic enzymes. We report here high-level expression of ZmOMT1 from maize in rice (Oryza sativa ssp. indica IR64). Increased activity of the transporter in transgenic rice was confirmed by reconstitution of transporter activity into proteoliposomes. Unexpectedly, overexpression of ZmOMT1 in rice negatively affected growth, CO2 assimilation rate, total free amino acid content, tricarboxylic acid cycle metabolites, as well as sucrose and starch contents. Accumulation of high amounts of aspartate and the impaired growth phenotype of OMT1 rice lines could be suppressed by simultaneous overexpression of ZmDiT2. Implications for engineering C4 rice are discussed.

Using Interactome Big Data to Crack Genetic Mysteries and Enhance Future Crop Breeding

The functional genes underlying phenotypic variation and their interactions represent "genetic mysteries". Understanding and utilizing these genetic mysteries are key solutions for mitigating the current threats to agriculture posed by population growth and individual food preferences. Due to advances in high-throughput multi-omics technologies, we are stepping into an Interactome Big Data era that is certain to revolutionize genetic research. In this article, we provide a brief overview of current strategies to explore genetic mysteries. We then introduce the methods for constructing and analyzing the Interactome Big Data and summarize currently available interactome resources. Next, we discuss how Interactome Big Data can be used as a versatile tool to dissect genetic mysteries. We propose an integrated strategy that could revolutionize genetic research by combining Interactome Big Data with machine learning, which involves mining information hidden in Big Data to identify the genetic models or networks that control various traits, and also provide a detailed procedure for systematic dissection of genetic mysteries,. Finally, we discuss three promising future breeding strategies utilizing the Interactome Big Data to improve crop yields and quality.

The 21st Century Agriculture: When Rice Research Draws Attention to Climate Variability and How Weedy Rice and Underutilized Grains Come in Handy

Rice, the first crop to be fully sequenced and annotated in the mid-2000s, is an excellent model species for crop research due mainly to its relatively small genome and rich genetic diversity. The 130-million-year-old cereal came into the limelight in the 1960s when the semi-dwarfing gene sd-1, better known as the "green revolution" gene, resulted in the establishment of a high-yielding semi-dwarf variety IR8. Deemed as the miracle rice, IR8 saved millions of lives and revolutionized irrigated rice farming particularly in the tropics. The technology, however, spurred some unintended negative consequences, especially in prompting ubiquitous monoculture systems that increase agricultural vulnerability to extreme weather events and climate variability. One feasible way to incorporate resilience in modern rice varieties with narrow genetic backgrounds is by introgressing alleles from the germplasm of its weedy and wild relatives, or perhaps from the suitable underutilized species that harbor novel genes responsive to various biotic and abiotic stresses. This review reminisces the fascinating half-century journey of rice research and highlights the potential utilization of weedy rice and underutilized grains in modern breeding programs. Other possible alternatives to improve the sustainability of crop production systems in a changing climate are also discussed.

Engineering Improved Photosynthesis in the Era of Synthetic Biology

Much attention has been given to the enhancement of photosynthesis as a strategy for the optimization of crop productivity. As traditional plant breeding is most likely reaching a plateau, there is a timely need to accelerate improvements in photosynthetic efficiency by means of novel tools and biotechnological solutions. The emerging field of synthetic biology offers the potential for building completely novel pathways in predictable directions and, thus, addresses the global requirements for higher yields expected to occur in the 21st century. Here, we discuss recent advances and current challenges of engineering improved photosynthesis in the era of synthetic biology toward optimized utilization of solar energy and carbon sources to optimize the production of food, fiber, and fuel.

Photosynthetic Metabolism under Stressful Growth Conditions as a Bases for Crop Breeding and Yield Improvement

Increased periods of water shortage and higher temperatures, together with a reduction in nutrient availability, have been proposed as major factors that negatively impact plant development. Photosynthetic CO2 assimilation is the basis of crop production for animal and human food, and for this reason, it has been selected as a primary target for crop phenotyping/breeding studies. Within this context, knowledge of the mechanisms involved in the response and acclimation of photosynthetic CO2 assimilation to multiple changing environmental conditions (including nutrients, water availability, and rising temperature) is a matter of great concern for the understanding of plant behavior under stress conditions, and for the development of new strategies and tools for enhancing plant growth in the future. The current review aims to analyze, from a multi-perspective approach (ranging across breeding, gas exchange, genomics, etc.) the impact of changing environmental conditions on the performance of the photosynthetic apparatus and, consequently, plant growth.

Oxytree Pruned Biomass Torrefaction: Process Kinetics

Oxytree is a fast-growing energy crop with C4 photosynthesis. In this research, for the first time, the torrefaction kinetic parameters of pruned Oxytree biomass (Paulownia clon in Vitro 112) were determined. The influence of the Oxytree cultivation method and soil class on the kinetic parameters of the torrefaction was also investigated. Oxytree pruned biomass from a first-year plantation was subjected to torrefaction within temperature range from 200 to 300 °C and under anaerobic conditions in the laboratory-scale batch reactor. The mass loss was measured continuously during the process. The relative mass loss increased from 1.22% to 19.56% with the increase of the process temperature. The first-order constant rate reaction (k) values increased from 1.26 × 10⁻⁵ s⁻¹ to 7.69 × 10⁻⁵ s⁻¹ with the increase in temperature. The average activation energy for the pruned biomass of Oxytree torrefaction was 36.5 kJ∙mol⁻¹. Statistical analysis showed no significant (p < 0.05) effect of the Oxytree cultivation method and soil class on the k value. The results of this research could be useful for the valorization of energy crops such as Oxytree and optimization of waste-to-carbon and waste-to-energy processes.

Integration of sulfate assimilation with carbon and nitrogen metabolism in transition from C3 to C4 photosynthesis

The first product of sulfate assimilation in plants, cysteine, is a proteinogenic amino acid and a source of reduced sulfur for plant metabolism. Cysteine synthesis is the convergence point of the three major pathways of primary metabolism: carbon, nitrate, and sulfate assimilation. Despite the importance of metabolic and genetic coordination of these three pathways for nutrient balance in plants, the molecular mechanisms underlying this coordination, and the sensors and signals, are far from being understood. This is even more apparent in C4 plants, where coordination of these pathways for cysteine synthesis includes the additional challenge of differential spatial localization. Here we review the coordination of sulfate, nitrate, and carbon assimilation, and show how they are altered in C4 plants. We then summarize current knowledge of the mechanisms of coordination of these pathways. Finally, we identify urgent questions to be addressed in order to understand the integration of sulfate assimilation with carbon and nitrogen metabolism particularly in C4 plants. We consider answering these questions to be a prerequisite for successful engineering of C4 photosynthesis into C3 crops to increase their efficiency.

Redundant SCARECROW genes pattern distinct cell layers in roots and leaves of maize

The highly efficient C₄ photosynthetic pathway is facilitated by ‘Kranz’ leaf anatomy. In Kranz leaves, closely spaced veins are encircled by concentric layers of photosynthetic bundle sheath (inner) and mesophyll (outer) cells. Here, we demonstrate that, in the C₄ monocot maize, Kranz patterning is regulated by redundant function of SCARECROW 1 (ZmSCR1) and a previously uncharacterized homeologue: ZmSCR1h. ZmSCR1 and ZmSCR1h transcripts accumulate in ground meristem cells of developing leaf primordia and in Zmscr1;Zmscr1h mutant leaves, most veins are separated by one rather than two mesophyll cells; many veins have sclerenchyma above and/or below instead of mesophyll cells; and supernumerary bundle sheath cells develop. The mutant defects are unified by compromised mesophyll cell development. In addition to Kranz defects, Zmscr1;Zmscr1h mutants fail to form an organized endodermal layer in the root. Collectively, these data indicate that ZmSCR1 and ZmSCR1h redundantly regulate cell-type patterning in both the leaves and roots of maize. Leaf and root pathways are distinguished, however, by the cell layer in which they operate – mesophyll at a two-cell distance from leaf veins versus endodermis immediately adjacent to root vasculature.

Summary: Two duplicated maize SCARECROW genes control the development of the endodermis in roots and the mesophyll in leaves.

ZmbHLH80 and ZmbHLH90 transcription factors act antagonistically and contribute to regulate PEPC1 cell-specific gene expression in maize

Compartmentation of photosynthetic reactions between mesophyll and bundle sheath cells is a key feature of C₄ photosynthesis and depends on the cell-specific accumulation of major C₄ enzymes, such as phosphoenolpyruvate carboxylase 1. The ZmPEPC1 upstream region, which drives light-inducible and mesophyll-specific gene expression in maize, has been shown to keep the same properties when introduced into rice (C₃ plant), indicating that rice has the transcription factors (TFs) needed to confer C₄ -like gene expression. Using a yeast one-hybrid approach, we identified OsbHLH112, a rice basic Helix-Loop-Helix (bHLH) TF that interacts with the maize ZmPEPC1 upstream region. Moreover, we found that maize OsbHLH112 homologues, ZmbHLH80, and ZmbHLH90, also interact with the ZmPEPC1 upstream region, suggesting that these C₄ regulators were co-opted from C₃ plants. A transactivation assay in maize mesophyll protoplasts revealed that ZmbHLH80 represses, whereas ZmbHLH90 activates, ZmPEPC1 expression. In addition, ZmbHLH80 was shown to impair the ZmPEPC1 promoter activation caused by ZmbHLH90. We showed that ZmbHLH80 and ZmbHLH90 bind to the same cis-element within the ZmPEPC1 upstream region either as homodimers or heterodimers. The formation of homo- and heterodimers with higher oligomeric forms promoted by ZmbHLH80 may explain its negative effect on gene transcription. Gene expression analysis revealed that ZmbHLH80 is preferentially expressed in bundle sheath cells, whereas ZmbHLH90 does not show a clear cell-specific expression pattern. Altogether, our results led us to propose a model in which ZmbHLH80 contributes to mesophyll-specific ZmPEPC1 gene expression by impairing ZmbHLH90-mediated ZmPEPC1 activation in the bundle sheath cells.

Using natural variation to understand the evolutionary pressures on plant photosynthesis

Photosynthesis is the gateway of the Sun's energy into the biosphere and the source of the ozone layer; thus it is both provider and protector of life as we know it. Despite its pivotal role we know surprisingly little about the genetic basis of variation in photosynthesis and the selective pressures giving rise to or maintaining this variation. In this review, I will briefly summarise our current knowledge of intraspecific and interspecific variation in photosynthesis to understand the main selective constraints on photosynthesis and what this means for the future of nature and agriculture in a changing world.

Understanding the Genetic Basis of C4 Kranz Anatomy with a View to Engineering C3 Crops

One of the most remarkable examples of convergent evolution is the transition from C₃ to C₄ photosynthesis, an event that occurred on over 60 independent occasions. The evolution of C₄ is particularly noteworthy because of the complexity of the developmental and metabolic changes that took place. In most cases, compartmentalized metabolic reactions were facilitated by the development of a distinct leaf anatomy known as Kranz. C₄ Kranz anatomy differs from ancestral C₃ anatomy with respect to vein spacing patterns across the leaf, cell-type specification around veins, and cell-specific organelle function. Here we review our current understanding of how Kranz anatomy evolved and how it develops, with a focus on studies that are dissecting the underlying genetic mechanisms. This research field has gained prominence in recent years because understanding the genetic regulation of Kranz may enable the C₃-to-C₄ transition to be engineered, an endeavor that would significantly enhance crop productivity.

Characterization of maize leaf pyruvate orthophosphate dikinase using high throughput sequencing

In C₄ photosynthesis, pyruvate orthophosphate dikinase (PPDK) catalyzes the regeneration of phosphoenolpyruvate in the carbon shuttle pathway. Although the biochemical function of PPDK in maize is well characterized, a genetic analysis of PPDK has not been reported. In this study, we use the maize transposable elements Mutator and Ds to generate multiple mutant alleles of PPDK. Loss-of-function mutants are seedling lethal, even when plants were grown under 2% CO₂ , and they show very low capacity for CO₂ assimilation, indicating C₄ photosynthesis is essential in maize. Using RNA-seq and GC-MS technologies, we examined the transcriptional and metabolic responses to a deficiency in PPDK activity. These results indicate loss of PPDK results in downregulation of gene expression of enzymes of the C₄ cycle, the Calvin cycle, and components of photochemistry. Furthermore, the loss of PPDK did not change Kranz anatomy, indicating that this metabolic defect in the C₄ cycle did not impinge on the morphological differentiation of C₄ characters. However, sugar metabolism and nitrogen utilization were altered in the mutants. An interaction between light intensity and genotype was also detected from transcriptome profiling, suggesting altered transcriptional and metabolic responses to environmental and endogenous signals in the PPDK mutants.

Genome-Wide Identification and Analysis of Biotic and Abiotic Stress Regulation of C4 Photosynthetic Pathway Genes in Rice

Photosynthetic fixation of CO₂ is more efficient in C₄ than in C₃ plants. Rice is a C₃ plant and a potential target for genetic engineering of the C₄ pathway. It is known that genes encoding C₄ enzymes are present in C₃ plants. However, no systematic analysis has been conducted to determine if these C₄ gene family members are expressed in diverse rice genotypes. In this study, we identified 15 genes belonging to the five C₄ gene families in rice genome through BLAST search using known maize C₄ photosynthetic pathway genes. Phylogenetic relationship of rice C₄ photosynthetic pathway genes and their isoforms with other grass genomes (Brachypodium, maize, Sorghum and Setaria), showed that these genes were highly conserved across grass genomes. Spatiotemporal, hormone, and abiotic stress specific expression pattern of the identified genes revealed constitutive as well as inductive responses of the C₄ photosynthetic pathway in different tissues and developmental stages of rice. Expression levels of C₄ specific gene family members in flag leaf during tillering stage were quantitatively analyzed in five rice genotypes covering three species, viz. Oryza sativa, ssp. japonica (cv. Nipponbare), Oryza sativa, ssp. indica (cv IR64, Swarna), and two wild species Oryza barthii and Oryza australiensis. The results showed that all the identified genes expressed in rice and exhibited differential expression pattern during different growth stages, and in response to biotic and abiotic stress conditions and hormone treatments. Our study concludes that C₄ photosynthetic pathway genes present in rice play a crucial role in stress regulation and might act as targets for C₄ pathway engineering via CRISPR-mediated breeding.

Engineering photosynthesis: progress and perspectives

Photosynthesis is the basis of primary productivity on the planet. Crop breeding has sustained steady improvements in yield to keep pace with population growth increases. Yet these advances have not resulted from improving the photosynthetic process per se but rather of altering the way carbon is partitioned within the plant. Mounting evidence suggests that the rate at which crop yields can be boosted by traditional plant breeding approaches is wavering, and they may reach a “yield ceiling” in the foreseeable future. Further increases in yield will likely depend on the targeted manipulation of plant metabolism. Improving photosynthesis poses one such route, with simulations indicating it could have a significant transformative influence on enhancing crop productivity. Here, we summarize recent advances of alternative approaches for the manipulation and enhancement of photosynthesis and their possible application for crop improvement.

Elevated auxin biosynthesis and transport underlie high vein density in C4 leaves

High vein density, a distinctive trait of C4 leaves, is central to both C3-to-C4 evolution and conversion of C3 to C4-like crops. We tested the hypothesis that high vein density in C4 leaves is due to elevated auxin biosynthesis and transport in developing leaves. Up-regulation of genes in auxin biosynthesis pathways and higher auxin content were found in developing C4 leaves compared with developing C3 leaves. The same observation held for maize foliar (C4) and husk (C3) leaf primordia. Moreover, auxin content and vein density were increased in loss-of-function mutants of Arabidopsis MYC2, a suppressor of auxin biosynthesis. Treatment with an auxin biosynthesis inhibitor or an auxin transport inhibitor led to much fewer veins in new leaves. Finally, both Arabidopsis thaliana auxin efflux transporter pin1 and influx transporter lax2 mutants showed reduced vein numbers. Thus, development of high leaf vein density requires elevated auxin biosynthesis and transport.

Photorespiration and the potential to improve photosynthesis

The photorespiratory pathway, in short photorespiration, is an essential metabolite repair pathway that allows the photosynthetic CO₂ fixation of plants to occur in the presence of oxygen. It is necessary because oxygen is a competing substrate of the CO₂-fixing enzyme ribulose 1,5-bisphosphate carboxylase, forming 2-phosphoglycolate that negatively interferes with photosynthesis. Photorespiration very efficiently recycles 2-phosphoglycolate into 3-phosphoglycerate, which re-enters the Calvin-Benson cycle to drive sustainable photosynthesis. Photorespiration however requires extra energy and re-oxidises one quarter of the 2-phosphoglycolate carbon to CO₂, lowering potential maximum rates of photosynthesis in most plants including food and energy crops. This review discusses natural and artificial strategies to reduce the undesired impact of air oxygen on photosynthesis and in turn plant growth.