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

Physiological and molecular responses of poplar to salt stress and functional analysis of PagGRXC9 to salt tolerance

Soil salinization is increasingly recognized as a critical environmental challenge that significantly threatens plant survival and agricultural productivity. To elucidate the mechanism of salt resistance in poplar, physiological and transcriptomic analyses were conducted on 84K poplar (Populus alba × Populus glandulosa) under varying salt concentrations (0, 100, 200 and 300 mM NaCl). As salt levels increased, observable damage to poplar progressively intensified. Differentially expressed genes under salt stress were primarily enriched in photosynthesis, redox activity and glutathione metabolism pathways. Salt stress reduced chlorophyll content and net photosynthetic rate, accompanied by the downregulation of photosynthesis-related genes. NaCl (300 mM) significantly inhibited the photochemical activity of photosystems. The higher photochemical activity under 100 and 200 mM NaCl was attributed to the activated PGR5-cyclic electron flow photoprotective mechanism. However, the NAD(P)H dehydrogenase-like (NDH)-cyclic electron flow was inhibited under all salt levels. Salt stress led to reactive oxygen species accumulation, activating the ASA-GSH cycle and antioxidant enzymes to mitigate oxidative damage. Weighted gene co-expression network analysis showed that five photosynthesis-related hub genes (e.g., FNR and TPI) were down-regulated and nine antioxidant-related hub genes (e.g., GRX, GPX and GST) were up-regulated under salt stress conditions. PagGRXC9 encodes glutaredoxin and was found to be differentially expressed during the salt stress condition. Functional studies showed that overexpressing PagGRXC9 enhanced salt tolerance in yeast, and in poplar, it improved growth, FV/FM, non-photochemical quenching values and resistance to H2O2-induced oxidative stress under salt stress. This study constructed the photosynthetic and antioxidant response network for salt stress in poplar, revealing that PagGRXC9 enhances salt tolerance by reducing photoinhibition and increasing antioxidant capacity. These findings provide valuable insights for breeding salt-tolerant forest trees.

CsABF8 mediates drought-induced ABA signaling in the regulation of raffinose biosynthesis in Camellia sinensis leaves

Drought has become an important environmental stress limiting the growth and development of Camellia sinensis due to its moisture-loving and temperature-tolerant nature. ABA-response element binding factor (ABFs) is a key transcriptional regulator in the ABA signaling pathway that regulates plant responses to hormones and adversity. However, their roles and regulatory mechanisms in tea tree remain unknown. To investigate the drought response in Camellia sinensis, drought-sensitive (Fuyun No.6, FY) and drought-tolerant (Taicha No.12, TC) tea cultivars were treated with exogenous PEG and ABA and subjected to non-targeted metabolomics by Ultra Performance Liquid Chromatography-Electrospray Ionization-Triple Quadrupole tandem Mass Spectrometry (UPLC/ESI-Q TRAP-MS/MS). The bioactive carbohydrates galactinol and raffinose were identified as potential drought regulators. Analysis of transcriptomics data identified potential drought tolerant target genes, namely CsGolS1/2, encoding galactinol synthases, CsRaf6, a raffinose synthase, and CsABF8, a transcriptional regulator in the ABA-response element binding factor family. The tea CsSnRK2.8-CsABF8-CsGolS1/CsGolS2/CsRaf6 regulatory module induced in response to drought stress was constructed using multiple molecular validation tools. This preliminary analysis of the molecular mechanism by which CsABF8, a regulator on the ABA signaling pathway, mediates the differences in drought tolerance in different tea cultivars provides a theoretical basis for the selection and breeding of drought-resistant varieties.

A Zea genus-specific micropeptide controls kernel dehydration in maize

Kernel dehydration rate (KDR) is a crucial production trait that affects mechanized harvesting and kernel quality in maize; however, the underlying mechanisms remain unclear. Here, we identified a quantitative trait locus (QTL), qKDR1, as a non-coding sequence that regulates the expression of qKDR1 REGULATED PEPTIDE GENE (RPG). RPG encodes a 31 amino acid micropeptide, microRPG1, which controls KDR by precisely modulating the expression of two genes, ZmETHYLENE-INSENSITIVE3-like 1 and 3, in the ethylene signaling pathway in the kernels after filling. microRPG1 is a Zea genus-specific micropeptide and originated de novo from a non-coding sequence. Knockouts of microRPG1 result in faster KDR in maize. By contrast, overexpression or exogenous application of the micropeptide shows the opposite effect both in maize and Arabidopsis. Our findings reveal the molecular mechanism of microRPG1 in kernel dehydration and provide an important tool for future crop breeding.

Methane-derived microbial biostimulant reduces greenhouse gas emissions and improves rice yield

Introduction

More than half of the world's population consumes rice as their primary food. The majority of rice production is concentrated in Asia, with the top 10 rice-growing countries accounting for 84% of the world's total rice cultivation. However, rice production is also strongly linked to environmental changes. Among all the global sources of greenhouse gas (GHG) emissions, paddy cultivation stands out as a significant contributor to global methane (CH4) and nitrous oxide (N2O) emissions. This contribution is expected to increase further with the projected increase of 28% in global rice output by 2050. Hence, modifications to rice management practices are necessary both to increase yield and mitigate GHG emissions.

Methods

We investigated the effect of seedling treatment, soil application, and foliar application of a methane-derived microbial biostimulant on grain yield and GHG emissions from rice fields over three seasons under 100% fertilizer conditions. Further, microbial biostimulant was also tested under 75% nitrogen (N) levels to demonstrate its effect on grain yield. To understand the mechanism of action of microbial biostimulant on crop physiology and yield, a series of physiological, transcript, and metabolite analyses were also performed.

Results

Our three-season open-field studies demonstrated a significant enhancement of grain yield, up to 39%, with a simultaneous reduction in CH4 (31%-60%) and N2O (34%-50%) emissions with the use of methane-derived microbial biostimulant. Under 75% N levels, a 34% increase in grain yield was observed with microbial biostimulant application. Based on the physiological, transcript, and metabolite analyses data, we were further able to outline the potential mechanisms for the diverse synergistic effects of methane-derived microbial biostimulant on paddy, including indole-3-acetic acid production, modulation of photosynthesis, tillering, and panicle development, ultimately translating to superior yield.

Conclusion

The reduction in GHG emission and enhanced yield observed under both recommended and reduced N conditions demonstrated that the methane-derived biostimulant can play a unique and necessary role in the paddy ecosystem. The consistent improvements seen across different field trials established that the methane-derived microbial biostimulant could be a scalable solution to intensify rice productivity with a lower GHG footprint, thus creating a win-win-win solution for farmers, customers, and the environment.

Strategies for adaptation to high light in plants

Plants absorb light energy for photosynthesis via photosystem complexes in their chloroplasts. However, excess light can damage the photosystems and decrease photosynthetic output, thereby inhibiting plant growth and development. Plants have developed a series of light acclimation strategies that allow them to withstand high light. In the first line of defense against excess light, leaves and chloroplasts move away from the light and the plant accumulates compounds that filter and reflect the light. In the second line of defense, known as photoprotection, plants dissipate excess light energy through non-photochemical quenching, cyclic electron transport, photorespiration, and scavenging of excess reactive oxygen species. In the third line of defense, which occurs after photodamage, plants initiate a cycle of photosystem (mainly photosystem II) repair. In addition to being the site of photosynthesis, chloroplasts sense stress, especially light stress, and transduce the stress signal to the nucleus, where it modulates the expression of genes involved in the stress response. In this review, we discuss current progress in our understanding of the strategies and mechanisms employed by plants to withstand high light at the whole-plant, cellular, physiological, and molecular levels across the three lines of defense.

Physiological and Molecular Mechanisms of Rice Tolerance to Salt and Drought Stress: Advances and Future Directions

Rice, a globally important food crop, faces significant challenges due to salt and drought stress. These abiotic stresses severely impact rice growth and yield, manifesting as reduced plant height, decreased tillering, reduced biomass, and poor leaf development. Recent advances in molecular biology and genomics have uncovered key physiological and molecular mechanisms that rice employs to cope with these stresses, including osmotic regulation, ion balance, antioxidant responses, signal transduction, and gene expression regulation. Transcription factors such as DREB, NAC, and bZIP, as well as plant hormones like ABA and GA, have been identified as crucial regulators. Utilizing CRISPR/Cas9 technology for gene editing holds promise for significantly enhancing rice stress tolerance. Future research should integrate multi-omics approaches and smart agriculture technologies to develop rice varieties with enhanced stress resistance, ensuring food security and sustainable agriculture in the face of global environmental changes.

OsBBP1, a newly identified protein containing DUF630 and DUF632 domains confers drought tolerance in rice

Domain of unknown function (DUF) protein families, which are uncharacterized and numerous within the Pfam database. Recently, studies have demonstrated that DUFs played crucial roles in plant development, but whether, or how, they function in drought resistance remain unclear. In this study, we identified the Os03g0321500 gene, encoding OsbZIP72 binding protein 1 (OsBBP1), as a target of OsbZIP72 using chromatin immunoprecipitation sequencing in rice. OsBBP1 is a novel member of DUFs, which localize both in the nuclei and cytoplasm of rice protoplasts. Furthermore, yeast one-hybrid and electrophoretic mobility shift assays confirmed the specific binding between OsbZIP72 and OsBBP1. Additionally, a luciferase reporter analysis illustrated that OsbZIP72 activated the expression of OsBBP1. Drought tolerance experiments demonstrate that the OsBBP1 CRISPER-CAS9 transgenic mutants were sensitive to drought stress, but the transgenic OsBBP1 over-expressing rice plants showed enhanced drought resistance. Moreover, drought tolerance experiments in a paddy field suggested that OsBBP1 contributed to less yield or yield-related losses under drought conditions. Mechanistically, OsBBP1 might confer drought resistance by inducing more efficient reactive oxygen species (ROS) scavenging. Several ROS scavenging-related genes showed increased expression levels in OsBBP1 overexpression lines and decreased expression levels in OsBBP1 CRISPER-CAS9 mutants under drought conditions. Thus, OsBBP1, acting downstream of OsbZIP72, contributes to drought resistance and causes less yield or yield-related losses under drought conditions.

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

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

The role of priming and memory in rice environmental stress adaptation: Current knowledge and perspectives

Plant responses to abiotic stresses are dynamic, following the unpredictable changes of physical environmental parameters such as temperature, water and nutrients. Physiological and phenotypical responses to stress are intercalated by periods of recovery. An earlier stress can be remembered as 'stress memory' to mount a response within a generation or transgenerationally. The 'stress priming' phenomenon allows plants to respond quickly and more robustly to stressors to increase survival, and therefore has significant implications for agriculture. Although evidence for stress memory in various plant species is accumulating, understanding of the mechanisms implicated, especially for crops of agricultural interest, is in its infancy. Rice is a major food crop which is susceptible to abiotic stresses causing constraints on its cultivation and yield globally. Advancing the understanding of the stress response network will thus have a significant impact on rice sustainable production and global food security in the face of climate change. Therefore, this review highlights the effects of priming on rice abiotic stress tolerance and focuses on specific aspects of stress memory, its perpetuation and its regulation at epigenetic, transcriptional, metabolic as well as physiological levels. The open questions and future directions in this exciting research field are also laid out.

Physiological and transcriptomic analysis of OsLHCB3 knockdown lines in rice

The photosystem II (PSII) outer antenna LHCB3 protein plays critical roles in distributing the excitation energy and modulating the rate of state transition for photosynthesis. Here, OsLHCB3 knockdown mutants were produced using the RNAi system. Phenotypic analyses showed that OsLHCB3 knockdown led to pale green leaves and lower chlorophyll contents at both tillering and heading stages. In addition, mutant lines exhibited decreased non-photochemical quenching (NPQ) capacity and net photosynthetic rate (Pn) by downregulating the expression of PSII-related genes. Moreover, RNA-seq experiments were performed at both tillering and heading stages. The differentially expressed genes (DEGs) mainly involved in chlorophyll binding response to abscisic acid, photosystem II, response to chitin, and DNA-binding transcription factor. Besides, our transcriptomic and physiological data indicated that OsLHCB3 was essential for binding chlorophyll, but not for the metabolism of chlorophyll in rice. OsLHCB3 RNAi knockdown plants affected the expression of PS II-related genes, but not PS I-related genes. Overall, these results suggest that OsLHCB3 also plays vital roles in regulating photosynthesis and antenna proteins in rice as well as responses to environment stresses.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01387-z.

Water acidification weakens the carbon sink capacity of mixotrophic organisms

Mixotrophs combine both autotrophic and heterotrophic cell structures, and their highly plastic nutritional modes can shape the structure of food web and affect the carbon sink capacity of aquatic ecosystems. As pH affects the growth of phytoplankton by altering the carbonate balance system, water acidification caused by environmental pollution and global climate change may affect the nutritional modes of mixotrophs and bring a serious environmental consequence. In this study, we cultured mixotrophic Ochromonas gloeopara under autotrophic, mixotrophic, and heterotrophic conditions at different pH levels to test the tendency of its nutritional model and the changes in photosynthetic carbon fixation capacity. Results showed that: (1) with decreasing pH, carbon uptake of Ochromonas through phagocytosis gradually replaced the carbon fixation of photosynthesis; (2) with increasing pH, Ochromonas grazing rate decreased, and the relative contribution of photosynthetic carbon fixation to total carbon acquisition increased for Ochromonas; (3) Ochromonas became more heterotrophic under water acidification, which was involved in the up-regulated expression of genes encoding key enzymes that regulate nutrient perception, movement ability, and cell repair. These findings suggested that acidification caused mixotrophic organisms to become more heterotrophic, which can change their functional role and weaken their carbon sink capacity.

eQTLs play critical roles in regulating gene expression and identifying key regulators in rice

The regulation of gene expression plays an essential role in both the phenotype and adaptation of plants. Transcriptome sequencing enables simultaneous identification of exonic variants and quantification of gene expression. Here, we sequenced the leaf transcriptomes of 287 rice accessions from around the world and obtained a total of 177 853 high-quality single nucleotide polymorphisms after filtering. Genome-wide association study identified 44 354 expression quantitative trait loci (eQTLs), which regulate the expression of 13 201 genes, as well as 17 local eQTL hotspots and 96 distant eQTL hotspots. Furthermore, a transcriptome-wide association study screened 21 candidate genes for starch content in the flag leaves at the heading stage. HS002 was identified as a significant distant eQTL hotspot with five downstream genes enriched for diterpene antitoxin synthesis. Co-expression analysis, eQTL analysis, and linkage mapping together demonstrated that bHLH026 acts as a key regulator to activate the expression of downstream genes. The transgenic assay revealed that bHLH026 is an important regulator of diterpenoid antitoxin synthesis and enhances the disease resistance of rice. These findings improve our knowledge of the regulatory mechanisms of gene expression variation and complex regulatory networks of the rice genome and will facilitate genetic improvement of cultivated rice varieties.

miR2105 and the kinase OsSAPK10 co-regulate OsbZIP86 to mediate drought-induced ABA biosynthesis in rice

Mediating induced abscisic acid (ABA) biosynthesis is important for enhancing plant stress tolerance. Here, we found that rice (Oryza sativa L.) osa-miR2105 (miR2105) and the Stress/ABA-activated protein kinase (OsSAPK10) coordinately regulate the rice basic region-leucine zipper transcription factor (bZIP TF; OsbZIP86) at the posttranscriptional and posttranslational levels to control drought-induced ABA biosynthesis via modulation of rice 9-cis-epoxycarotenoid dioxygenase (OsNCED3) expression. OsbZIP86 expression is regulated by miR2105-directed cleavage of the OsbZIP86 mRNA. OsbZIP86 encodes a nuclear TF that binds to the promoter of the ABA biosynthetic gene OsNCED3. OsSAPK10 can phosphorylate and activate OsbZIP86 to enhance the expression of OsNCED3. Under normal growth conditions, altered expression of miR2105 and OsbZIP86 displayed no substantial effect on rice growth. However, under drought conditions, miR2105 knockdown or OsbZIP86 overexpression transgenic rice plants showed higher ABA content, enhanced tolerance to drought, lower rates of water loss, and more stomatal closure of seedlings, compared with wild-type rice Zhonghua 11; in contrast, miR2105 overexpression, OsbZIP86 downregulation, and OsbZIP86 knockout plants displayed opposite phenotypes. Collectively, our results show that the "miR2105-(OsSAPK10)-OsbZIP86-OsNCED3" module regulates the drought-induced ABA biosynthesis without penalty on rice growth under normal conditions, suggesting candidates for improving drought tolerance in rice.

H3K36 demethylase JMJ710 negatively regulates drought tolerance by suppressing MYB48-1 expression in rice

The homeostasis of histone methylation is maintained by histone methyltransferases and demethylases, which are important for the regulation of gene expression. Here, we report a histone demethylase from rice (Oryza sativa), Jumonji C domain-containing protein (JMJ710), which belongs to the JMJD6 group and plays an important role in the response to drought stress. Overexpression of JMJ710 causes a drought-sensitive phenotype, while RNAi and clustered regularly interspaced short palindromic repeats (CRISPR)-knockout mutant lines show drought tolerance. In vitro and in vivo assays showed that JMJ710 is a histone demethylase. It targets to MYB TRANSCRIPTION FACTOR 48 (MYB48-1) chromatin, demethylates H3K36me2, and negatively regulates the expression of MYB48-1, a positive regulator of drought tolerance. Under drought stress, JMJ710 is downregulated and the expression of MYB48-1 increases, and the subsequent activation of its downstream drought-responsive genes leads to drought tolerance. This research reports a negative regulator of drought stress-responsive genes, JMJ710, that ensures that the drought tolerance mechanism is not mis-activated under normal conditions but allows quick activation upon drought stress.

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

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

Light Deficiency Inhibits Growth by Affecting Photosynthesis Efficiency as well as JA and Ethylene Signaling in Endangered Plant Magnolia sinostellata

The endangered plant Magnolia sinostellata largely grows in the understory of forest and suffers light deficiency stress. It is generally recognized that the interaction between plant development and growth environment is intricate; however, the underlying molecular regulatory pathways by which light deficiency induced growth inhibition remain obscure. To understand the physiological and molecular mechanisms of plant response to shading caused light deficiency, we performed photosynthesis efficiency analysis and comparative transcriptome analysis in M. sinostellata leaves, which were subjected to shading treatments of different durations. Most of the parameters relevant to the photosynthesis systems were altered as the result of light deficiency treatment, which was also confirmed by the transcriptome analysis. Gene Ontology and KEGG pathway enrichment analyses illustrated that most of differential expression genes (DEGs) were enriched in photosynthesis-related pathways. Light deficiency may have accelerated leaf abscission by impacting the photosynthesis efficiency and hormone signaling. Further, shading could repress the expression of stress responsive transcription factors and R-genes, which confer disease resistance. This study provides valuable insight into light deficiency-induced molecular regulatory pathways in M. sinostellata and offers a theoretical basis for conservation and cultivation improvements of Magnolia and other endangered woody plants.

Rapid Hormetic Responses of Photosystem II Photochemistry of Clary Sage to Cadmium Exposure

Five-day exposure of clary sage (Salvia sclarea L.) to 100 μM cadmium (Cd) in hydroponics was sufficient to increase Cd concentrations significantly in roots and aboveground parts and affect negatively whole plant levels of calcium (Ca) and magnesium (Mg), since Cd competes for Ca channels, while reduced Mg concentrations are associated with increased Cd tolerance. Total zinc (Zn), copper (Cu), and iron (Fe) uptake increased but their translocation to the aboveground parts decreased. Despite the substantial levels of Cd in leaves, without any observed defects on chloroplast ultrastructure, an enhanced photosystem II (PSII) efficiency was observed, with a higher fraction of absorbed light energy to be directed to photochemistry (ΦPSΙΙ). The concomitant increase in the photoprotective mechanism of non-photochemical quenching of photosynthesis (NPQ) resulted in an important decrease in the dissipated non-regulated energy (ΦNO), modifying the homeostasis of reactive oxygen species (ROS), through a decreased singlet oxygen (1O2) formation. A basal ROS level was detected in control plant leaves for optimal growth, while a low increased level of ROS under 5 days Cd exposure seemed to be beneficial for triggering defense responses, and a high level of ROS out of the boundaries (8 days Cd exposure), was harmful to plants. Thus, when clary sage was exposed to Cd for a short period, tolerance mechanisms were triggered. However, exposure to a combination of Cd and high light or to Cd alone (8 days) resulted in an inhibition of PSII functionality, indicating Cd toxicity. Thus, the rapid activation of PSII functionality at short time exposure and the inhibition at longer duration suggests a hormetic response and describes these effects in terms of "adaptive response" and "toxicity", respectively.