GID1 modulates stomatal response and submergence tolerance involving abscisic acid and gibberellic acid signaling in rice

Mitigating growth-stress tradeoffs via elevated TOR signaling in rice

Rice production accounts for approximately half of the freshwater resources utilized in agriculture, resulting in greenhouse gas emissions such as methane (CH4) from flooded paddy fields. To address this challenge, environmentally friendly and cost-effective water-saving techniques have become widely adopted in rice cultivation. However, the implementation of water-saving treatments (WSTs) in paddy-field rice has been associated with a substantial yield loss of up to 50% as well as a reduction in nitrogen use efficiency (NUE). In this study, we discovered that the target of rapamycin (TOR) signaling pathway is compromised in rice under WST. Polysome profiling-coupled transcriptome sequencing (polysome-seq) analysis unveiled a substantial reduction in global translation in response to WST associated with the downregulation of TOR activity. Molecular, biochemical, and genetic analyses revealed new insights into the impact of the positive TOR-S6K-RPS6 and negative TOR-MAF1 modules on translation repression under WST. Intriguingly, ammonium exhibited a greater ability to alleviate growth constraints under WST by enhancing TOR signaling, which simultaneously promoted uptake and utilization of ammonium and nitrogen allocation. We further demonstrated that TOR modulates the ammonium transporter AMT1;1 as well as the amino acid permease APP1 and dipeptide transporter NPF7.3 at the translational level through the 5' untranslated region. Collectively, these findings reveal that enhancing TOR signaling could mitigate rice yield penalty due to WST by regulating the processes involved in protein synthesis and NUE. Our study will contribute to the breeding of new rice varieties with increased water and fertilizer utilization efficiency.

The JASMONATE ZIM-domain-OPEN STOMATA1 cascade integrates jasmonic acid and abscisic acid signaling to regulate drought tolerance by mediating stomatal closure in poplar

Drought, which directly affects the yield of crops and trees, is a natural stress with a profound impact on the economy. Improving water use efficiency (WUE) and drought tolerance are relatively effective strategies to alleviate drought stress. OPEN STOMATA1 (OST1), at the core of abscisic acid (ABA) signaling, can improve WUE by regulating stomatal closure and photosynthesis. Methyl jasmonate (MeJA) and ABA crosstalk is considered to be involved in the response to drought stress, but the detailed molecular mechanism is insufficiently known. Here, Populus euphratica, which naturally grows in arid and semiarid regions, was selected as the species for studying MeJA and ABA crosstalk under drought. A yeast two-hybrid assay was performed using PeOST1 as bait and a nucleus-localized factor, JASMONATE ZIM-domain protein 2 (PeJAZ2), was found to participate in MeJA signaling by interacting with PeOST1. Overexpression of PeJAZ2 in poplar notably increased water deficit tolerance and WUE in both severe and mild drought stress by regulating ABA signaling rather than ABA synthesis. Furthermore, a PeJAZ2 overexpression line was shown to have greater ABA-induced stomatal closure and hydrogen peroxide (H2O2) production. Collectively, this evidence establishes a mechanism in which PeJAZ2 acts as a positive regulator in response to drought stress via ABA-induced stomatal closure caused by H2O2 production. Our study presents a new insight into the crosstalk of ABA and jasmonic acid signaling in regulating WUE and drought stress, providing a basis of the drought tolerance mechanism of P. euphratica.

ZmLBD5, a class-II LBD gene, negatively regulates drought tolerance by impairing abscisic acid synthesis

Lateral organ boundaries domain (LBD) proteins are plant-specific transcription factors. Class-I LBD genes have been widely demonstrated to play pivotal roles in organ development; however, knowledge on class-II genes remains limited. Here, we report that ZmLBD5, a class-II LBD gene, is involved in the regulation of maize (Zea mays) growth and the drought response by affecting gibberellin (GA) and abscisic acid (ABA) synthesis. ZmLBD5 is mainly involved in regulation of the TPS-KS-GA2ox gene module, which is comprised of key enzyme-encoding genes involved in GA and ABA biosynthesis. ABA insufficiency increases stomatal density and aperture in overexpression plants and causes a drought-sensitive phenotype by promoting water transpiration. Increased GA₁ levels promotes seedling growth in overexpression plants. Accordingly, CRISPR/Cas9 knockout lbd5 seedlings are dwarf but drought-tolerant. Moreover, lbd5 has a higher grain yield under drought stress conditions and shows no penalty in well-watered conditions compared to the wild type. On the whole, ZmLBD5 is a negative regulator of maize drought tolerance, and it is a potentially useful target for drought resistance breeding.

Proteomic and Biochemical Approaches Elucidate the Role of Millimeter-Wave Irradiation in Wheat Growth under Flooding Stress

Flooding impairs wheat growth and considerably affects yield productivity worldwide. On the other hand, irradiation with millimeter waves enhanced the growth of chickpea and soybean under flooding stress. In the current work, millimeter-wave irradiation notably enhanced wheat growth, even under flooding stress. To explore the protective mechanisms of millimeter-wave irradiation on wheat under flooding, quantitative proteomics was performed. According to functional categorization, proteins whose abundances were changed significantly with and without irradiation under flooding stress were correlated to glycolysis, reactive-oxygen species scavenging, cell organization, and hormonal metabolism. Immunoblot analysis confirmed that fructose-bisphosphate aldolase and β tubulin accumulated in root and leaf under flooding; however, even in such condition, their accumulations were recovered to the control level in irradiated wheat. The abundance of ascorbate peroxidase increased in leaf under flooding and recovered to the control level in irradiated wheat. Because the abundance of auxin-related proteins changed with millimeter-wave irradiation, auxin was applied to wheat under flooding, resulting in the application of auxin improving its growth, even in such condition. These results suggest that millimeter-wave irradiation on wheat seeds improves the recovery of plant growth from flooding via the regulation of glycolysis, reactive-oxygen species scavenging, and cell organization. Additionally, millimeter-wave irradiation could promote tolerance against flooding through the regulation of auxin contents in wheat.

Integrated Transcriptomic and Proteomic Analyses Uncover the Regulatory Mechanisms of Myricaria laxiflora Under Flooding Stress

Flooding is one of the major environmental stresses that severely influence plant survival and development. However, the regulatory mechanisms underlying flooding stress remain largely unknown in Myricaria laxiflora, an endangered plant mainly distributed in the flood zone of the Yangtze River, China. In this work, transcriptome and proteome were performed in parallel in roots of M. laxiflora during nine time-points under the flooding and post-flooding recovery treatments. Overall, highly dynamic and stage-specific expression profiles of genes/proteins were observed during flooding and post-flooding recovery treatment. Genes related to auxin, cell wall, calcium signaling, and MAP kinase signaling were greatly down-regulated exclusively at the transcriptomic level during the early stages of flooding. Glycolysis and major CHO metabolism genes, which were regulated at the transcriptomic and/or proteomic levels with low expression correlations, mainly functioned during the late stages of flooding. Genes involved in reactive oxygen species (ROS) scavenging, mitochondrial metabolism, and development were also regulated exclusively at the transcriptomic level, but their expression levels were highly up-regulated upon post-flooding recovery. Moreover, the comprehensive expression profiles of genes/proteins related to redox, hormones, and transcriptional factors were also investigated. Finally, the regulatory networks of M. laxiflora in response to flooding and post-flooding recovery were discussed. The findings deepen our understanding of the molecular mechanisms of flooding stress and shed light on the genes and pathways for the preservation of M. laxiflora and other endangered plants in the flood zone.

Identification of the Regulators of Epidermis Development under Drought- and Salt-Stressed Conditions by Single-Cell RNA-Seq

As sessile organisms, plants constantly face challenges from the external environment. In order to meet these challenges and survive, plants have evolved a set of sophisticated adaptation strategies, including changes in leaf morphology and epidermal cell development. These developmental patterns are regulated by both light and hormonal signaling pathways. However, our mechanistic understanding of the role of these signaling pathways in regulating plant response to environmental stress is still very limited. By applying single-cell RNA-Seq, we determined the expression pattern of PHYTOCHROME INTERACTING FACTOR (PIF) 1, PIF3, PIF4, and PIF5 genes in leaf epidermal pavement cells (PCs) and guard cells (GCs). PCs and GCs are very sensitive to environmental stress, and our previous research suggests that these PIFs may be involved in regulating the development of PCs, GCs, and leaf morphology under environmental stress. Growth analysis showed that pif1/3/4/5 quadruple mutant maintained tolerance to drought and salt stress, and the length to width ratio of leaves and petiole length under normal growth conditions were similar to those of wild-type (WT) plants under drought and salt treatment. Analysis of the developmental patterns of PCs and GCs, and whole leaf morphology, further confirmed that these PIFs may be involved in mediating the development of epidermal cells under drought and salt stress, likely by regulating the expression of MUTE and TOO MANY MOUTHS (TMM) genes. These results provide new insights into the molecular mechanism of plant adaptation to adverse growth environments.

De novo transcriptome sequencing, assembly, and gene expression profiling of a salt-stressed halophyte (Salsola drummondii) from a saline habitat

Salsola drummondii is a perennial habitat-indifferent halophyte growing in saline and nonsaline habitats of the Arabian hyperarid deserts. It offers an invaluable opportunity to examine the molecular mechanisms of salt tolerance. The present study was conducted to elucidate these mechanisms through transcriptome profiling of seedlings grown from seeds collected in a saline habitat. The Illumina Hiseq 2500 platform was employed to sequence cDNA libraries prepared from shoots and roots of nonsaline-treated plants (controls) and plants treated with 1200 mM NaCl. Transcriptomic comparison between salt-treated and control samples resulted in 17,363 differentially expressed genes (DEGs), including 12,000 upregulated genes (7870 in roots, 4130 in shoots) and 5363 downregulated genes (4258 in roots and 1105 in shoots). The majority of identified DEGs are known to be involved in transcription regulation (79), signal transduction (82), defense metabolism (101), transportation (410), cell wall metabolism (27), regulatory processes (392), respiration (85), chaperoning (9), and ubiquitination (98) during salt tolerance. This study identified potential genes associated with the salt tolerance of S. drummondii and demonstrated that this tolerance may depend on the induction of certain genes in shoot and root tissues. These gene expressions were validated using reverse-transcription quantitative PCR, the results of which were consistent with transcriptomics results. To the best of our knowledge, this is the first study providing genetic information on salt tolerance mechanisms in S. drummondii.

Plant Morphological, Physiological and Anatomical Adaption to Flooding Stress and the Underlying Molecular Mechanisms

Globally, flooding is a major threat causing substantial yield decline of cereal crops, and is expected to be even more serious in many parts of the world due to climatic anomaly in the future. Understanding the mechanisms of plants coping with unanticipated flooding will be crucial for developing new flooding-tolerance crop varieties. Here we describe survival strategies of plants adaptation to flooding stress at the morphological, physiological and anatomical scale systemically, such as the formation of adventitious roots (ARs), aerenchyma and radial O₂ loss (ROL) barriers. Then molecular mechanisms underlying the adaptive strategies are summarized, and more than thirty identified functional genes or proteins associated with flooding-tolerance are searched out and expounded. Moreover, we elaborated the regulatory roles of phytohormones in plant against flooding stress, especially ethylene and its relevant transcription factors from the group VII Ethylene Response Factor (ERF-VII) family. ERF-VIIs of main crops and several reported ERF-VIIs involving plant tolerance to flooding stress were collected and analyzed according to sequence similarity, which can provide references for screening flooding-tolerant genes more precisely. Finally, the potential research directions in the future were summarized and discussed. Through this review, we aim to provide references for the studies of plant acclimation to flooding stress and breeding new flooding-resistant crops in the future.

Improving Nitrogen Use Efficiency Through Overexpression of Alanine Aminotransferase in Rice, Wheat, and Barley

Nitrogen is an essential nutrient for plants, but crop plants are inefficient in the acquisition and utilization of applied nitrogen. This often results in producers over applying nitrogen fertilizers, which can negatively impact the environment. The development of crop plants with more efficient nitrogen usage is, therefore, an important research goal in achieving greater agricultural sustainability. We utilized genetically modified rice lines over-expressing a barley alanine aminotransferase (HvAlaAT) to help characterize pathways which lead to more efficient use of nitrogen. Under the control of a stress-inducible promoter OsAnt1, OsAnt1:HvAlaAT lines have increased above-ground biomass with little change to both nitrate and ammonium uptake rates. Based on metabolic profiles, carbon metabolites, particularly those involved in glycolysis and the tricarboxylic acid (TCA) cycle, were significantly altered in roots of OsAnt1:HvAlaAT lines, suggesting higher metabolic turnover. Moreover, transcriptomic data revealed that genes involved in glycolysis and TCA cycle were upregulated. These observations suggest that higher activity of these two processes could result in higher energy production, driving higher nitrogen assimilation, consequently increasing biomass production. Other potential mechanisms contributing to a nitrogen-use efficient phenotype include involvements of phytohormonal responses and an alteration in secondary metabolism. We also conducted basic growth studies to evaluate the effect of the OsAnt1:HvAlaAT transgene in barley and wheat, which the transgenic crop plants increased seed production under controlled environmental conditions. This study provides comprehensive profiling of genetic and metabolic responses to the over-expression of AlaAT and unravels several components and pathways which contribute to its nitrogen-use efficient phenotype.

Alternate wetting and drying irrigation increases water and phosphorus use efficiency independent of substrate phosphorus status of vegetative rice plants

Sustainable approaches to rice cultivation that apply less irrigation and chemical fertilisers are required to increase crop resource use efficiency. Although alternate wetting and drying (AWD) has been widely promoted as a water-saving irrigation technique, its interactions with phosphorus (P) nutrition have attracted little attention. Vegetative rice plants were grown with two phosphorus levels, fertilised (HP) or un-fertilised (LP), and either continuous flooding (CF) or AWD irrigation. Treatment effects on substrate P bioavailability (measured by Diffusive Gradients in Thin films - DGT-P), plant and substrate water relations, and foliar phytohormone status, were assessed along with P partitioning in planta. Shoot biomass and leaf area under different irrigation treatments depended on substrate P status (significant P x irrigation interaction), since LP decreased these variables under CF, but had no significant effect on plants grown under AWD. AWD maintained DGT-P concentrations and increased maximal root length, but decreased root P concentrations and P offtake. Substrate drying decreased stomatal conductance (g_s) and leaf water potential (Ψ_leaf) but re-flooding increased g_s. AWD increased foliar abscisic acid (ABA), isopentenyl adenine (iP) and 1-aminocyclopropane-1-carboxylic acid (ACC) concentrations, but decreased trans-zeatin (tZ) and gibberellin A1 (GA1) concentrations. Low P increased ACC and jasmonic acid (JA) concentrations but decreased gibberellin A4 (GA4) concentrations. Across all treatments, stomatal conductance was negatively correlated with foliar ABA concentration but positively correlated with GA1 concentration. Changes in shoot phytohormone concentrations were associated with increased water and phosphorus use efficiency (WUE and PUE) of vegetative rice plants grown under AWD.

Chloroplastic Os3BGlu6 contributes significantly to cellular ABA pools and impacts drought tolerance and photosynthesis in rice

Cellular abscisic acid (ABA) concentration is determined by both de novo biosynthesis and recycling via β-glucosidase(s). However, which rice β-glucosidase(s) are involved in this process remains unknown. Here, we report on a chloroplastic β-glucosidase isoenzyme, Os3BGlu6, that functions in ABA recycling in rice. Disruption of Os3BGlu6 in rice resulted in dwarfism, lower ABA content in leaves, drought-sensitivity, lower photosynthesis rate and higher intercellular CO₂ concentration. Os3BGlu6 could hydrolyze ABA-GE to ABA in vitro. The reversion and overexpression rice lines restored or increased the drought tolerance as shown by the higher β-glucosidase activity, ABA concentrations and expressions of ABA- and drought-responsive genes. Drought induced Os3BGlu6 to form dimers, and the degree of polymerization correlated well with the increase in cellular ABA concentrations and drought tolerance in rice. Os3BGlu6 was responsive to drought and ABA treatments, and the protein was localized to the chloroplast. Disruption of Os3BGlu6 resulted in the increased stomatal density and impaired stomatal movement. Transcriptomics revealed that disruption of Os3BGlu6 resulted in chloroplastic oxidative stress and lowered Rubisco activity even under normal conditions. Taken together, these results suggest that chloroplastically localized Os3BGlu6 significantly affects cellular ABA pools, thereby affecting drought tolerance and photosynthesis in rice.

Transcriptomic data-driven discovery of global regulatory features of rice seeds developing under heat stress

Plants respond to abiotic stressors through a suite of strategies including differential regulation of stress-responsive genes. Hence, characterizing the influences of the relevant global regulators or on stress-related transcription factors is critical to understand plant stress response. Rice seed development is highly sensitive to elevated temperatures. To elucidate the extent and directional hierarchy of gene regulation in rice seeds under heat stress, we developed and implemented a robust multi-level optimization-based algorithm called Minimal Regulatory Network identifier (MiReN). MiReN could predict the minimal regulatory relationship between a gene and its potential regulators from our temporal transcriptomic dataset. MiReN predictions for global regulators including stress-responsive gene Slender Rice 1 (SLR1) and disease resistance gene XA21 were validated with published literature. It also predicted novel regulatory influences of other major regulators such as Kinesin-like proteins KIN12C and STD1, and WD repeat-containing protein WD40. Out of the 228 stress-responsive transcription factors identified, we predicted de novo regulatory influences on three major groups (MADS-box M-type, MYB, and bZIP) and investigated their physiological impacts during stress. Overall, MiReN results can facilitate new experimental studies to enhance our understanding of global regulatory mechanisms triggered during heat stress, which can potentially accelerate the development of stress-tolerant cultivars.

Abscisic acid induced cellular responses of sub1A QTL to aluminium toxicity in rice (Oryza sativa L.)

Involvement of abscisic acid (ABA) was studied for aluminium (Al) sensitivity through functioning of sub1A quantitative trait loci in rice cultivars. sub1A quantitative trait loci bearing cv. Swarna Sub1 was found almost compatible with non sub1A quantitative trait loci bearing cv. Swarna for abscisic acid accumulation all through the aluminium concentrations. However, abscisic acid was self inductive by over expression of its biosynthetic gene in nine-cis-epoxycarotenoid dioxygenase 3 (NCED3) more in cv. Swarna than other. The effect of abscisic acid pretreatment was variable for specific leaf weight, leaf mass ratio and others for the cultivars. Bio-accumulation of aluminium had revealed the sensitivity of toxicity more in cv. Swarna than other. In connection to oxidative stress generation of reactive oxygen species was detected by both histochemical and in vitro assays through hematoxylin, Evans blue and schiff's reactions. Abscisic acid pretreatment had significantly reversed the effects of aluminium toxicity for reactive oxygen species generation. Regardless of varieties sensitivity of aluminium was more prone in shoot than root as detected by nitro blue tetrazolium and 3,3'-diaminobenzidine mediated signalling. Activity in metal chelation in extra cellular spaces monitored through esterase activity and that also established independence of abscisic acid pretreatment for cv. Swarna Sub1. The specific polymorphism of esterase at protein level strengthened the bio-monitoring of aluminium through the rice varieties as well its modulation with abscisic acid. Abscisic acid has been discussed an important effectors to modulate the tolerance pathway of rice cultivars through intrusion of sub1A quantitative trait loci.

Homologous genes of epidermal patterning factor regulate stomatal development in rice

Stomata are microscopic pores on the surface of leaves through which water as vapor passes to the atmosphere and CO₂ uptake for the photosynthesis. The signaling peptides of the epidermal patterning factor (EPF) family regulate stomatal development and density in Arabidopsis. Several putative homologs of EPF/EPFL exist in rice genome. To understand their possible involvement in stomatal formation, in this study we generated a series of transgenic lines including reporter promoter fusions, down-regulation and overexpression and demonstrated drastic differences in stomatal densities between different genotypes, as elevated expression of OsEPF1 or OsEPF2 greatly reduced stomatal density in rice, whereas ectopic overexpression of either OsEPF1 or OsEPF2 significantly decreased the high stomatal frequency of both mutant lines of epf2 and epf1epf2 Arabidopsis. Conversely, knocking down OsEPFL9 transcription conferred transgenic plants with fewer stomata than WT in rice, whereas overexpressing rice OsEPFL9 gene could cause excessive production of stomata in Arabidopsis. In conclusion, homologs of EPF/EPFL regulate stomatal development in a generally highly conserved way yet there exist function distinctions between dicot and monocot plants.

Phytohormone-Mediated Stomatal Response, Escape and Quiescence Strategies in Plants under Flooding Stress

Generally, flooding causes waterlogging or submergence stress which is considered as one of the most important abiotic factors that severely hinders plant growth and development. Plants might not complete their life cycle even in short duration of flooding. As biologically intelligent organisms, plants always try to resist or survive under such adverse circumstances by adapting a wide array of mechanisms including hormonal homeostasis. Under this mechanism, plants try to adapt through diverse morphological, physiological and molecular changes, including the closing of stomata, elongating of petioles, hollow stems or internodes, or maintaining minimum physiological activity to store energy to combat post-flooding stress and to continue normal growth and development. Mainly, ethylene, gibberellins (GA) and abscisic acid (ABA) are directly and/or indirectly involved in hormonal homeostasis mechanisms. Responses of specific genes or transcription factors or reactive oxygen species (ROS) maintain the equilibrium between stomatal opening and closing, which is one of the fastest responses in plants when encountering flooding stress conditions. In this review paper, the sequential steps of some of the hormone-dependent survival mechanisms of plants under flooding stress conditions have been critically discussed.

Rice SDSFL1 plays a critical role in the regulation of plant structure through the control of different phytohormones and altered cell structure

Semi-dwarfism is one of the most important agronomic traits for many cereal crops. In the present study, a mutant with semi-dwarf and short flag leaf 1, sdsfl1, was identified and characterized. The sdsfl1 mutant demonstrated some distinguished structural alterations, including shorter plant height and flag leaf length, increased tiller numbers and flag leaf width, and decreased panicle length compared with those of wild type (WT). Genetic analysis suggested that the mutant traits were completely controlled by a single recessive gene. The SDSFL1 gene was mapped to the long arm of chromosome 3 within a region of 44.6 kb between InDel markers A3P8.3 and A3P8.4. The DNA sequence analysis revealed that there was only a T to C substitution in the coding region of LOC_Os03g63970, resulting in the substitution of Tryptophan (Try) to Arginine (Arg) and encoding a GA 20 oxidase 1 protein of 372 amino acid residues. Photosynthesis analysis showed that the photosynthetic rate (Pn), stomatal conductance (Gs), and intercellular CO₂ concentration (Ci) were significantly increased in sdsfl1. Chlorophyll a (Chl a), total Chl, and carotenoid contents were significantly increased in sdsfl1 compared with those in WT. sdsfl1 carried a reduced level of GA₃ but reacted to exogenously applied gibberellins (GA). Moreover, the levels of abscisic acid (ABA), indole 3-acetic acid (IAA), and salicylic acid (SA) were notably improved in sdsfl1, whereas there was no noteworthy change in jasmonic acid (JA). The results thus offer a visible foundation for the molecular and physiological analysis of the SDSFL1 gene, which might participate in various functional pathways for controlling plant height and leaf length in rice breeding.

Overexpression of OsGID1 Enhances the Resistance of Rice to the Brown Planthopper Nilaparvata lugens

Gibberellins (GAs) play pivotal roles in plant growth and development, and in defenses against pathogens. Thus far, how the GA-mediated signaling pathway regulates plant defenses against herbivores remains largely unknown. In this study, we cloned the rice GA receptor gene OsGID1, whose expression was induced by damage from the brown planthopper (BPH) Niaparvata lugens, mechanical wounding, and treatment with salicylic acid (SA), but not jasmonic acid. The overexpression of OsGID1 (oe-GID1) decreased BPH-induced levels of SA, H₂O₂, and three SA-pathway-related WRKY transcripts, but enhanced BPH-induced levels of ethylene. Bioassays in the laboratory revealed that gravid BPH females preferred to feed and lay eggs on wild type (WT) plants than on oe-GID1 plants. Moreover, the hatching rate of BPH eggs on oe-GID1 plants was significantly lower than that on WT plants. In the field, population densities of BPH adults and nymphs were consistently and significantly lower on oe-OsGID1 plants than on WT plants. The increased resistance in oe-GID1 plants was probably due to the increased lignin level mediated by the GA pathway, and to the decrease in the expression of the three WRKY genes. Our findings illustrated that the OsGID1-mediated GA pathway plays a positive role in mediating the resistance of rice to BPH.

Abscisic Acid Signaling Inhibits Brassinosteroid Signaling through Dampening the Dephosphorylation of BIN2 by ABI1 and ABI2

Abscisic acid (ABA) and brassinosteroid (BR) antagonistically regulate many aspects of plant growth and development. Previous physiological studies have revealed that the inhibition of BR signaling by ABA is largely dependent on ABI1 and ABI2. However, the genetic and molecular basis of how ABI1 and ABI2 are involved in inhibiting BR signaling remains unclear. Although it is known that in the BR signaling pathway the ABA-BR crosstalk occurs in the downstream of BR receptor complex but upstream of BIN2 kinase, a negative regulator of BR signaling, the component that acts as the hub to directly mediate their crosstalk remains a big mystery. Here, we found that ABI1 and ABI2 interact with and dephosphorylate BIN2 to regulate its activity toward the phosphorylation of BES1. By in vitro mimicking ABA signal transduction, we found that ABA can promote BIN2 phosphorylation by inhibiting ABI2 through ABA receptors. RNA-sequencing analysis further demonstrated that ABA inhibits BR signaling through the ABA primary signaling components, including its receptors and ABI2, and that ABA and GSK3s co-regulate a common set of stress-responsive genes. Because BIN2 can interact with and phosphorylate SnRK2s to activate its kinase activity, our study also reveals there is a module of PP2Cs-BIN2-SnRK2s in the ABA signaling pathway. Collectively, these findings provide significant insights into how plants balance growth and survival by coordinately regulating the growth-promoting signaling pathway and stress responses under abiotic stresses.

Constitutive gibberellin response in grafted tomato modulates root-to-shoot signaling under drought stress

Plants are sessile organisms that must perceive and respond to various environmental constraints throughout their life cycle. Among these constraints, drought stress has become the main limiting factor to crop production around the world. Water deprivation is perceived primarily by the roots, which efficiently signal the shoot to trigger drought responses in order to maximize a plant's ability to survive. In this study, the tomato (Solanum lycopersicum L.) mutant procera (pro), with a constitutive response to gibberellin (GA), and its near isogenic line cv. Micro-Tom (MT), were used in reciprocal grafting under well-watered and water stress conditions to evaluate the role of GA signaling in root-to-shoot communication during drought stress. Growth, oxidative stress, gene expression, water relations and hormonal content were measured in order to provide insights into GA-mediated adjustments to water stress. All graft combinations with pro (i.e. pro/pro, MT/pro and pro/MT) prevented the reduction of growth under stress conditions without a reduction in oxidative stress. The increase of oxidative stress was followed by upregulation of SlDREB2, a drought-tolerance related gene, in all drought-stressed plants. Scions harboring the pro mutation tended to increase the abscisic acid (ABA) content, independent of the rootstock. Moreover, the GA sensitivity of the rootstock modulated stomatal conductance and water use efficiency under drought stress, indicating GA and ABA crosstalk in the adjustment of growth and water economy.

Differential transcriptome profiling of chilling stress response between shoots and rhizomes of Oryza longistaminata using RNA sequencing

Rice (Oryza sativa) is very sensitive to chilling stress at seedling and reproductive stages, whereas wild rice, O. longistaminata, tolerates non-freezing cold temperatures and has overwintering ability. Elucidating the molecular mechanisms of chilling tolerance (CT) in O. longistaminata should thus provide a basis for rice CT improvement through molecular breeding. In this study, high-throughput RNA sequencing was performed to profile global transcriptome alterations and crucial genes involved in response to long-term low temperature in O. longistaminata shoots and rhizomes subjected to 7 days of chilling stress. A total of 605 and 403 genes were respectively identified as up- and down-regulated in O. longistaminata under 7 days of chilling stress, with 354 and 371 differentially expressed genes (DEGs) found exclusively in shoots and rhizomes, respectively. GO enrichment and KEGG pathway analyses revealed that multiple transcriptional regulatory pathways were enriched in commonly induced genes in both tissues; in contrast, only the photosynthesis pathway was prevalent in genes uniquely induced in shoots, whereas several key metabolic pathways and the programmed cell death process were enriched in genes induced only in rhizomes. Further analysis of these tissue-specific DEGs showed that the CBF/DREB1 regulon and other transcription factors (TFs), including AP2/EREBPs, MYBs, and WRKYs, were synergistically involved in transcriptional regulation of chilling stress response in shoots. Different sets of TFs, such as OsERF922, OsNAC9, OsWRKY25, and WRKY74, and eight genes encoding antioxidant enzymes were exclusively activated in rhizomes under long-term low-temperature treatment. Furthermore, several cis-regulatory elements, including the ICE1-binding site, the GATA element for phytochrome regulation, and the W-box for WRKY binding, were highly abundant in both tissues, confirming the involvement of multiple regulatory genes and complex networks in the transcriptional regulation of CT in O. longistaminata. Finally, most chilling-induced genes with alternative splicing exclusive to shoots were associated with photosynthesis and regulation of gene expression, while those enriched in rhizomes were primarily related to stress signal transduction; this indicates that tissue-specific transcriptional and post-transcriptional regulation mechanisms synergistically contribute to O. longistaminata long-term CT. Our findings provide an overview of the complex regulatory networks of CT in O. longistaminata.

Identification of novel stress-responsive biomarkers from gene expression datasets in tomato roots

Abiotic stresses such as heat, drought or salinity have been widely studied individually. Nevertheless, in the nature and in the field, plants and crops are commonly exposed to a different combination of stresses, which often result in a synergistic response mediated by the activation of several molecular pathways that cannot be inferred from the response to each individual stress. By screening microarray data obtained from different plant species and under different stresses, we identified several conserved stress-responsive genes whose expression was differentially regulated in tomato (Solanum lycopersicum L.) roots in response to one or several stresses. We validated 10 of these genes as reliable biomarkers whose expression levels are related to different signalling pathways involved in adaptive stress responses. In addition, the genes identified in this work could be used as general salt-stress biomarkers to rapidly evaluate the response of salt-tolerant cultivars and wild species for which sufficient genetic information is not yet available.

EARLY SENESCENCE1 Encodes a SCAR-LIKE PROTEIN2 That Affects Water Loss in Rice

The global problem of drought threatens agricultural production and constrains the development of sustainable agricultural practices. In plants, excessive water loss causes drought stress and induces early senescence. In this study, we isolated a rice (Oryza sativa) mutant, designated as early senescence1 (es1), which exhibits early leaf senescence. The es1-1 leaves undergo water loss at the seedling stage (as reflected by whitening of the leaf margin and wilting) and display early senescence at the three-leaf stage. We used map-based cloning to identify ES1, which encodes a SCAR-LIKE PROTEIN2, a component of the suppressor of cAMP receptor/Wiskott-Aldrich syndrome protein family verprolin-homologous complex involved in actin polymerization and function. The es1-1 mutants exhibited significantly higher stomatal density. This resulted in excessive water loss and accelerated water flow in es1-1, also enhancing the water absorption capacity of the roots and the water transport capacity of the stems as well as promoting the in vivo enrichment of metal ions cotransported with water. The expression of ES1 is higher in the leaves and leaf sheaths than in other tissues, consistent with its role in controlling water loss from leaves. GREEN FLUORESCENT PROTEIN-ES1 fusion proteins were ubiquitously distributed in the cytoplasm of plant cells. Collectively, our data suggest that ES1 is important for regulating water loss in rice.

Overexpression of Rat Neurons Nitric Oxide Synthase in Rice Enhances Drought and Salt Tolerance

Nitric oxide (NO) has been shown to play an important role in the plant response to biotic and abiotic stresses in Arabidopsis mutants with lower or higher levels of endogenous NO. The exogenous application of NO donors or scavengers has also suggested an important role for NO in plant defense against environmental stress. In this study, rice plants under drought and high salinity conditions showed increased nitric oxide synthase (NOS) activity and NO levels. Overexpression of rat neuronal NO synthase (nNOS) in rice increased both NOS activity and NO accumulation, resulting in improved tolerance of the transgenic plants to both drought and salt stresses. nNOS-overexpressing plants exhibited stronger water-holding capability, higher proline accumulation, less lipid peroxidation and reduced electrolyte leakage under drought and salt conditions than wild rice. Moreover, nNOS-overexpressing plants accumulated less H2O2, due to the observed up-regulation of OsCATA, OsCATB and OsPOX1. In agreement, the activities of CAT and POX were higher in transgenic rice than wild type. Additionally, the expression of six tested stress-responsive genes including OsDREB2A, OsDREB2B, OsSNAC1, OsSNAC2, OsLEA3 and OsRD29A, in nNOS-overexpressing plants was higher than that in the wild type under drought and high salinity conditions. Taken together, our results suggest that nNOS overexpression suppresses the stress-enhanced electrolyte leakage, lipid peroxidation and H2O2 accumulation, and promotes proline accumulation and the expression of stress-responsive genes under stress conditions, thereby promoting increased tolerance to drought and salt stresses.