TaERF87 and TaAKS1 synergistically regulate TaP5CS1/TaP5CR1-mediated proline biosynthesis to enhance drought tolerance in wheat

TaDTGIP1-TaDTG6-BDel574-TaPIF1 module regulates drought stress response in wheat

Drought is a major environmental constraint to wheat production, yet the genetic and molecular mechanisms underlying drought tolerance remain poorly understood. A gain-of-function protein variant TaDTG6-BDel574 has been identified and positively regulates TaPIF1 transcription to enhance wheat drought tolerance. However, the precise molecular pathways driving this response are yet to be fully characterized. In this study, we demonstrate that TaPIF1 plays a crucial role in mediating wheat drought tolerance by regulating stomatal aperture to control transpiration. RNA sequencing combined with biochemical assays revealed that TaPIF1 directly binds to E-box elements to activate the expression of key stress-responsive genes, including TaABI5, TaRD17, and TaP5CS1. Notably, overexpression of TaABI5 enhances wheat drought tolerance by promoting stomatal closure, thereby reducing water loss. Furthermore, TaPIF1 interacts with TaABI5 and the bHLH transcription factor TaAKS1 to synergistically enhancing the transcriptional activation of TaABI5, TaRD17, and TaP5CS1. Additionally, our findings verified that TaDTGIP1 interacts with TaDTG6-BDel574 to attenuate its binding affinity and regulatory activity on the TaPIF1 promoter, thereby negatively regulating drought tolerance. Together, our findings unveil the molecular mechanisms underlying wheat drought stress response mediated by the TaDTGIP1-TaDTG6-BDel574-TaPIF1/TaABI5/TaAKS1-target regulatory module and identify potential candidate genes for breeding elite drought-tolerant wheat varieties.

The ERF072 Transcription Factor Directly Regulates MtSOC1-Like Expression and Mediates Drought-Accelerated Flowering in Medicago truncatula

Flowering time is a key agricultural trait that indicates the yield of Medicago truncatula. Although drought stress affects flowering time in this species, the molecular mechanism underlying the enhancement of flowering to facilitate drought tolerance remains unclear. Accelerated flowering at the onset of drought enables drought escape in Medicago truncatula, ethylene-responsive factors are an important class of transcription factors whose members are involved in drought stress processes in numerous plants. In this study, MfERF072 overexpression accelerated flowering in Medicago truncatula. In addition, the knockdown of this gene did not affect flowering time, MfERF072 overexpression enhanced drought and decreased the flowering time of Medicago truncatula under drought stress. Moreover, a more pronounced phenotype was observed. In contrast, the knockdown of this transcription factor reduced drought tolerance and delayed flowering time. Furthermore, yeast one-hybrid and two-luciferase assays confirmed that ERF072 binds directly to the promoter of the flowering integration MtSOC1-like gene in Medicago truncatula. This consequently promotes floral transition under drought conditions. Our preliminarily data revealed that ERF072 regulates flowering under drought stress. These results may provide insights into new genetic resources for the molecular breeding of Medicago truncatula, ultimately supporting stress tolerance by balancing drought stress responses and flowering time.

FtbHLH1, a transcription factor that interacts with FtATG8a, enhances the drought stress response in Tartary buckwheat

Tartary buckwheat (Fagopyrum tataricum) is a traditional cereal crop cultivated in hilly, arid, cool mountainous regions. The bHLH transcription factors play a pivotal role in regulating flavonoid metabolism and enhancing resistance to extreme environments in Tartary buckwheat. However, the functional characterization of bHLH genes in this species remains incomplete. Previous research identified FtbHLH1 as an interacting partner of the key autophagy protein FtATG8a through yeast library screening. Yeast two-hybrid, bimolecular fluorescence complementation, and luciferase complementation imaging assays confirmed that FtbHLH1 interacts with FtATG8a. This interaction depends on the AIM motifs (LEWYYL and QSWHFV) present in FtbHLH1, with both proteins co-localizing in the nucleus. The expression of FtbHLH1 was significantly induced by drought stress (P < 0.05), and its overexpression led to increased drought tolerance in transgenic Tartary buckwheat hairy roots. RNA sequencing revealed that FtbHLH1 up-regulated genes associated with stress response (e.g., FtCu/ZnSOD) as well as those involved in abscisic acid and methyl jasmonate biosynthesis and signaling pathways (e.g., FtCYP707As, FtRD29B, and FtJAZs). Further analysis indicated that the overexpression of FtbHLH1 enhances drought stress tolerance by altering the activities of antioxidant enzymes and promoting proline accumulation in both transgenic Arabidopsis and Tartary buckwheat hairy roots. This study provides theoretical support for selecting drought-resistant Tartary buckwheat varieties by elucidating the role of FtbHLH1 in the response to drought stress.

The IbDof2.1-IbABF2 module regulates abscisic acid responses and proline biosynthesis to enhance drought tolerance in sweetpotato

Drought is a major abiotic stress that impairs plant growth and development. Developing drought-tolerant crop varieties is an important goal of breeders. Transcription factors belonging to the DNA-binding with one zinc finger (Dof) family regulate plant stress responses and development. However, the roles and regulatory mechanisms of Dof2.1 members in plant stress tolerance are still unclear. Here, we cloned the IbDof2.1 gene from sweetpotato and found that its overexpression significantly enhanced drought tolerance of sweetpotato, whereas IbDof2.1-RNA interference (RNAi) plants displayed the opposite phenotype. The IbDof2.1-overexpression plants showed increased abscisic acid (ABA) and proline contents and stomatal sensitivity to ABA and decreased H2O2 accumulation. Furthermore, we found that IbDof2.1 interacted with ABA-binding factor 2 (IbABF2) and promoted the expression of the proline biosynthesis gene IbP5CS1 to increase proline content, further activating the reactive oxygen species (ROS) scavenging system. These results suggest that the IbDof2.1-IbABF2 module induces stomatal closure and activates the ROS scavenging system by regulating ABA responses and proline biosynthesis to enhance drought tolerance in sweetpotato. Our findings provide novel insights into the roles and regulatory mechanisms of Dof2.1 in plants.

The drought-responsive wheat AP2/ERF transcription factor TaRAP2-13L and its interacting protein TaWRKY10 enhance drought tolerance in transgenic Arabidopsis and wheat (Triticum aestivum L.)

AP2/ERF transcription factors (TFs) are one of the largest TF families involved in plant growth, development, and stress responses. Drought, a major abiotic stress, severely impacts wheat yield and quality. In this study, we identified a wheat AP2/ERF gene, TaRAP2-13L, which was significantly upregulated in response to drought stress. Subcellular localization and transcriptional activity assays indicated that TaRAP2-13L localizes in the nucleus but lacks transcriptional activity. Overexpression of TaRAP2-13L in Arabidopsis enhanced drought tolerance, while silencing TaRAP2-13L in wheat reduced drought tolerance by modulating the ABA signaling pathway and reactive oxygen species homeostasis. Through yeast two-hybrid screening, TaWRKY10 was identified as an interacting protein of TaRAP2-13L, and their interaction was further confirmed by bimolecular fluorescence complementation, luciferase complementation imaging assays, and GST pull-down assays. Functional analysis revealed that TaWRKY10 exhibited a similar role to TaRAP2-13L in drought response. Transcriptional regulation analysis showed that co-expression of TaRAP2-13L and TaWRKY10 complex significantly enhanced transcriptional activity, particularly under drought conditions induced by PEG6000. Moreover, dual-luciferase assays demonstrated that TaRAP2-13L and TaWRKY10 can activate the expression of TaSOD3-2A, TaSOD3-2D, TaGPX1-D, and TaNCED2-5B, with co-expression of both TFs enhancing this activation. Further assays revealed that TaRAP2-13L binds to the DRE motif, TaSOD3-2A, and TaSOD3-2D promoters, while TaWRKY10 binds to the W-box, and TaSOD3-2A promoter. These findings highlight a synergistic mechanism by which TaRAP2-13L and TaWRKY10 regulate drought tolerance, offering potential targets for improving drought tolerance in wheat through transgenic strategies.

Genome-Wide Identification, Characterization, and Expression Analysis of the BTB domain-Containing Protein Gene Family in Poplar

In recent years, the BTB (Bric-a-brac/Tramtrack/Broad complex) gene family in plants has garnered widespread attention for its regulatory roles in plant growth and development. However, knowledge regarding BTBs in poplar trees remains limited. Here, we identified 94 BTB gene family members across the genome of Populus alba L. Through phylogenetic analysis, these members were classified into seven subfamilies and 16 branches, followed by comprehensive bioinformatics and biological analyses. Structural analysis revealed that poplar BTB gene family exhibits both high conservation and diversity, with distinct gene structures and protein features. Expression pattern analysis demonstrated differential expression of poplar BTB genes across various tissues, hormone treatments, and under drought stress, suggesting their potential roles in poplar growth and development and drought response. This study provides a vital foundation and reference for unraveling the BTB-involved regulatory mechanisms underlying poplar growth and development and drought response.

Lipid metabolism improves salt tolerance of Salicornia europaea

BACKGROUND AND AIMS

Salicornia europaea L., a succulent euhalophyte plant, has been found to exhibit optimal reproductive capabilities under appropriate salinity concentrations. However, the underlying metabolic changes are not yet fully understood.

METHODS

In this study, we conducted a comprehensive analysis combining transcriptomic and lipidomic techniques to investigate the molecular mechanisms of lipid metabolism in response to different NaCl concentrations (0 and 200 mM).

RESULTS

Transcriptomic data demonstrated that salt treatment mainly affected processes including lipid biosynthesis, phosphatidylinositol signalling and glycerophospholipid metabolism. The expression levels of several key genes involved in salt tolerance, namely SeSOS1, SeNHX1, SeVHA-A, SeVP1 and SePSS, were found to be upregulated upon NaCl treatment. A total of 485 lipid compounds were identified, of which 27 changed in abundance during salt treatment, including the enrichment of phospholipids and sphingolipids. Moreover, the increase in the double-bond index was mainly attributable to phospholipids and sphingolipids. Comparing the acyl chain length showed that the acyl chain length coefficient of sphingosine-1-phosphate decreased significantly in the presence of 200 mM NaCl.

CONCLUSIONS

This study suggests that S. europaea adapts to saline environments by altering phospholipids and sphingolipids to improve salt tolerance. The salinity response of S. europaea can provide important insights into the action of lipids and their salt adaptation mechanisms.

MsERF17 Promotes Ethylene-Induced Anthocyanin Biosynthesis Under Drought Conditions in Malus spectabilis Leaves

Drought is an important factor that affects plant anthocyanin biosynthesis. However, the underlying molecular mechanisms remain elusive. Ethylene response factors (ERFs) are pivotal regulators in plant growth and environmental responses, particularly in anthocyanin biosynthesis. This study investigated the leaf colour transition from green to red in Malus spectabilis under drought conditions. This transition was primarily attributed to the accumulation of anthocyanins, specifically cyanidin-3,5-diglucoside and cyanidin-3-O-galactoside. Our findings elucidate the pivotal role of MsERF17 in drought-induced anthocyanin biosynthesis. Biochemical and molecular analyses showed that MsERF17 positively regulates anthocyanin synthesis by binding to promoters of MsbHLH3 and MsF3' H, thereby activating their expression. Moreover, transient overexpression and virus-induced gene silencing of MsERF17 in fruit peel and leaves, respectively, regulated anthocyanin synthesis. The stable transformation of calli further corroborated the positive regulatory function of MsERF17 in anthocyanin biosynthesis. Our results provide novel insights into the mechanism by which MsERF17, induced by ethylene, promotes anthocyanin accumulation through the positive regulation of MsbHLH3 and MsF3'H expression under drought conditions in M. spectabilis leaves.

TaERFL1a enhances drought resilience through DHAR-mediated ASA-GSH biosynthesis in wheat

Wheat is one of the important cereal crops around the world, but it often suffers from abiotic stresses, which threaten food security. Thus, it is critical to identify the genes that determine drought tolerance in wheat. AP2/ERFs are known to regulate drought stress in various crops. In this study, TaERFL1a-overexpressing wheat transgenic lines (TaERFL1a-OEs) were used to determine drought resilience mechanism. After 12 d without watering, the growth phenotype of TaERFL1a-OEs was better than that of the wild type (WT), whose activities of superoxide dismutase and catalase, and contents of ascorbate acid (ASA) and glutathione (GSH) were significantly increased, while malondialdehyde content was significantly decreased. Transcriptome analysis revealed that 28,520 genes were differentially expressed between TaERFL1a-OEs and WT under drought condition. Further analysis found that these DEGs were involved in multiple stress-response processes, especially in the ASA-GSH pathway. qPCR revealed that the expression levels of GPX, DHAR, and MDHAR, which are suggested to be participated in ASA-GSH biosynthesis, were significantly up-regulated in TaERFL1a-OEs under drought stress, especially the DHAR gene. Moreover, dual-luciferase and luciferase complementation imaging revealed that TaERFL1a was more promoted DHAR transcription to a greater extent than other genes. Furthermore, yeast one-hybrid, electrophoretic mobility shift assay, and chromatin immunoprecipitation combined with qPCR revealed that TaERFL1a regulates DHAR expression by binding to the cis-element ERF in DHAR promoter and promotes the transcription of later in vivo and in vitro. Overall, our results provided molecular regulatory evidence for TaERFL1a in wheat drought stress and suggested candidate genes for improving drought-tolerant wheat breeding.

Identification of Ethylene Response Factors in Wheat Reveals That TaERF16-B Contributes to Salt Tolerance

Soil salinization is a major abiotic stressor that significantly reduces wheat yield. Identifying novel salt-tolerance genes and integrating them into wheat breeding programs can enhance wheat productivity in saline soils. Ethylene response factor (ERF) plays an important role in plant response to salt stress, and thus far, four wheat ERF genes have been identified to be involved in salt stress response. To systematically identify salt tolerance-related ERF genes in wheat, in this study, 213 ERF sequences were isolated from the whole genome of common wheat and classified into 54 members based on subgenome homology, named TaERF1 to TaERF54. Transcriptome sequencing results showed different expression patterns of TaERF members in leaves after 1, 6, 24, and 48 h of NaCl treatment. Based on association analysis, nine TaERF genes were correlated with the leaf salt injury index. Among them, five SNPs of TaERF16-B formed two haplotypes: Hap1 and Hap2. RT-qPCR results showed that the expression level of TaERF16-B was significantly higher in Hap2-typed germplasms than that in Hap1-typed germplasms after 1 and 6 h of NaCl treatment. A Kompetitive Allele-Specific PCR marker K52 was developed for genotyping TaERF16-B haplotypes, which further confirmed the significant correlation between TaERF16-B and salt tolerance-related phenotypes in mapping population and wheat germplasms. This study provides new genes and molecular markers for improving salt tolerance in wheat.

The transcription factor CitPH4 regulates plant defense-related metabolite biosynthesis in citrus

Wild citrus (Citrus L.) exhibits high disease resistance accompanied by high-acidity fruit, whereas cultivated citrus produces tastier fruit but is more susceptible to disease. This is a common phenomenon, but the underlying molecular mechanisms remain unknown. Citrus PH4 (CitPH4) is a key transcription factor promoting citric acid accumulation in fruits. Accordingly, CitPH4 expression decreased during citrus domestication, along with a reduction in citric acid levels. Here, we demonstrate that a CitPH4-knockout mutant exhibits an acidless phenotype and displays substantially lower resistance to citrus diseases. Metabolome and transcriptome analyses of CitPH4-overexpressing citrus callus, Arabidopsis, and CitPH4-knockout citrus fruits revealed that quercetin, pipecolic acid (Pip), and N-hydroxypipecolic acid (NHP) are pivotal defense-related metabolites. Application of quercetin and Pip inhibited the growth of Xcc and Penicillium italicum, while NHP inhibited the growth of P. italicum and Huanglongbing. Biochemical experiments demonstrated that CitPH4 enhances the expression of quercetin and NHP biosynthesis genes by binding to their promoters. Moreover, Pip and quercetin contents were positively associated with citric acid content in the pulp of fruits from natural citrus populations. Finally, the heterologous expression of CitPH4 in Arabidopsis promoted the expression of stress response genes and enhanced its resistance to the fungal pathogen Botrytis cinerea. The overexpression of CitPH4 in tobacco (Nicotiana tabacum) enhanced disease resistance. This study reveals the mechanism by which CitPH4 regulates disease resistance and fruit acidity, providing a conceptual strategy to control fruit acidity and resistance to devastating diseases.

Wheat2035: Integrating pan-omics and advanced biotechnology for future wheat design

Wheat (Triticum aestivum) production is vital for global food security, providing energy and protein to millions of people worldwide. Recent advancements in wheat research have led to significant increases in production, fueled by technological and scientific innovation. Here, we summarize the major advancements in wheat research, particularly the integration of biotechnologies and a deeper understanding of wheat biology. The shift from multi-omics to pan-omics approaches in wheat research has greatly enhanced our understanding of the complex genome, genomic variations, and regulatory networks to decode complex traits. We also outline key scientific questions, potential research directions, and technological strategies for improving wheat over the next decade. Since global wheat production is expected to increase by 60% in 2050, continued innovation and collaboration are crucial. Integrating biotechnologies and a deeper understanding of wheat biology will be essential for addressing future challenges in wheat production, ensuring sustainable practices and improved productivity.

PdbCRF5 Overexpression Negatively Regulates Salt Tolerance by Downregulating PdbbZIP61 to Mediate Reactive Oxygen Species Scavenging and ABA Synthesis in Populus davidiana × P. bolleana

Salt stress is the main factor limiting the large-scale cultivation of Shanxin poplar; therefore, improving its salt tolerance is crucial. In this study, we identified and characterized a CRF gene (PdbCRF5) in Shanxin poplar. Compared with the wild-type poplar, the Shanxin poplar overexpressing PdbCRF5 were more sensitive to salt stress. The PdbCRF5-silenced plants exhibited improved salt tolerance. ChIP‒PCR, EMSA, and Y1H confirmed that PdbCRF5 can regulate the expression of the PdbbZIP61 by binding to ABRE element. Further analysis revealed that the overexpression of PdbbZIP61 can reduce cell damage by increasing ROS scavenging, and on the other hand, overexpression of PdbbZIP61 can improve the salt tolerance of Shanxin poplar by regulating the expression of the PdbNCED genes to increase the ABA content. In addition, we also demonstrated that PdbCRF5 can inhibit the expression of the PdbbZIP61 in combination with PdbCRF6. The overexpression of PdbCRF6 also reduced the salt tolerance of Shanxin poplar. Therefore, we found that PdbCRF5 negatively regulates the salt tolerance of Shanxin poplar by inhibiting the PdbbZIP61, indicating that PdbCRF5 plays an important role in the tolerance of Shanxin poplar to salt stress and is an important candidate gene for gene editing and breeding in forest trees.

Unveiling the Role of GhP5CS1 in Cotton Salt Stress Tolerance: A Comprehensive Genomic and Functional Analysis of P5CS Genes

Proline, a critical osmoregulatory compound, is integral to various plant stress responses. The P5CS gene, which encodes the rate-limiting enzyme in proline biosynthesis, known as ∆1-pyrroline-5-carboxylate synthetase, is fundamental to these stress response pathways. While the functions of P5CS genes in plants have been extensively documented, their specific roles in cotton remain inadequately characterized. In this study, we identified 40 P5CS genes across four cotton species with diverse sequence lengths and molecular weights. Phylogenetic analysis of 100 P5CS genes from nine species revealed three subgroups, with Gossypium hirsutum closely related to Gossypium barbadense. Collinearity analysis highlighted significant differences in collinear gene pairs, indicating evolutionary divergence among P5CS genes in tetraploid and diploid cotton. Exon-intron structures and conserved motifs correlated with phylogenetic relationships, suggesting functional differentiation. Stress-responsive elements in P5CS promoters suggest involvement in abiotic stress. Expression analysis under salt stress revealed differential expressions of GhP5CS genes, with GhP5CS1 emerging as a potential key regulator. Virus-induced gene silencing confirmed the pivotal role of GhP5CS1 in cotton's salt stress response, as evidenced by increased salt sensitivity in the silenced plants. This study enhances our understanding of the functional diversity and roles of P5CS genes in cotton under stress conditions.

Exogenous SNP Alleviates Drought Stress in Wheat During the Grain-Filling Stage by Modulating TaP5CS Gene Transcription

Drought stress severely damages wheat growth and photosynthesis, and plants at the grain-filling stage are the most sensitive to drought throughout the entire period of development. Exogenous spraying of sodium nitroprusside (SNP) can alleviate the damage to wheat caused by drought stress, but the mechanism regulating the proline pathway remains unknown. Two wheat cultivars, drought-sensitive Zhoumai 18 and drought-tolerant Zhengmai 1860, were used as materials when the plants were cultivated to the grain-filling stage. The results show that under drought stress, SNP pretreatment effectively improved the physiological basis of photosynthesis and water use efficiency of the two cultivars, increased their tolerance to photosystem II (PSII) damage, and maintained a normal photosynthetic rate and yield. Drought stress induced an increase in pyrroline-5-carboxylate synthase (TaP5CS) gene transcription, and a comparatively greater increase was detected in Zhengmai 1860. When SNP treatment was applied before drought exposure, TaP5CS transcription was further enhanced. Induction of TaP5CS transcription promoted proline accumulation in response to drought stress, increased osmotic ability, and maintained the net photosynthetic rate, thereby increasing the accumulation of dry matter and yield traits. In this study, exogenous SNP regulates the transcription of genes related to the proline metabolism pathway and provides a theoretical basis for the establishment of wheat cultivation technology using SNP to resist drought stress.

Insight into the transcriptional regulation of key genes involved in proline metabolism in plants under osmotic stress

Proline biosynthesis and catabolism pathways are executed by powerful action of specific enzymes that are subjected to environmental fluctuations at the transcriptional level. Previous researches have demonstrated that osmotic stress-induced upstream events can affect the expression of proline metabolism-related genes, which results in adjustable free proline accumulation to protect plant cells from severe damage. Here, we mainly describe the mechanisms for how some key factors, such as transcription factors, ABA (abscisic acid), Ca2+, MAPK cascades, CK (cytokinin) and phospholipase, in a phosphorylated manner, vividly function in the transcriptional regulation of proline metabolism under osmotic stress. These mechanisms reveal that sustaining of proline homeostasis is an efficient way for plants to adapt to osmotic stress.

The transcription factor TGA2 orchestrates salicylic acid signal to regulate cold-induced proline accumulation in Citrus

Plants subjected to cold stress have been observed to accumulate proline, but the underlying regulatory mechanism remains to be elucidated. In this study, we identified a pyrroline-5-carboxylate synthetase (P5CS)-encoding gene (CtrP5CS1) from trifoliate orange (Citrus trifoliata L.), a cold-hardy citrus species, as a critical gene for cold-induced proline accumulation. CtrTGA2 bound directly to the TGACG motif of the CtrP5CS1 promoter and activated its expression. Moreover, CtrTGA2 functioned positively in cold tolerance via modulation of proline synthesis by regulating CtrP5CS1 expression. Up-regulation of CtrP5CS1 and CtrTGA2 under cold stress was dependent on salicylic acid (SA) biosynthesis. CtrTGA2 directly regulated the expression of CtrICS1, a gene encoding isochorismate synthase (ICS) involved in SA biosynthesis, forming a positive feedback loop to intensify the CtrTGA2-mediated transcriptional activation of CtrP5CS1. The cold-induced SA receptor NONEXPRESSOR OF PATHOGENESIS-RELATED GENES3 (CtrNPR3) interacted with CtrTGA2 to inhibit its transcriptional activation activity; however, the inhibition was released by SA. Our results uncover the CtrTGA2-CtrP5CS1/CtrICS1 regulatory module that orchestrates the SA signal to regulate proline synthesis, giving important insights into the transcriptional mechanism underlying proline accumulation in plants under cold stress.

Genome-Wide Identification of the GbUBC Gene Family in Sea-Island Cotton (Gossypium barbadense) and the Active Regulation of Drought Resistance in Cotton by GbUBC23

Cotton is an economically critical crop worldwide, and drought stress strongly affects its growth and development. Ubiquitination modifies protein activity and is crucial in numerous biological processes. Ubiquitin-conjugating enzymes serve as intermediaries in the protein ubiquitination process and play important roles in plant responses to abiotic stress. However, the impact of ubiquitination on the response of cotton to abiotic stress is not fully understood. Bioinformatic methods were employed in this study to analyze the physiochemical characteristics, gene structure, collinearity, expression patterns, and evolutionary relationships of GbUBC gene family members in sea-island cotton. In sea-island cotton, a minimum of 125 GbUBC genes are irregularly distributed across the 26 chromosomes, with multiple instances of gene duplication observed among the members. Phylogenetic analysis categorized the GbUBC gene family into 15 ubiquitin-conjugating enzyme (E2) subgroups, one ubiquitin E2 enzyme variant (UEV) subgroup, and one COP10 subgroup. GbUBC gene expression pattern analyses revealed that most GbUBC genes responded differently to cold, heat, NaCl, and polyethylene glycol (PEG) treatments, with certain GbUBC genes exhibiting high expression levels in specific fiber development period and organs. Furthermore, molecular biology methods were employed to elucidate the biological functions of GbUBC23. The GbUBC23 gene was highly expressed in the cotyledons of sea-island cotton and was activated by PEG treatment. GbUBC23 is localized to the nucleus and cytomembrane. The silencing of the GbUBC23 gene under drought conditions led to decreased drought tolerance and survival rates in sea-island cotton. Compared with those in the control plants, the activity of proline and superoxide dismutase and the expression levels of the drought-induced genes GbNCED3, GbRD22, GbRD26 were significantly lower, but the levels of malondialdehyde and hydrogen peroxide were significantly higher. Our findings revealed 125 members of the GbUBC gene family in sea-island cotton, with the GbUBC23 gene critically contributing to the abiotic stress response. These findings indicate that the GbUBC gene family may play a crucial role in the drought stress response in sea-island cotton.

Saussurea involucrata SiLEA5 Enhances Tolerance to Drought Stress in Solanum lycopersicum

Drought adversely affects plant growth, which leads to reduced crop yields and exacerbates food insecurity. Late embryogenesis abundant (LEA) proteins are crucial for plants' responses to abiotic stresses. This research further investigates the role of SiLEA5 by utilizing transgenic tomatoes under drought stress. The expression of SiLEA5 was upregulated under drought and abscisic acid (ABA) treatment, resulting in decreased electrolyte leakage and malondialdehyde content, alongside increased levels of osmotic regulators and antioxidant enzyme activity. These biochemical alterations reduce oxidative damage and enhance drought resistance. qRT-PCR analysis revealed the upregulation of ABA signaling genes and key enzymes involved in proline biosynthesis (P5CS) and dehydrin (DHN) synthesis under drought stress. Additionally, overexpression of SiLEA5 increased the net photosynthetic rate (Pn) and fruit yield of tomatoes by regulating stomatal density and aperture. These findings suggest that SiLEA5 may be a potential target for improving drought tolerance in tomatoes and other crops.

Transcriptome and molecular evidence of HvMORF8 conferring drought-tolerance in barley

Drought is one of the most devastating abiotic stresses worldwide, which severely limits crop yield. Tibetan wild barley is a treasure trove of useful genes for crop improvement including drought tolerance. Here, we detected large-scale changes of gene expression in response to drought stress with a substantial difference among contrasting Tibetan barley genotypes XZ5 (drought-tolerant), XZ54 (drought-sensitive) and cv. Tadmor (drought-tolerant). Drought stress led to upregulations of 142 genes involved in transcription, metabolism, protein synthesis, stress defense, transport and signal transduction in XZ5, but those genes were down-regulated or unchanged in XZ54 and Tadmor. We identified and functionally characterized a novel multiple organellar RNA editing factors 8 (HvMORF8), which was up-regulated by drought stress in XZ5, but unchanged in XZ54 and Tadmor under drought stress. Phylogenetic analysis showed that orthologues of HvMORF8 can be traced back to the closest gymnosperm species such as Cycas micholitzii, implicating a potential evolutionary origin for MORF8 from a common ancestor in early seed plants. Virus-induced HvMORF8 silencing in XZ5 led to hypersensitivity to drought stress, demonstrating it is a positive regulator of drought tolerance in barley. RNA sequencing of BSMV:HvMORF8 and control plants reveals that silencing of HvMORF8 suppresses genes involved in osmolytes transport, cell wall modification and antioxidants, resulting in water metabolism disorder and overaccumulation of reactive oxygen species (ROS) under drought stress. Therefore, we propose HvMORF8-mediated regulatory drought tolerance mechanisms at transcriptomic level in XZ5, providing new insight into the genetic basis of plastid RNA editing function of HvMORF8 for barley drought tolerance.

Overexpression of TdNACB improves the drought resistance of rice

Drought stress greatly affects disrupts the productivity, ecological structure, physiological and biochemical activities of wheat at different growth stages. However, drought stress tolerance is a complex quantitative trait and involves multiple metabolic pathways. We found that a wild emmer introgression line BAd7-209 had stronger drought resistance compared with drought resistant wheat Zhongmai 175. The transcriptome analysis found 14,284, 22,383 and 21,451 genes had expression corresponding responsed to drought stress at 24h, 48h, 120h, respectively and significantly enriched in 'Arginine and proline metabolism' and 'Peroxisome' in BAd7-209. 1666 transcription factors (TFs) related responsed to drought stress in which TdNACB showed high expression at 24h, 48h and 120h and had the closest relationship with TaNAC48 and OsNAC6 in phylogenetic analysis. Overexpression of TdNACB significantly enhanced drought resistance in rice and overexpression lines had significantly higher CAT, POD and SOD activity, Pro content and lower MDA content than those of the WT under drought stress. The result demonstrated that TdNACB positively regulates drought resistance through increasing proline content and enhancing activity of enzyme related to ROS scavenging. The results of this study provides candidate genes for improving wheat drought resistance and guide as reference for studying the molecular mechanisms of wheat drought resistance.

Silencing of SlMYB78-like Reduces the Tolerance to Drought and Salt Stress via the ABA Pathway in Tomato

The MYB transcription factor family plays a crucial regulatory role in plant growth, development, biological progress, and stress responses. Here, we identified a R2R3-MYB transcription factor gene, SlMYB78-like, from tomato and characterized its function by gene silencing via RNA interference (RNAi). The results exhibited that the silencing of SlMYB78-like reduced the sensitivity of tomato seedlings to exogenous ABA. In addition, when exposed to drought and salt stresses, the RNAi lines grown in soil showed decreased tolerance, with lower ABA accumulation, relative water content, and chlorophyll content while displaying higher relative conductivity and malondialdehyde (MDA) content than the wild type. Moreover, the expression of genes related to chlorophyll biosynthesis, photosynthesis, and ABA biosynthesis/response were down-regulated in SlMYB78-like-silenced lines. Notably, the transcript level of SlCYP707-A2, which encodes a protein involved in ABA degradation, was up-regulated significantly after stresses. The transient expression assay Dual-luciferase (Dual-LUC) and a yeast one-hybrid (Y1H) assay demonstrated that SlMYB78-like bound to the promoter of SlCYP707-A2. Additionally, the physical interaction between SlMYB78-like and SlDREB3, which functioned in ABA signaling transduction, was identified through yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. Collectively, our study illustrates that SlMYB78-like participates in the abiotic stress response via the ABA pathway.

PpERF-CRF3 selected by transcriptomic analysis plays key roles in the regulation of ABA alleviating chilling injury in peach fruit

Abscisic acid (ABA) is widely utilized to mitigate chilling injury (CI) of fruit. However, the molecular mechanism of ABA alleviates CI in peach fruit remain unclear. Herein, 10-4 M ABA treatment significantly mitigated the CI of peach fruit by reducing relative conductivity and malondialdehyde content, while increasing proline and endogenous ABA content. Transcriptomic analysis indicated that an abundant number of differentially expressed genes were altered by ABA treatment, which primarily enriched pathways such as plant hormone signal transduction, glycerophospholipid metabolism and phenylpropanoid biosynthesis. RNA-Seq results indicate that ABA modulates the transcription of genes involved in auxin, ABA and ethylene signal transduction, as well as in cell wall degradation, antioxidant, fatty acid desaturation and proline metabolism. RT-qPCR confirmed the RNA-Seq results, ABA treatment induced the transcription of proline metabolism related genes (PpP5CR2, PpP5CS, PpP5CS1) and PpERF-CRF3. Particularly noteworthy, as a nuclear protein, PpERF-CRF3 activated the expression of PpP5CR2 and PpP5CS by directly binding to their promoters and over-expression PpERF-CRF3 increased proline content and enhanced PpP5CR2 and PpP5CS expression. Overall, these findings suggest that ABA mitigates CI in peach fruit may be by mediating these pathways, and PpERF-CRF3 potentially involves this process by stimulating the expression of genes related to proline synthesis.

Comparative analysis of physical traits, mineral compositions, antioxidant contents, and metabolite profiles in five cherry tomato cultivars

Cherry tomatoes (Solanum lycopersicum var. cerasiforme) are cultivated and consumed worldwide. While numerous cultivars have been bred to enhance fruit quality, few studies have comprehensively evaluated the fruit quality of cherry tomato cultivars. In this study, we assessed fruits of five cherry tomato cultivars (Qianxi, Fengjingling, Fushan88, Yanyu, and Qiyu) at the red ripe stage through detailed analysis of their physical traits, mineral compositions, antioxidant contents, and metabolite profiles. Significant variations were observed among the cultivars in terms of fruit size, shape, firmness, weight, glossiness, and sepal length, with each cultivar displaying unique attributes. Mineral analysis revealed distinct patterns of essential and trace element accumulation, with notable differences in calcium, sodium, manganese, and selenium concentrations. Fenjingling was identified as a selenium enriched cultivar. Analysis of antioxidant contents highlighted Yanyu as particularly rich in vitamin C and Fenjingling as having elevated antioxidant enzyme activities. Metabolomics analysis identified a total number of 3,396 annotated metabolites, and the five cultivars showed distinct metabolomics profiles. Amino acid analysis showed Fushan88 to possess a superior profile, while sweetness and tartness assessments indicated that Yanyu exhibited higher total soluble solids (TSS) and acidity. Notably, red cherry tomato cultivars (Fushan88, Yanyu, and Qiyu) accumulated significantly higher levels of eugenol and α-tomatine, compounds associated with undesirable flavors, compared to pink cultivars (Qianxi and Fengjingling). Taken together, our results provide novel insights into the physical traits, nutritional value, and flavor-associated metabolites of cherry tomatoes, offering knowledge that could be implemented for the breeding, cultivation, and marketing of cherry tomato cultivars.

Transcriptome and Metabolome Analyses Reveal the Molecular Mechanisms of Albizia odoratissima's Response to Drought Stress

Albizia odoratissima is a deciduous tree species belonging to the family Leguminosae. It is widely distributed in the southern subtropical and tropical areas of China and has important ecological and economic value. The growth and metabolic processes of A. odoratissima are affected by drought stress, but the molecular mechanisms remain unknown. Therefore, this study investigated the physicochemical properties, gene expression, and metabolites of A. odoratissima seedlings under drought stress. The results show that, in leaves of A. odoratissima seedlings, drought stress reduced the moisture content, chlorophyll content, photosynthetic efficiency, superoxide dismutase (SOD) activity, and gibberellin (GA) and indoleacetic acid (IAA) contents while increasing the catalase (CAT) and peroxidase (POD) activities and malondialdehyde (MDA), proline, soluble sugar, and soluble protein contents. Within the CK5 (Day 5 of control group) vs. T5 (Day 5 of drought treatment), CK10 vs. T10, CK15 vs. T15, and CK20 vs. T20 groups (CK: control group; T: drought treatment), a total of 676 differentially expressed genes (DEGs) were upregulated and 518 DEGs were downregulated, and a total of 228 and 143 differential accumulation metabolites (DAMs) were identified in the CK10 vs. T10 and CK20 vs. T20 groups. These were mainly involved in the amino acid and alkaloid metabolism pathways in the leaves of the A. odoratissima seedlings. In the amino acid and alkaloid biosynthesis pathways, the relative expression levels of the AoproA (Aod04G002740, ORTHODONTIC APPLIANCE), AoOAT (Aod07G015970, ORNITHINE-OXO-ACID TRANSAMINASE), and AoAOC3 (Aod12G005010/08G003360/05G023920/08G003000/08G003010, AMINE OXIDASE COPPER CONTAINING 3) genes increased, which concurrently promoted the accumulation of arginine, proline, piperine, cadaverine, and lysine. Furthermore, some key transcription factors in the response to drought were identified in the leaves using the weighted gene co-expression network analyses (WGCNA) method. These findings reveal that A. odoratissima seedlings respond to drought stress by improving the capacities of the antioxidant system and secondary metabolism.

Transcriptomic and Metabolomic Profiling of Root Tissue in Drought-Tolerant and Drought-Susceptible Wheat Genotypes in Response to Water Stress

Wheat is the most widely grown crop in the world; its production is severely disrupted by increasing water deficit. Plant roots play a crucial role in the uptake of water and perception and transduction of water deficit signals. In the past decade, the mechanisms of drought tolerance have been frequently reported; however, the transcriptome and metabolome regulatory network of root responses to water stress has not been fully understood in wheat. In this study, the global transcriptomic and metabolomics profiles were employed to investigate the mechanisms of roots responding to water stresses using the drought-tolerant (DT) and drought-susceptible (DS) wheat genotypes. The results showed that compared with the control group, wheat roots exposed to polyethylene glycol (PEG) had 25941 differentially expressed genes (DEGs) and more upregulated genes were found in DT (8610) than DS (7141). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs of the drought-tolerant genotype were preferably enriched in the flavonoid biosynthetic process, anthocyanin biosynthesis and suberin biosynthesis. The integrated analysis of the transcriptome and metabolome showed that in DT, the KEGG pathways, including flavonoid biosynthesis and arginine and proline metabolism, were shared by differentially accumulated metabolites (DAMs) and DEGs at 6 h after treatment (HAT) and pathways including alanine, aspartate, glutamate metabolism and carbon metabolism were shared at 48 HAT, while in DS, the KEGG pathways shared by DAMs and DEGs only included arginine and proline metabolism at 6 HAT and the biosynthesis of amino acids at 48 HAT. Our results suggest that the drought-tolerant genotype may relieve the drought stress by producing more ROS scavengers, osmoprotectants, energy and larger roots. Interestingly, hormone signaling plays an important role in promoting the development of larger roots and a higher capability to absorb and transport water in drought-tolerant genotypes.

An Integrated Framework for Drought Stress in Plants

With global warming, drought stress is becoming increasingly severe, causing serious impacts on crop yield and quality. In order to survive under adverse conditions such as drought stress, plants have evolved a certain mechanism to cope. The tolerance to drought stress is mainly improved through the synergistic effect of regulatory pathways, such as transcription factors, phytohormone, stomatal movement, osmotic substances, sRNA, and antioxidant systems. This study summarizes the research progress on plant drought resistance, in order to provide a reference for improving plant drought resistance and cultivating drought-resistant varieties through genetic engineering technology.

Integrated metabolomics and transcriptomics reveal that HhERF9 positively regulates salt tolerance in Hibiscus hamabo Siebold & Zuccarini

Hibiscus hamabo Siebold & Zuccarini is one of the few semi-mangrove plants in the genus Hibiscus that can survive in saline-alkali soil and flooded land, but the mechanism underlying its adaptation to salt soil remains unknown. Here, to uncover this unsolved mystery, we characterized the changes in the accumulation of specific metabolites under salt stress in H. hamabo by integrating physiological, metabolic, and transcriptomic data, and found that osmotic adjustment and abscisic acid (ABA) is highly associated with the salt stress response. Further, a weighted gene co-expression network analysis was performed on the root transcriptome data, which identified three key candidate transcription factors responsive to salt stress. Among them, the expression HhERF9 was significantly upregulated under salt stress and ABA treatment and was involved in regulating the expression of genes related to the salt stress response. Further research indicated that HhERF9 enhances the accumulation of proline and soluble sugars by regulating the expression of genes such as NHX2 and P5CS. These findings provide a reference for improving H. hamabo through targeted genetic engineering and lay a theoretical foundation for its future promotion and cultivation in saline-alkali areas.

Calcium-Dependent Protein Kinase GhCDPK16 Exerts a Positive Regulatory Role in Enhancing Drought Tolerance in Cotton

Cotton is essential for the textile industry as a primary source of natural fibers. However, environmental factors like drought present significant challenges to its cultivation, adversely affecting both production levels and fiber quality. Enhancing cotton's drought resilience has the potential to reduce yield losses and support the growth of cotton farming. In this study, the cotton calcium-dependent protein kinase GhCDPK16 was characterized, and the transcription level of GhCDPK16 was significantly upregulated under drought and various stress-related hormone treatments. Physiological analyses revealed that the overexpression of GhCDPK16 improved drought stress resistance in Arabidopsis by enhancing osmotic adjustment capacity and boosting antioxidant enzyme activities. In contrast, silencing GhCDPK16 in cotton resulted in increased dehydration compared with the control. Furthermore, reduced antioxidant enzyme activities and downregulation of ABA-related genes were observed in GhCDPK16-silenced plants. These findings not only enhanced our understanding of the biological functions of GhCDPK16 and the mechanisms underlying drought stress resistance but also underscored the considerable potential of GhCDPK16 in improving drought resilience in cotton.

MsABCG1, ATP-Binding Cassette G transporter from Medicago Sativa, improves drought tolerance in transgenic Nicotiana Tabacum

Drought has a devastating impact, presenting a formidable challenge to agricultural productivity and global food security. Among the numerous ABC transporter proteins found in plants, the ABCG transporters play a crucial role in plant responses to abiotic stress. In Medicago sativa, the function of ABCG transporters remains elusive. Here, we report that MsABCG1, a WBC-type transporter highly conserved in legumes, is critical for the response to drought in alfalfa. MsABCG1 is localized on the plasma membrane, with the highest expression observed in roots under normal conditions, and its expression is induced by drought, NaCl and ABA signalling. In transgenic tobacco, overexpression of MsABCG1 enhanced drought tolerance, evidenced by increased osmotic regulatory substances and reduced lipid peroxidation. Additionally, drought stress resulted in reduced ABA accumulation in tobacco overexpressing MsABCG1, demonstrating that overexpression of MsABCG1 enhanced drought tolerance was not via an ABA-dependent pathway. Furthermore, transgenic tobacco exhibited increased stomatal density and reduced stomatal aperture under drought stress, indicating that MsABCG1 has the potential to participate in stomatal regulation during drought stress. In summary, these findings suggest that MsABCG1 significantly enhances drought tolerance in plants and provides a foundation for developing efficient drought-resistance strategies in crops.

Functions of Basic Helix-Loop-Helix (bHLH) Proteins in the Regulation of Plant Responses to Cold, Drought, Salt, and Iron Deficiency: A Comprehensive Review

Abiotic stresses including cold, drought, salt, and iron deficiency severely impair plant development, crop productivity, and geographic distribution. Several bodies of research have shed light on the pleiotropic functions of BASIC HELIX-LOOP-HELIX (bHLH) proteins in plant responses to these abiotic stresses. In this review, we mention the regulatory roles of bHLH TFs in response to stresses such as cold, drought, salt resistance, and iron deficiency, as well as in enhancing grain yield in plants, especially crops. The bHLH proteins bind to E/G-box motifs in the target promoter and interact with various other factors to form a complex regulatory network. Through this network, they cooperatively activate or repress the transcription of downstream genes, thereby regulating various stress responses. Finally, we present some perspectives for future research focusing on the molecular mechanisms that integrate and coordinate these abiotic stresses. Understanding these molecular mechanisms is crucial for the development of stress-tolerant crops.

Transgenerational Seed Exposure to Elevated CO2 Involves Stress Memory Regulation at Metabolic Levels to Confer Drought Resistance in Wheat

Drought is the worst environmental stress constraint that inflicts heavy losses to global food production, such as wheat. The metabolic responses of seeds produced overtransgenerational exposure to e[CO2] to recover drought's effects on wheat are still unexplored. Seeds were produced constantly for four generations (F1 to F4) under ambient CO2 (a[CO2], 400 μmol L-1) and elevated CO2 (e[CO2], 800 μmol L-1) concentrations, and then further regrown under natural CO2 conditions to investigate their effects on the stress memory metabolic processes liable for increasing drought resistance in the next generation (F5). At the anthesis stage, plants were subjected to normal (100% FC, field capacity) and drought stress (60% FC) conditions. Under drought stress, plants of transgenerational e[CO2] exposed seeds showed markedly increased superoxide dismutase (16%), catalase (24%), peroxidase (9%), total antioxidants (14%), and proline (35%) levels that helped the plants to sustain normal growth through scavenging of hydrogen peroxide (11%) and malondialdehyde (26%). The carbohydrate metabolic enzymes such as aldolase (36%), phosphoglucomutase (12%), UDP-glucose pyrophosphorylase (25%), vacuolar invertase (33%), glucose-6-phosphate-dehydrogenase (68%), and cell wall invertase (17%) were decreased significantly; however, transgenerational seeds produced under e[CO2] showed a considerable increase in their activities in drought-stressed wheat plants. Moreover, transgenerational e[CO2] exposed seeds under drought stress caused a marked increase in leaf Ψw (15%), chlorophyll a (19%), chlorophyll b (8%), carotenoids (12%), grain spike (16%), hundred grain weight (19%), and grain yield (10%). Hence, transgenerational seeds exposed to e[CO2] upregulate the drought recovery metabolic processes to improve the grain yield of wheat under drought stress conditions.

Biochemical characterization and metabolic reprogramming of amino acids in Soybean roots under drought stress

Amino acids play important roles in stress resistance, plant growth, development, and quality, with roots serving as the primary organs for drought response. We conducted biochemical and multi-omics analyses to investigate the metabolic processes of root amino acids in drought-resistant (HN44) and drought-sensitive (HN65) soybean (Glycine max) varieties. Our analysis revealed an increase in total amino acid content in both varieties, with phenylalanine, proline, and methionine accumulating in both. Additionally, several amino acids exhibited significant decreases in HN65 but slight increases in HN44. Multi-omics association analysis identified 13 amino acid-related pathways. We thoroughly examined the changes in genes and metabolites involved in various amino acid metabolism/synthesis and determined core genes and metabolites through correlation networks. The phenylalanine, tyrosine, and tryptophan metabolic pathways and proline, glutamic acid and sulfur-containing amino acid pathways were particularly important for drought resistance. Some candidate genes, such as ProDH and P4HA family genes, and metabolites, such as O-acetyl-L-serine, directly affected up- and downstream metabolism to induce drought resistance. This study provided a basis for soybean drought resistance breeding.

Transcription factors as molecular switches regulating plant responses to drought stress

Plants often experience abiotic stress, which severely affects their growth. With the advent of global warming, drought stress has become a pivotal factor affecting crop yield and quality. Increasing numbers of studies have focused on elucidating the molecular mechanisms underlying plant responses to drought stress. As molecular switches, transcription factors (TFs) are key participants in drought-resistance regulatory networks in crops. TFs regulate the transcription of downstream genes and are regulated by various upstream regulatory factors. Therefore, understanding the mechanisms of action of TFs in regulating drought stress can help enhance the adaptive capacity of crops under drought conditions. In this review, we summarize the structural characteristics of several common TFs, their multiple drought-response pathways, and recently employed research strategies. We describe the application of new technologies such as analysis of stress granule dynamics and function, multi-omics data, gene editing, and molecular crosstalk between TFs in drought resistance. This review aims to familiarize readers with the regulatory network of TFs in drought resistance and to provide a reference for examining the molecular mechanisms of drought resistance in plants and improving agronomic traits.

VvERF117 positively regulates grape cold tolerance through direct regulation of the antioxidative gene BAS1

Cold stress significantly threatens grape quality, yield, and geographical distribution. Although ethylene-responsive factors (ERFs) are recognized for their pivotal roles in cold stress, the regulatory mechanisms of many ERFs contributing to tolerance remain unclear. In this study, we identified the cold-responsive gene VvERF117 and elucidated its positive regulatory function in cold tolerance. VvERF117 exhibits transcriptional activity and localizes to the nucleus. VvERF117 overexpression improved cold tolerance in transgenic Arabidopsis, grape calli, and grape leaves, whereas VvERF117 silencing increased cold sensitivity in grape calli and leaves. Furthermore, VvERF117 overexpression remarkably upregulated the expression of several stress-related genes. Importantly, BAS1, encoding a 2-Cys peroxidase (POD), was confirmed as a direct target gene of VvERF117. Meanwhile, compared to the wild-type, POD activity and H2O2 content were remarkably increased and decreased in VvERF117-overexpressing grape calli and leaves, respectively. Conversely, VvERF117 silencing displayed the opposite trend in grape calli and leaves under cold stress. These findings indicate that VvERF117 plays a positive role in cold resistance by, at least in part, enhancing antioxidant capacity through regulating the POD-encoding gene VvBAS1, leading to effective mitigation of reactive oxygen species.

Two transcription factors, RhERF005 and RhCCCH12, regulate rose resistance to Botrytis cinerea by modulating cytokinin levels

Gray mold caused by the necrotrophic fungal pathogen Botrytis cinerea is one of the most destructive diseases in rose (Rosa spp.). Rose infection by B. cinerea leads to severe economic losses due to necrosis, tissue collapse, and rot. In rose, cytokinins (CKs) positively regulate a defense response to B. cinerea, but little is known about the underlying molecular mechanisms. Here, we characterized two ethylene/jasmonic acid-regulated transcription factors, RhEFR005 and RhCCCH12, that bind to the promoter region of PATHOGENESIS-RELATED 10.1 (RhPR10.1) and promote its transcription, leading to decreased susceptibility to B. cinerea. The RhEFR005/RhCCCH12-RhPR10.1 module regulated cytokinin content in rose, and the susceptibility of RhEFR005-, RhCCCH12-, and RhPR10.1-silenced rose petals can be rescued by exogenous CK. In summary, our results reveal that the RhERF005/RhCCCH12-RhPR10.1 module regulates the CK-induced defense response of rose to B. cinerea.

A long non-coding RNA functions as a competitive endogenous RNA to modulate TaNAC018 by acting as a decoy for tae-miR6206

Increasing evidence indicates a strong correlation between the deposition of cuticular waxes and drought tolerance. However, the precise regulatory mechanism remains elusive. Here, we conducted a comprehensive transcriptome analysis of two wheat (Triticum aestivum) near-isogenic lines, the glaucous line G-JM38 rich in cuticular waxes and the non-glaucous line NG-JM31. We identified 85,143 protein-coding mRNAs, 4,485 lncRNAs, and 1,130 miRNAs. Using the lncRNA-miRNA-mRNA network and endogenous target mimic (eTM) prediction, we discovered that lncRNA35557 acted as an eTM for the miRNA tae-miR6206, effectively preventing tae-miR6206 from cleaving the NAC transcription factor gene TaNAC018. This lncRNA-miRNA interaction led to higher transcript abundance for TaNAC018 and enhanced drought-stress tolerance. Additionally, treatment with mannitol and abscisic acid (ABA) each influenced the levels of tae-miR6206, lncRNA35557, and TaNAC018 transcript. The ectopic expression of TaNAC018 in Arabidopsis also improved tolerance toward mannitol and ABA treatment, whereas knocking down TaNAC018 transcript levels via virus-induced gene silencing in wheat rendered seedlings more sensitive to mannitol stress. Our results indicate that lncRNA35557 functions as a competing endogenous RNA to modulate TaNAC018 expression by acting as a decoy target for tae-miR6206 in glaucous wheat, suggesting that non-coding RNA has important roles in the regulatory mechanisms responsible for wheat stress tolerance.

Exogenous 24-Epibrassinolide Enhanced Drought Tolerance and Promoted BRASSINOSTEROID-INSENSITIVE2 Expression of Quinoa

Brassinosteroids (BRs) are involved in the regulation of biotic and abiotic stresses in plants. The molecular mechanisms of BRs that alleviate the drought stress in quinoa have rarely been reported. Here, quinoa seedlings were treated with 24-epibrassinolide (EBR) and we transiently transferred CqBIN2 to the quinoa seedlings' leaves using VIGS technology to analyze the molecular mechanism of the BR mitigation drought stress. The results showed that EBR treatment significantly increased the root growth parameters, the antioxidant enzyme activities, and the osmolyte content, resulting in a decrease in the H2O2, O2∙-, and malondialdehyde content in quinoa. A transcriptome analysis identified 8124, 2761, and 5448 differentially expressed genes (DEGs) among CK and Drought, CK and EBR + Drought, and Drought and EBR + Drought groups. WGCNA divided these DEGs into 19 modules in which these characterized genes collectively contributed significantly to drought stress. In addition, the EBR application also up-regulated the transcript levels of CqBIN2 and proline biosynthesis genes. Silenced CqBIN2 by VIGS could reduce the drought tolerance, survival rate, and proline content in quinoa seedlings. These findings not only revealed that exogenous BRs enhance drought tolerance, but also provided insight into the novel functions of CqBIN2 involved in regulating drought tolerance in plants.

The E3 ligase TaGW2 mediates transcription factor TaARR12 degradation to promote drought resistance in wheat

Drought stress limits crop yield, but the molecular modulators and their mechanisms underlying the trade-off between drought resistance and crop growth and development remain elusive. Here, a grain width and weight2 (GW2)-like really interesting new gene finger E3 ligase, TaGW2, was identified as a pivotal regulator of both kernel development and drought responses in wheat (Triticum aestivum). TaGW2 overexpression enhances drought resistance but leads to yield drag under full irrigation conditions. In contrast, TaGW2 knockdown or knockout attenuates drought resistance but remarkably increases kernel size and weight. Furthermore, TaGW2 directly interacts with and ubiquitinates the type-B Arabidopsis response regulator TaARR12, promoting its degradation via the 26S proteasome. Analysis of TaARR12 overexpression and knockdown lines indicated that TaARR12 represses the drought response but does not influence grain yield in wheat. Further DNA affinity purification sequencing combined with transcriptome analysis revealed that TaARR12 downregulates stress-responsive genes, especially group-A basic leucine zipper (bZIP) genes, resulting in impaired drought resistance. Notably, TaARR12 knockdown in the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-mediated tagw2 knockout mutant leads to significantly higher drought resistance and grain yield compared to wild-type plants. Collectively, these findings show that the TaGW2-TaARR12 regulatory module is essential for drought responses, providing a strategy for improving stress resistance in high-yield wheat varieties.

Development of KASP markers assisted with soybean drought tolerance in the germination stage based on GWAS

Soybean [Glycine max(L.)Merr.] is a leading oil-bearing crop and cultivated globally over a vast scale. The agricultural landscape in China faces a formidable challenge with drought significantly impacting soybean production. In this study, we treated a natural population of 264 Chinese soybean accessions using 15% PEG-6000 and used GR, GE, GI, RGR, RGE, RGI and ASFV as evaluation index. Using the ASFV, we screened 17 strong drought-tolerant soybean germplasm in the germination stage. Leveraging 2,597,425 high-density SNP markers, we conducted Genome-Wide Association Studies (GWAS) and identified 92 SNPs and 9 candidate genes significantly associated with drought tolerance. Furthermore, we developed two KASP markers for S14_5147797 and S18_53902767, which closely linked to drought tolerance. This research not only enriches the pool of soybean germplasm resources but also establishes a robust foundation for the molecular breeding of drought tolerance soybean varieties.

RcMYB8 enhances salt and drought tolerance in rose (Rosa chinensis) by modulating RcPR5/1 and RcP5CS1

Plant Myeloblastosis (MYB) proteins function crucially roles upon variegated abiotic stresses. Nonetheless, their effects and mechanisms in rose (Rosa chinensis) are not fully clarified. In this study, we characterized the effects of rose RcMYB8 under salt and drought tolerances. For induction of the RcMYB8 expression, NaCl and drought stress treatment were adopted. Rose plants overexpressing RcMYB8 displayed enhanced tolerance to salinity and drought stress, while silencing RcMYB8 resulted in decreased tolerance, as evidenced by lowered intra-leaf electrolyte leakage and callose deposition, as well as photosynthetic sustainment under stressed conditions. Here, we further show that RcMYB8 binds similarly to the promoters of RcPR5/1 and RcP5C51 in vivo and in vitro. Inhibiting RcP5CS1 by virus-induced gene silencing led to decreased drought tolerance through the reactive oxygen species (ROS) homeostatic regulation. RcP5CS1-silenced plants showed an increase in ion leakage and reduce of proline content, together with the content of malondialdehyde (MDA) increased, lowered activities of Catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD). Our study highlights the transcriptional modulator role of RcMYB8 in drought and salinity tolerances, which bridges RcPR5/1 and RcP5CS1 by promoting ROS scavenging. Besides, it is probably applicable to the rose plant engineering for enhancing their abiotic stress tolerances.

Genome-wide identification and comprehensive analysis of the phytochrome-interacting factor (PIF) gene family in wheat

Phytochrome-interacting factors (PIFs) are essential transcription factors for plant growth, development, and stress responses. Although PIF genes have been extensively studied in many plant species, they have not been thoroughly investigated in wheat. Here, we identified 18 PIF genes in cultivated hexaploid wheat (Triticum aestivum L). Phylogenetic analysis, exon-intron structures, and motif compositions revealed the presence of four distinct groups of TaPIFs. Genome-wide collinearity analysis of PIF genes revealed the evolutionary history of PIFs in wheat, Oryza sativa, and Brachypodium distachyon. Cis-regulatory element analysis suggested that TaPIF genes indicated participated in plant development and stress responses. Subcellular localization assays indicated that TaPIF2-1B and TaPIF4-5B were transcriptionally active. Both were found to be localized to the nucleus. Gene expression analyses demonstrated that TaPIFs were primarily expressed in the leaves and were induced by various biotic and abiotic stresses and phytohormone treatments. This study provides new insights into PIF-mediated stress responses and lays a strong foundation for future investigation of PIF genes in wheat.

The NtDEGP5 gene improves drought tolerance in tobacco (Nicotiana tabacum L.) by dampening plastid extracellular Ca2+ and flagellin signaling and thereby reducing ROS production

Tobacco is an essential cash crop, but drought has become a major factor in the decline of global tobacco production as a result of changes in the global climate. The HtrA protease is an oligomeric serine endopeptidase that responds to stress in plants. DEGP5 is a member of the gene family that encodes HtrA protease, which promotes plant adaptation to adversity. The aim of this study was to investigate the role and mechanism employed by the DEGP5 gene in response to drought stress in tobacco. NtDEGP5-overexpression lines were obtained by genetic transformation and the phenotypes and transcriptomes of NtDEGP5-overexpression lines and wild-type (K326) tobacco seedlings were compared under drought stress. The results demonstrated that plants overexpressing NtDEGP5 exhibited greater drought tolerance. The differentially expressed genes involved in the regulation of drought tolerance by DEGP5 were enriched in metabolic pathways, such as plant-pathogen interaction and glutathione metabolism, with the plant-pathogen interaction pathway having the most differentially expressed genes. An analysis of the plant-pathogen interaction pathway revealed that these genes contributed to the suppression of plastid extracellular Ca2+ signaling and flagellin signaling to inhibit reactive oxygen species production, and that lower levels of reactive oxygen species act as a signal to regulate the activation of the antioxidant system, further balancing the production and removal of reactive oxygen species in tobacco seedlings under drought stress. These findings suggest that the NtDEGP5 gene can enhance the drought tolerance of tobacco by regulating the homeostasis of reactive oxygen species by inhibiting extracellular plastids.

Wheat adaptation to environmental stresses under climate change: Molecular basis and genetic improvement

Wheat (Triticum aestivum) is a staple food for about 40% of the world's population. As the global population has grown and living standards improved, high yield and improved nutritional quality have become the main targets for wheat breeding. However, wheat production has been compromised by global warming through the more frequent occurrence of extreme temperature events, which have increased water scarcity, aggravated soil salinization, caused plants to be more vulnerable to diseases, and directly reduced plant fertility and suppressed yield. One promising option to address these challenges is the genetic improvement of wheat for enhanced resistance to environmental stress. Several decades of progress in genomics and genetic engineering has tremendously advanced our understanding of the molecular and genetic mechanisms underlying abiotic and biotic stress responses in wheat. These advances have heralded what might be considered a "golden age" of functional genomics for the genetic improvement of wheat. Here, we summarize the current knowledge on the molecular and genetic basis of wheat resistance to abiotic and biotic stresses, including the QTLs/genes involved, their functional and regulatory mechanisms, and strategies for genetic modification of wheat for improved stress resistance. In addition, we also provide perspectives on some key challenges that need to be addressed.

Molecular Mechanism Underlying the Sorghum sudanense (Piper) Stapf. Response to Osmotic Stress Determined via Single-Molecule Real-Time Sequencing and Next-Generation Sequencing

Drought, as a widespread environmental factor in nature, has become one of the most critical factors restricting the yield of forage grass. Sudangrass (Sorghum sudanense (Piper) Stapf.), as a tall and large grass, has a large biomass and is widely used as forage and biofuel. However, its growth and development are limited by drought stress. To obtain novel insight into the molecular mechanisms underlying the drought response and excavate drought tolerance genes in sudangrass, the first full-length transcriptome database of sudangrass under drought stress at different time points was constructed by combining single-molecule real-time sequencing (SMRT) and next-generation transcriptome sequencing (NGS). A total of 32.3 Gb of raw data was obtained, including 20,199 full-length transcripts with an average length of 1628 bp after assembly and correction. In total, 11,921 and 8559 up- and down-regulated differentially expressed genes were identified between the control group and plants subjected to drought stress. Additionally, 951 transcription factors belonging to 50 families and 358 alternative splicing events were found. A KEGG analysis of 158 core genes exhibiting continuous changes over time revealed that 'galactose metabolism' is a hub pathway and raffinose synthase 2 and β-fructofuranosidase are key genes in the response to drought stress. This study revealed the molecular mechanism underlying drought tolerance in sudangrass. Furthermore, the genes identified in this study provide valuable resources for further research into the response to drought stress.

Transcriptomic and co-expression network analyses on diverse wheat landraces identifies candidate master regulators of the response to early drought

Introduction

Over four billion people around the world rely on bread wheat (Triticum aestivum L.) as a major constituent of their diet. The changing climate, however, threatens the food security of these people, with periods of intense drought stress already causing widespread wheat yield losses. Much of the research into the wheat drought response has centred on the response to drought events later in development, during anthesis or grain filling. But as the timing of periods of drought stress become increasingly unpredictable, a more complete understanding of the response to drought during early development is also needed.

Methods

Here, we utilized the YoGI landrace panel to identify 10,199 genes which were differentially expressed under early drought stress, before weighted gene co-expression network analysis (WGCNA) was used to construct a co-expression network and identify hub genes in modules particularly associated with the early drought response.

Results

Of these hub genes, two stood out as novel candidate master regulators of the early drought response - one as an activator (TaDHN4-D1; TraesCS5D02G379200) and the other as a repressor (uncharacterised gene; TraesCS3D02G361500).

Discussion

As well as appearing to coordinate the transcriptional early drought response, we propose that these hub genes may be able to regulate the physiological early drought response due to potential control over the expression of members of gene families well-known for their involvement in the drought response in many plant species, namely dehydrins and aquaporins, as well as other genes seemingly involved in key processes such as, stomatal opening, stomatal closing, stomatal morphogenesis and stress hormone signalling.

PagMYB151 facilitates proline accumulation to enhance salt tolerance of poplar

Poplar is one of the main urban and rural greening and shade tree species in the northern hemisphere, but its growth and development is always restricted by salt stress. R2R3-MYB transcription factor family is commonly involved in many biological processes during plant growth and stress endurance. In this study, PagMYB151 (Potri.014G035100) one of R2R3-MYB members related to salt stress and expressed in both nucleus and cell membrane was cloned from Populus alba × P. glandulosa to perfect the salt tolerance mechanism. Morphological and physiological indexes regulated by PagMYB151 were detected using the PagMYB151 overexpression (OX) and RNA interference (RNAi) transgenic poplar lines. Under salt stress conditions, compared with RNAi and the non-transgenic wild-type (WT) plants, the plant height, both aboveground and underground part fresh weight of OX was significantly increased. In addition, OX has a longer and finer root structure and a larger root surface area. The root activity of OX was also enhanced, which was significantly different from RNAi but not from WT under salt treatment. Under normal conditions, the stomatal aperture of OX was larger than WT, whereas this phenotype was not obvious after salt stress treatment. In terms of physiological indices, OX enhanced the accumulation of proline but reduced the toxicity of malondialdehyde to plants under salt stress. Combing with the transcriptome sequencing data, 6 transcription factors induced by salt stress and co-expressed with PagMYB151 were identified that may cooperate with PagMYB151 to function in salt stress responding process. This study provides a basis for further exploring the molecular mechanism of poplar PagMYB151 transcription factor under abiotic stress.

Transcriptome Analysis of Roots from Wheat (Triticum aestivum L.) Varieties in Response to Drought Stress

Under climate change, drought is one of the most limiting factors that influences wheat (Triticum aestivum L.) production. Exploring stress-related genes is vital for wheat breeding. To identify genes related to the drought tolerance response, two common wheat cultivars, Zhengmai 366 (ZM366) and Chuanmai 42 (CM42), were selected based on their obvious difference in root length under 15% PEG-6000 treatment. The root length of the ZM366 cultivar was significantly longer than that of CM42. Stress-related genes were identified by RNA-seq in samples treated with 15% PEG-6000 for 7 days. In total, 11,083 differentially expressed genes (DEGs) and numerous single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) were identified. GO enrichment analysis revealed that the upregulated genes were mainly related to the response to water, acidic chemicals, oxygen-containing compounds, inorganic substances, and abiotic stimuli. Among the DEGs, the expression levels of 16 genes in ZM366 were higher than those in CM42 after the 15% PEG-6000 treatment based on RT-qPCR. Furthermore, EMS-induced mutants in Kronos (T. turgidum L.) of 4 representative DEGs possessed longer roots than the WT after the 15% PEG-6000 treatment. Altogether, the drought stress genes identified in this study represent useful gene resources for wheat breeding.

Transcriptome and Proteome Analysis Revealed That Hormone and Reactive Oxygen Species Synergetically Regulate Dormancy of Introgression Line in Rice (Oryza sativa L.)

Dormancy is a complex agronomy phenotype controlled by multiple signaling and a key trait repressing pre-harvest sprouting (PHS). However, the signaling network of dormancy remains unclear. In this study, we used Zhonghua11 (ZH11) with a weak dormancy, and Introgression line (IL) with a strong dormancy to study the mechanism of hormones and reactive oxygen species (ROS) crosstalk regulating rice dormancy. The germination experiment showed that the germination rate of ZH11 was 76.86%, while that of IL was only 1.25%. Transcriptome analysis showed that there were 1658 differentially expressed genes (DEGs) between IL and ZH11, of which 577 were up-regulated and 1081 were down-regulated. Additionally, DEGs were mainly enriched in oxidoreductase activity, cell periphery, and plant hormone signal transduction pathways. Tandem mass tags (TMT) quantitative proteomics analysis showed 275 differentially expressed proteins (DEPs) between IL and ZH11, of which 176 proteins were up-regulated, 99 were down-regulated, and the DEPs were mainly enriched in the metabolic process and oxidation-reduction process. The comprehensive transcriptome and proteome analysis showed that their correlation was very low, and only 56 genes were co-expressed. Hormone content detection showed that IL had significantly lower abscisic acid (ABA) contents than the ZH11 while having significantly higher jasmonic acid (JA) contents than the ZH11. ROS content measurement showed that the hydrogen peroxide (H₂O₂) content of IL was significantly lower than the ZH11, while the production rate of superoxide anion (O₂^.-) was significantly higher than the ZH11. These results indicate that hormones and ROS crosstalk to regulate rice dormancy. In particular, this study has deepened our mechanism of ROS and JA crosstalk regulating rice dormancy and is conducive to our precise inhibition of PHS.