Transcription factor WRKY22 promotes aluminum tolerance via activation of OsFRDL4 expression and enhancement of citrate secretion in rice (Oryza sativa)

Strigolactones alleviate AlCl3 stress by vacuolar compartmentalization and cell wall blocking in apple

Poor management and excess fertilization of apple (Malus domestica Borkh.) orchards are causing increasingly serious soil acidification, resulting in Al toxicity and direct poisoning of roots. Strigolactones (SLs) are reported to be involved in plant responses to abiotic stress, but their role and mechanism under AlCl3 stress remain unknown. Here, we found that applying 1 μm GR24 (an SL analoge) significantly alleviated AlCl3 stress of M26 apple rootstock, mainly by blocking the movement of Al through cell wall and by vacuolar compartmentalization of Al. RNA-seq analysis identified the core transcription factor gene MdWRKY53, and overexpressing MdWRKY53 enhanced AlCl3 tolerance in transgenic apple plants through the same mechanism as GR24. Subsequently, we identified MdPMEI45 (encoding pectin methylesterase inhibitor) and MdALS3 (encoding an Al transporter) as downstream target genes of MdWRKY53 using chromatin immunoprecipitation followed by sequencing (ChIP-seq). GR24 enhanced the interaction between MdWRKY53 and the transcription factor MdTCP15, further increasing the binding of MdWRKY53 to the MdPMEI45 promoter and inducing MdPMEI45 expression to prevent Al from crossing cell wall. MdWRKY53 also bound to the promoter of MdALS3 and enhanced its transcription to compartmentalize Al in vacuoles under AlCl3 stress. We therefore identified two modules involved in alleviating AlCl3 stress in woody plant apple: the SL-WRKY+TCP-PMEI module required for excluding external Al by blocking the entry of Al3+ into cells and the SL-WRKY-ALS module allowing internal detoxification of Al through vacuolar compartmentalization. These findings lay a foundation for the practical application of SLs in agriculture.

OsAlR3 regulates aluminum tolerance through promoting the secretion of organic acids and the expression of antioxidant genes in rice

In acidic soils, aluminum (Al) toxicity inhibits the growth and development of plant roots and affects nutrient and water absorption, leading to reduced yield and quality. Therefore, it is crucial to investigate and identify candidate genes for Al tolerance and elucidate their physiological and molecular mechanisms under Al stress. In this study, we identified a new gene OsAlR3 regulating Al tolerance, and analyzed its mechanism from physiological, transcriptional and metabolic levels. Compared with the WT, malondialdehyde (MDA) and hydrogen peroxide (H2O2) content were significantly increased, superoxide dismutase (SOD) activity and citric acid (CA) content were significantly decreased in the osalr3 mutant lines when exposed to Al stress. Under Al stress, the osalr3 exhibited decreased expression of antioxidant-related genes and lower organic acid content compared with WT. Integrated transcriptome and metabolome analysis showed the phenylpropanoid biosynthetic pathway plays an important role in OsAlR3-mediated Al tolerance. Exogenous CA and oxalic acid (OA) could increase total root length and enhance the antioxidant capacity in the mutant lines under Al stress. Conclusively, we found a new gene OsAlR3 that positively regulates Al tolerance by promoting the chelation of Al ions through the secretion of organic acids, and increasing the expression of antioxidant genes.

Comparative transcriptome analyses reveal regulatory network and hub genes of aluminum response in roots of elephant grass (Cenchrus purpureus)

Aluminum (Al) toxicity severely restricts the growth and productivity of elephant grass in acidic soils around the world. However, the molecular mechanisms of Al response have not been investigated in elephant grass. In this study, we conducted phenotype, physiology, and transcriptome analysis of elephant grass roots in response to Al stress. Phenotypic analysis revealed that a low concentration of Al stress improved root growth while higher Al concentrations inhibit root growth. Al stress significantly increased the citrate (CA) content in roots, while the expression levels of genes related to citrate synthesis were substantially changed. The multidrug and toxic compound extrusion (MATE) family were identified as hub genes in the co-expression network of Al response in elephant grass roots. Phylogenetic analysis showed that hub genes CpMATE93 and CpMATE158 belonged to the same clade as other MATE genes reported to be involved in citrate transport. Additionally, overexpression of CpMATE93 conferred Al resistance in yeast cells. These results provide a theoretical basis for further studies of molecular mechanisms in the elephant grass response to Al stress and could help breeders develop elite cultivars with Al tolerance.

WRKY Transcription Factor Responses and Tolerance to Abiotic Stresses in Plants

Plants are subjected to abiotic stresses throughout their developmental period. Abiotic stresses include drought, salt, heat, cold, heavy metals, nutritional elements, and oxidative stresses. Improving plant responses to various environmental stresses is critical for plant survival and perpetuation. WRKY transcription factors have special structures (WRKY structural domains), which enable the WRKY transcription factors to have different transcriptional regulatory functions. WRKY transcription factors can not only regulate abiotic stress responses and plant growth and development by regulating phytohormone signalling pathways but also promote or suppress the expression of downstream genes by binding to the W-box [TGACCA/TGACCT] in the promoters of their target genes. In addition, WRKY transcription factors not only interact with other families of transcription factors to regulate plant defence responses to abiotic stresses but also self-regulate by recognising and binding to W-boxes in their own target genes to regulate their defence responses to abiotic stresses. However, in recent years, research reviews on the regulatory roles of WRKY transcription factors in higher plants have been scarce and shallow. In this review, we focus on the structure and classification of WRKY transcription factors, as well as the identification of their downstream target genes and molecular mechanisms involved in the response to abiotic stresses, which can improve the tolerance ability of plants under abiotic stress, and we also look forward to their future research directions, with a view of providing theoretical support for the genetic improvement of crop abiotic stress tolerance.

GmMYB183, a R2R3-MYB Transcription Factor in Tamba Black Soybean (Glycine max. cv. Tamba), Conferred Aluminum Tolerance in Arabidopsis and Soybean

Aluminum (Al) toxicity is one of the environmental stress factors that affects crop growth, development, and productivity. MYB transcription factors play crucial roles in responding to biotic or abiotic stresses. However, the roles of MYB transcription factors in Al tolerance have not been clearly elucidated. Here, we found that GmMYB183, a gene encoding a R2R3 MYB transcription factor, is involved in Al tolerance. Subcellular localization studies revealed that GmMYB183 protein is located in the nucleus, cytoplasm and cell membrane. Overexpression of GmMYB183 in Arabidopsis and soybean hairy roots enhanced plant tolerance towards Al stress compared to the wild type, with higher citrate secretion and less Al accumulation. Furthermore, we showed that GmMYB183 binds the GmMATE75 gene promoter encoding for a plasma-membrane-localized citrate transporter. Through a dual-luciferase reporter system and yeast one hybrid, the GmMYB183 protein was shown to directly activate the transcription of GmMATE75. Furthermore, the expression of GmMATE75 may depend on phosphorylation of Ser36 residues in GmMYB183 and two MYB sites in P3 segment of the GmMATE75 promoter. In conclusion, GmMYB183 conferred Al tolerance by promoting the secretion of citrate, which provides a scientific basis for further elucidating the mechanism of plant Al resistance.

Identification of responsive genes to multiple abiotic stresses in rice (Oryza sativa): a meta-analysis of transcriptomics data

Abiotic stresses limit the quantity and quality of rice grain production, which is considered a strategic crop in many countries. In this study, a meta-analysis of different microarray data at seedling stage was performed to investigate the effects of multiple abiotic stresses (drought, salinity, cold situation, high temperature, alkali condition, iron, aluminum, and heavy metal toxicity, nitrogen, phosphorus, and potassium deficiency) on rice. Comparative analysis between multiple abiotic stress groups and their control groups indicated 561 differentially expressed genes (DEGs), among which 422 and 139 genes were up-regulated and down-regulated, respectively. Gene Ontology analysis showed that the process of responding to stresses and stimuli was significantly enriched. In addition, pathways such as metabolic process and biosynthesis of secondary metabolites were identified by KEGG pathway analysis. Weighted correlation network analysis (WGCNA) uncovered 17 distinct co-expression modules. Six modules were significantly associated with genes involved in response to abiotic stresses. Finally, to validate the results of the meta-analysis, five genes, including TIFY9 (JAZ5), RAB16B, ADF3, Os01g0124650, and Os05g0142900 selected for qRT-PCR analysis. Expression patterns of selected genes confirmed the results of the meta-analysis. The outcome of this study could help introduce candidate genes that may be beneficial for use in genetic engineering programs to produce more tolerant crops or as markers for selection.

Insight into the relationship between metabolic enzymes and oxadiazon degradation in Oryza sativa for reducing environmental risks

Oxadiazon (ODZ) is extensively utilized in agricultural fields for weed control owing to its strong effectiveness. However, excessive loading of ODZ in water bodies and agricultural soils can lead to various environmental concerns. Therefore, it is crucial to understand the ODZ metabolic process and associated mechanisms in crops to assess the likelihood of ODZ contamination in the environment. This study aimed to assess the effects of ODZ on the growth and toxicological responses of rice (Oryza sativa). The growth of rice tissues was notably compromised with the increase in ODZ concentrations. RNA sequencing in combination with liquid chromatography-quadrupole-time-of-flight-high-resolution mass spectrometry/mass spectrometry (LC-Q-TOF-HRMS/MS) analysis allowed for the identification of numerous transcriptional components associated with ODZ metabolism. Four libraries comprising rice roots and shoots exposed to ODZ were RNA-sequenced in triplicate. The application of environmentally realistic ODZ concentrations upregulated the expression of 844 genes in shoots and 1476 genes in roots. Gene enrichment analysis revealed the presence of multiple enzymes involved in ODZ metabolism and detoxification. These enzymes play a critical role in mitigating environmental stress and facilitating xenobiotic metabolism. Notably, among differentially expressed genes, several key enzymes were identified, including cytochrome P450s, protein kinases, aminotransferases, and ATP-binding cassette transporters involved in the metabolic process. Using LC-Q-TOF-HRMS/MS, 3 metabolites and 13 conjugates were identified in multiple metabolic pathways involving oxidation, hydrolysis, glycosylation, acetylation, and methylation. This study successfully established a potential link between the specific metabolic products of ODZ and increased activities of their corresponding enzymes. Moreover, this study considerably elucidates the detailed pathways and mechanisms involved in ODZ metabolism. The study findings provide valuable insights into the development of genotypes for reducing ODZ residues in paddy fields and minimizing their accumulation in rice crops.

Genome-wide profiling of genetic variations reveals the molecular basis of aluminum stress adaptation in Tibetan wild barley

Aluminum (Al) toxicity in acidic soil is a major factor affecting crop productivity. The extensive genetic diversity found in Tibetan wild barley germplasms offers a valuable reservoir of alleles associated with aluminum tolerance. Here, resequencing of two Al-tolerant barley genotypes (Tibetan wild barley accession XZ16 and cultivated barley Dayton) identified a total of 19,826,182 and 16,287,277 single nucleotide polymorphisms (SNPs), 1628,052 and 1386,973 insertions/deletions (InDels), 61,532 and 57,937 structural variations (SVs), 248,768 and 240,723 copy number variations (CNVs) in XZ16 and Dayton, respectively, and uncovered approximately 600 genes highly related to Al tolerance in barley. Comparative genomic analyses unveiled 71 key genes that contain unique genetic variants in XZ16 and are predominantly associated with organic acid exudation, Al sequestration, auxin response, and transcriptional regulation. Manipulation of these key genes at the genetic and transcriptional level is a promising strategy for developing optimal haplotype combinations and new barley cultivars with improved Al tolerance. This study represents the first comprehensive examination of genetic variation in Al-tolerant Tibetan wild barley through genome-wide profiling. The obtained results make the deep insight into the mechanisms underlying barley adaptation to Al toxicity, and identified the candidate genes useful for improvement of Al tolerance in barley.

Aluminum phytotoxicity in acidic environments: A comprehensive review of plant tolerance and adaptation strategies

Aluminum (Al), a non-essential metal for plant growth, exerts significant phytotoxic effects, particularly on root growth. Anthropogenic activities would intensify Al's toxic effects by releasing Al3+ into the soil solution, especially in acidic soils with a pH lower than 5.5 and rich mineral content. The severity of Al-induced phytotoxicity varies based on factors such as Al concentration, ionic form, plant species, and growth stages. Al toxicity leads to inhibited root and shoot growth, reduced plant biomass, disrupted water uptake causing nutritional imbalance, and adverse alterations in physiological, biochemical, and molecular processes. These effects collectively lead to diminished plant yield and quality, along with reduced soil fertility. Plants employ various mechanisms to counter Al toxicity under stress conditions, including sequestering Al in vacuoles, exuding organic acids (OAs) like citrate, oxalate, and malate from root tip cells to form Al-complexes, activating antioxidative enzymes, and overexpressing Al-stress regulatory genes. Recent advancements focus on enhancing the exudation of OAs to prevent Al from entering the plant, and developing Al-tolerant varieties. Gene transporter families, such as ATP-Binding Cassette (ABC), Aluminum-activated Malate Transporter (ALMT), Natural resistance-associated macrophage protein (Nramp), Multidrug and Toxic compounds Extrusion (MATE), and aquaporin, play a crucial role in regulating Al toxicity. This comprehensive review examined recent progress in understanding the cytotoxic impact of Al on plants at the cellular and molecular levels. Diverse strategies developed by both plants and scientists to mitigate Al-induced phytotoxicity were discussed. Furthermore, the review explored recent genomic developments, identifying candidate genes responsible for OAs exudation, and delved into genome-mediated breeding initiatives, isolating transgenic and advanced breeding lines to cultivate Al-tolerant plants.

Harnessing the power of exogenous factors to enhance plant resistance to aluminum toxicity; a critical review

Aluminum (Al) is the most prevalent element in the earth crust and is toxic to plants in acidic soils. However, plants can address Al toxicity through external exclusion (which prevents Al from entering roots) and internal detoxification (which counterbalances the toxic-Al absorbed by roots). Nowadays, certain categories of exogenously added regulatory factors (EARF), such as nutritional elements, organic acids, amino acids, phytohormones, or biochar, etc. play a critical role in reducing the bioavailability/toxicity of Al in plants. Numerous studies suggest that regulating factors against Al toxicity mediate the expression of Al-responsive genes and transcription factors, thereby regulating the secretion of organic acids, alkalizing rhizosphere pH, modulating cell wall (CW) modifications, improving antioxidant defense systems, and promoting the compartmentalization of non-toxic Al within intracellular. This review primarily discusses recent and older published papers to demonstrate the basic concepts of Al phytotoxicity. Furthermore, we provide a comprehensive explanation of the crucial roles of EARF-induced responses against Al toxicity in plants. This information may serve as a foundation for improving plant resistance to Al and enhancing the growth of susceptible species in acidic soils. And this review holds significant theoretical significance for EARF to improve the quality of acidic soils cultivated land, increase crop yield and quality, and ensure food security.

Identification and characterization of long noncoding RNAs in two contrasting olive (Olea europaea L.) genotypes subjected to aluminum toxicity

Aluminum (Al) toxcity is considered to be the primary factor limiting crop productivity in acidic soil. Many studies indicate that long non-coding RNAs (lncRNAs) fulfil a crucial role in plant growth and responses to different abiotic stress. However, identification and characterization of lncRNAs responsive to Al stress at a genome-wide level in olive tree is still lacking. Here, we performed comparative analysis on lncRNA transcriptome between Zhonglan (an Al-tolerant genotype) and Frantoio selezione (Al-sensitive) responding to Al exposure. A total of 19,498 novel lncRNAs were identified from both genotypes, and 6900 lncRNA-target pairs were identified as cis-acting and 2311 supposed to be trans-acting. Among them, 2076 lncRNAs were appraised as Al tolerance-associated lncRNAs due to their distinctly genotype-specific expression profiles under Al exposure. Target prediction and functional analyses revealed several key lncRNAs are related to genes encoding pectinesterases, xyloglucan endotransglucosylase/hydrolase, WRKY and MYB transcription factors, which mainly participate in the modification of cell wall for Al tolerance. Furthermore, gene co-expression network analysis showed 8 lncRNA-mRNA-miRNA modules participate in transcriptional regulation of downstream Al resistant genes. Our findings increased our understanding about the function of lncRNAs in responding to Al stress in olive and identified potential promising lncRNAs for further investigation.

Two Sweet Sorghum (Sorghum bicolor L.) WRKY Transcription Factors Promote Aluminum Tolerance via the Reduction in Callose Deposition

Aluminum (Al) toxicity is a primary limiting factor for crop production in acidic soils. The WRKY transcription factors play important roles in regulating plant growth and stress resistance. In this study, we identified and characterized two WRKY transcription factors, SbWRKY22 and SbWRKY65, in sweet sorghum (Sorghum bicolor L.). Al induced the transcription of SbWRKY22 and SbWRKY65 in the root apices of sweet sorghum. These two WRKY proteins were localized in the nucleus and exhibited transcriptional activity. SbWRKY22 showed the significant transcriptional regulation of SbMATE, SbGlu1, SbSTAR1, SbSTAR2a, and SbSTAR2b, which are major known Al tolerance genes in sorghum. Interestingly, SbWRKY65 had almost no effect on the aforementioned genes, but it significantly regulated the transcription of SbWRKY22. Therefore, it is speculated that SbWRKY65 might indirectly regulate Al-tolerance genes mediated by SbWRKY22. The heterologous expression of SbWRKY22 and SbWRKY65 greatly improved the Al tolerance of transgenic plants. The enhanced Al tolerance phenotype of transgenic plants is associated with reduced callose deposition in their roots. These findings suggest the existence of SbWRKY22- and SbWRKY65-mediated Al tolerance regulation pathways in sweet sorghum. This study extends our understanding of the complex regulatory mechanisms of WRKY transcription factors in response to Al toxicity.

Linking plant functional genes to rhizosphere microbes: a review

The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.

Exogenous application of salicylic acid improves freezing stress tolerance in alfalfa

Freezing stress is one of the most detrimental environmental factors that can seriously impact the growth, development, and distribution of alfalfa (Medicago sativa L.). Exogenous salicylic acid (SA) has been revealed as a cost-effective method of improving defense against freezing stress due to its predominant role in biotic and abiotic stress resistance. However, how the molecular mechanisms of SA improve freezing stress resistance in alfalfa is still unclear. Therefore, in this study, we used leaf samples of alfalfa seedlings pretreatment with 200 μM and 0 μM SA, which were exposed to freezing stress (-10°C) for 0, 0.5, 1, and 2h and allowed to recover at normal temperature in a growth chamber for 2 days, after which we detect the changes in the phenotypical, physiological, hormone content, and performed a transcriptome analysis to explain SA influence alfalfa in freezing stress. The results demonstrated that exogenous SA could improve the accumulation of free SA in alfalfa leaves primarily through the phenylalanine ammonia-lyase pathway. Moreover, the results of transcriptome analysis revealed that the mitogen-activated protein kinase (MAPK) signaling pathway-plant play a critical role in SA alleviating freezing stress. In addition, the weighted gene co-expression network analysis (WGCNA) found that MPK3, MPK9, WRKY22 (downstream target gene of MPK3), and TGACG-binding factor 1 (TGA1) are candidate hub genes involved in freezing stress defense, all of which are involved in the SA signaling pathway. Therefore, we conclude that SA could possibly induce MPK3 to regulate WRKY22 to participate in freezing stress to induced gene expression related to SA signaling pathway (NPR1-dependent pathway and NPR1-independent pathway), including the genes of non-expresser of pathogenesis-related gene 1 (NPR1), TGA1, pathogenesis-related 1 (PR1), superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX), glutathione-S-transferase (GST), and heat shock protein (HSP). This enhanced the production of antioxidant enzymes such as SOD, POD, and APX, which increases the freezing stress tolerance of alfalfa plants.

Salt-responsive bermudagrass microRNAs and insights into light reaction photosynthetic performance

INTRODUCTION

Bermudagrass (Cynodon dactylon L.) is a warm-season grass with high drought and salt tolerance. However, its cultivation as a silage crop is limited by its lower forage value when compared to other C4 crops. Because of its high genetic variability in abiotic stress tolerance, bermudagrass-mediated genetic breeding offers significant promise for introducing alternative fodder crops in saline and drought-affected regions, and improved photosynthetic capacity is one way for increasing forage yield.

METHODS

Here, we used RNA sequencing to profile miRNAs in two bermudagrass genotypes with contrasting salt tolerance growing under saline conditions.

RESULTS

Putatively, 536 miRNA variants were salt-inducible, with the majority being downregulated in salt-tolerant vs sensitive varieties. Also, seven miRNAs putatively targeted 6 genes which were significantly annotated to light reaction photosynthesis. Among the microRNAs, highly abundant miRNA171f in the salt tolerant regime targeted Pentatricopeptide repeat-containing protein and dehydrogenase family 3 member F1 both annotated to electron transport and Light harvesting protein complex 1 genes annotated to light photosynthetic reaction in salt tolerant regime vs salt sensitive counterparts. To facilitate genetic breeding for photosynthetic capacity, we overexpressed miR171f in Medicago tracantula which resulted in a substantial increase in the chlorophyll transient curve, electron transport rate, quantum yield of photosystem II non photochemical quenching, NADPH and biomass accumulation under saline conditions while its targets were downregulated. At ambient light level the electron transport was negatively correlated with all parameters while the NADPH was positively associated higher dry matter in mutants.

DISCUSSION

These results demonstrate that miR171f improves photosynthetic performance and dry matter accumulation via transcriptional repression of genes in the electron transport pathway under saline conditions and thus a target for breeding.

Deciphering Interactions between Phosphorus Status and Toxic Metal Exposure in Plants and Rhizospheres to Improve Crops Reared on Acid Soil

Acid soils are characterized by deficiencies in essential nutrient elements, oftentimes phosphorus (P), along with toxicities of metal elements, such as aluminum (Al), manganese (Mn), and cadmium (Cd), each of which significantly limits crop production. In recent years, impressive progress has been made in revealing mechanisms underlying tolerance to high concentrations of Al, Mn, and Cd. Phosphorus is an essential nutrient element that can alleviate exposure to potentially toxic levels of Al, Mn, and Cd. In this review, recent advances in elucidating the genes responsible for the uptake, translocation, and redistribution of Al, Mn, and Cd in plants are first summarized, as are descriptions of the mechanisms conferring resistance to these toxicities. Then, literature highlights information on interactions of P nutrition with Al, Mn, and Cd toxicities, particularly possible mechanisms driving P alleviation of these toxicities, along with potential applications for crop improvement on acid soils. The roles of plant phosphate (Pi) signaling and associated gene regulatory networks relevant for coping with Al, Mn, and Cd toxicities, are also discussed. To develop varieties adapted to acid soils, future work needs to further decipher involved signaling pathways and key regulatory elements, including roles fulfilled by intracellular Pi signaling. The development of new strategies for remediation of acid soils should integrate the mechanisms of these interactions between limiting factors in acid soils.

Aluminum in plant: Benefits, toxicity and tolerance mechanisms

Aluminum (Al) is the third most ubiquitous metal in the earth's crust. A decrease in soil pH below 5 increases its solubility and availability. However, its impact on plants depends largely on concentration, exposure time, plant species, developmental age, and growing conditions. Although Al can be beneficial to plants by stimulating growth and mitigating biotic and abiotic stresses, it remains unknown how Al mediates these effects since its biological significance in cellular systems is still unidentified. Al is considered a major limiting factor restricting plant growth and productivity in acidic soils. It instigates a series of phytotoxic symptoms in several Al-sensitive crops with inhibition of root growth and restriction of water and nutrient uptake as the obvious symptoms. This review explores advances in Al benefits, toxicity and tolerance mechanisms employed by plants on acidic soils. These insights will provide directions and future prospects for potential crop improvement.

Low-acidity ALUMINUM-DEPENDENT MALATE TRANSPORTER4 genotype determines malate content in cultivated jujube

Jujube (Ziziphus jujuba Mill.), the most economically important fruit tree in Rhamnaceae, was domesticated from sour jujube (Z. jujuba Mill. var. spinosa (Bunge) Hu ex H.F.Chow.). During domestication, fruit sweetness increased and acidity decreased. Reduction in organic acid content is crucial for the increase in sweetness of jujube fruit. In this study, the determination of malate content among 46 sour jujube and 35 cultivated jujube accessions revealed that malate content varied widely in sour jujube (0.90-13.31 mg g-1) but to a lesser extent in cultivated jujube (0.33-2.81 mg g-1). Transcriptome sequencing analysis showed that the expression level of Aluminum-Dependent Malate Transporter 4 (ZjALMT4) was substantially higher in sour jujube than in jujube. Correlation analysis of mRNA abundance and fruit malate content and transient gene overexpression showed that ZjALMT4 participates in malate accumulation. Further sequencing analyses revealed that three genotypes of the W-box in the promoter of ZjALMT4 in sour jujube associated with malate content were detected, and the genotype associated with low malate content was fixed in jujube. Yeast one-hybrid screening showed that ZjWRKY7 binds to the W-box region of the high-acidity genotype in sour jujube, whereas the binding ability was weakened in jujube. Transient dual-luciferase and overexpression analyses showed that ZjWRKY7 directly binds to the promoter of ZjALMT4, activating its transcription, and thereby promoting malate accumulation. These findings provide insights into the mechanism by which ZjALMT4 modulates malate accumulation in sour jujube and jujube. The results are of theoretical and practical importance for the exploitation and domestication of germplasm resources.

Global transcriptomic analysis reveals candidate genes associated with different phosphorus acquisition strategies among soybean varieties

Introduction

Soybean adapts to phosphorus-deficient soils through three important phosphorus acquisition strategies, namely altered root conformation, exudation of carboxylic acids, and symbiosis with clumping mycorrhizal fungi. However, the trade-offs and regulatory mechanisms of these three phosphorus acquisition strategies in soybean have not been researched.

Methods

In this study, we investigated the responses of ten different soybean varieties to low soil phosphorus availability by determining biomass, phosphorus accumulation, root morphology, exudation, and mycorrhizal colonization rate. Furthermore, the molecular regulatory mechanisms underlying root phosphorus acquisition strategies were examined among varieties with different low-phosphorus tolerance using transcriptome sequencing and weighted gene co-expression network analysis.

Results and discussion

The results showed that two types of phosphorus acquisition strategies-"outsourcing" and "do-it-yourself"-were employed by soybean varieties under low phosphorus availability. The "do-it-yourself" varieties, represented by QD11, Zh30, and Sd, obtained sufficient phosphorus by increasing their root surface area and secreting carboxylic acids. In contrast, the "outsourcing" varieties, represented by Zh301, Zh13, and Hc6, used increased symbiosis with mycorrhizae to obtain phosphorus owing to their large root diameters. Transcriptome analysis showed that the direction of acetyl-CoA metabolism could be the dividing line between the two strategies of soybean selection. ERF1 and WRKY1 may be involved in the regulation of phosphorus acquisition strategies for soybeans grown under low P environments. These findings will enhance our understanding of phosphorus acquisition strategies in soybeans. In addition, they will facilitate the development of breeding strategies that are more flexible to accommodate a variety of production scenarios in agriculture under low phosphorus environments.

Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources

Eleusine coracana, finger millet, is a multipurpose crop cultivated in arid and semi-arid regions of Africa and Asia. RNA sequencing (RNA-seq) was used in this study to obtain valuable genomic resources and identify genes differentially expressed between Al-tolerant and Al-susceptible genotypes. Two groups of finger millet genotypes were used: Al-tolerant (215836, 215845, and 229722) and Al-susceptible (212462, 215804 and 238323). The analysis of the RNA-seq data resulted in 198,546 unigenes, 56.5% of which were annotated with significant hits in one or more of the following six databases: NR (48.8%), GO (29.7%), KEGG (45%), PlantTFDB (19.0%), Uniprot (49.2%), and NT (46.2%). It is noteworthy that only 220 unigenes in the NR database had significant hits against finger millet sequences suggesting that finger millet's genomic resources are scarce. The gene expression analysis revealed that 322 genes were significantly differentially expressed between the Al-tolerant and Al-susceptible genotypes, of which 40.7% were upregulated while 59.3% were downregulated in Al-tolerant genotypes. Among the significant DEGs, 54.7% were annotated in the GO database with the top hits being ATP binding (GO:0005524) and DNA binding (GO:0003677) in the molecular function, DNA integration (GO:0015074) and cell redox homeostasis in the biological process, as well as cellular anatomical entity and intracellular component in the cellular component GO classes. Several of the annotated DEGs were significantly enriched for their corresponding GO terms. The KEGG pathway analysis resulted in 60 DEGs that were annotated with different pathway classes, of which carbohydrate metabolism and signal transduction were the most prominent. The homologs of a number of significant DEGs have been previously reported as being associated with Al or other abiotic stress responses in various crops, including carboxypeptidase SOL1, HMA3, AP2, bZIP, C3H, and WRKY TF genes. A more detailed investigation of these and other DEGs will enable genomic-led breeding for Al tolerance in finger millet. RNA-seq data analysis also yielded 119,073 SNP markers, the majority of which had PIC values above 0.3, indicating that they are highly informative. Additionally, 3,553 single-copy SSR markers were identified, of which trinucleotide SSRs were the most prevalent. These genomic resources contribute substantially to the enrichment of genomic databases for finger millet, and facilitate future research on this crop.

The transcription factor SlWRKY37 positively regulates jasmonic acid- and dark-induced leaf senescence in tomato

Initiation and progression of leaf senescence are triggered by various environmental stressors and phytohormones. Jasmonic acid (JA) and darkness accelerate leaf senescence in plants. However, the mechanisms that integrate these two factors to initiate and regulate leaf senescence have not been identified. Here, we report a transcriptional regulatory module centred on a novel tomato WRKY transcription factor, SlWRKY37, responsible for both JA- and dark-induced leaf senescence. The expression of SlWRKY37, together with SlMYC2, encoding a master transcription factor in JA signalling, was significantly induced by both methyl jasmonate (MeJA) and dark treatments. SlMYC2 binds directly to the promoter of SlWRKY37 to activate its expression. Knock out of SlWRKY37 inhibited JA- and dark-induced leaf senescence. Transcriptome analysis and biochemical experiments revealed SlWRKY53 and SlSGR1 (S. lycopersicum senescence-inducible chloroplast stay-green protein 1) as direct transcriptional targets of SlWRKY37 to control leaf senescence. Moreover, SlWRKY37 interacted with a VQ motif-containing protein SlVQ7, and the interaction improved the stability of SlWRKY37 and the transcriptional activation of downstream target genes. Our results reveal the physiological and molecular functions of SlWRKY37 in leaf senescence, and offer a target gene to retard leaf yellowing by reducing sensitivity to external senescence signals, such as JA and darkness.

Malate-mediated CqMADS68 enhances aluminum tolerance in quinoa seedlings through interaction with CqSTOP6, CqALMT6 and CqWRKY88

Aluminum (Al) stress in acidic soils has severe negative effects on crop productivity. In this study, the alleviating effect and related mechanism of malate on Al stress in quinoa (Chenopodium quinoa) seedlings were investigated. The findings indicated that malate alleviated the growth inhibition of quinoa seedlings under Al stress, maintained the enzymatic and nonenzymatic antioxidant systems, and aided resistance to the damage caused by excessive reactive oxygen species (ROS). Under Al stress, malate significantly increased the contents of chlorophyll and carotenoids in quinoa shoots by 103.8% and 240.7%, and significantly increased the ratios of glutathione (GSH)/oxidized glutathione (GSSG), and ascorbate (AsA)/dehydroascorbate (DHA) in roots by 59.9% and 699.2%, respectively. However, malate significantly decreased the superoxide radical (O₂•^-), hydrogen peroxide (H₂O₂), malondialdehyde (MDA) and Al contents in quinoa roots under Al stress by 32.7%, 60.9%, 63.1% and 49%, respectively. Moreover, the CqMADS family and the Al stress-responsive gene families (CqSTOP, CqALMT, and CqWRKY) were identified from the quinoa genome. Comprehensive expression profiling identified CqMADS68 as being involved in malate-mediated Al resistance. Transient overexpression of CqMADS68 increased Al tolerance in quinoa seedlings. More importantly, we found that CqMADS68 regulated the expression of CqSTOP6, CqALMT6 and CqWRKY88 and further demonstrated the interaction of CqMADS68 with CqSTOP6, CqALMT6 and CqWRKY88 by bimolecular fluorescence complementation (BIFC) experiments. Moreover, transient overexpression and physiological and biochemical analyses demonstrated that CqSTOP6, CqALMT6 and CqWRKY88 could also improve Al tolerance by maintaining the antioxidant capacity of quinoa seedlings. Taken together, these findings reveal that CqMADS68, CqSTOP6, CqALMT6 and CqWRKY88 may be important contributors to the Al tolerance regulatory network in quinoa, providing new insights into Al stress resistance.

The OsWRKY63-OsWRKY76-OsDREB1B module regulates chilling tolerance in rice

Rice (Oryza sativa) is sensitive to low temperatures, which affects the yield and quality of rice. Therefore, uncovering the molecular mechanisms behind chilling tolerance is a critical task for improving cold tolerance in rice cultivars. Here, we report that OsWRKY63, a WRKY transcription factor with an unknown function, negatively regulates chilling tolerance in rice. OsWRKY63-overexpressing rice lines are more sensitive to cold stress. Conversely, OsWRKY63-knockout mutants generated using a CRISPR/Cas9 genome editing approach exhibited increased chilling tolerance. OsWRKY63 was expressed in all rice tissues, and OsWRKY63 expression was induced under cold stress, dehydration stress, high salinity stress, and ABA treatment. OsWRKY63 localized in the nucleus plays a role as a transcription repressor and downregulates many cold stress-related genes and reactive oxygen species scavenging-related genes. Molecular, biochemical, and genetic assays showed that OsWRKY76 is a direct target gene of OsWRKY63 and that its expression is suppressed by OsWRKY63. OsWRKY76-knockout lines had dramatically decreased cold tolerance, and the cold-induced expression of five OsDREB1 genes was repressed. OsWRKY76 interacted with OsbHLH148, transactivating the expression of OsDREB1B to enhance chilling tolerance in rice. Thus, our study suggests that OsWRKY63 negatively regulates chilling tolerance through the OsWRKY63-OsWRKY76-OsDREB1B transcriptional regulatory cascade in rice.

FaAKR23 Modulates Ascorbic Acid and Anthocyanin Accumulation in Strawberry (Fragaria × ananassa) Fruits

Strawberry (Fragaria × ananassa) fruits are rich in ascorbic acid (AsA) and anthocyanin, which are essential antioxidants for human health. However, the underlying regulatory mechanism of these antioxidant accumulation, especially AsA accumulation in strawberry fruits, remains largely unknown. In this study, we identified FaAKR23 was a regulator of AsA and anthocyanin accumulation. We transiently expressed FaAKR23 in strawberry fruits and conducted metabolic and molecular analyses to explore the role of FaAKR23 in AsA and anthocyanin accumulation. Transient silencing of FaAKR23 (FaAKR23-RNAi) in strawberry fruits significantly decreased the AsA and anthocyanin contents compared with control (empty vector-RNAi, EV-RNAi). Correspondingly, expression of some structural genes and regulatory factors involved in these two antioxidants’ accumulation was dramatically repressed. In addition, transcriptome analysis of EV-RNAi and FaAKR23-RNAi fruits suggested that FaAKR23 was also involved in starch and sucrose metabolism as well as plant–pathogen interaction. Overall, these results not only provide the coordinated regulatory function of FaAKR23 on AsA and anthocyanin accumulation but also offer a promising candidate gene for strawberry breeding with high antioxidants.

The TaWRKY22–TaCOPT3D Pathway Governs Cadmium Uptake in Wheat

Cadmium (Cd) is a heavy metal nonessential for plants; this toxic metal accumulation in crops has significant adverse effects on human health. The crosstalk between copper (Cu) and Cd has been reported; however, the molecular mechanisms remain unknown. The present study investigated the function of wheat Cu transporter 3D (TaCOPT3D) in Cd tolerance. The TaCOPT3D transcripts significantly accumulated in wheat roots under Cd stress. Furthermore, TaCOPT3D-overexpressing lines were compared to wildtype (WT) plants to test the role of TaCOPT3D in Cd stress response. Under 20 mM Cd treatment, TaCOPT3D-overexpressing lines exhibited more biomass and lower root, shoot, and grain Cd accumulation than the WT plants. In addition, overexpression of TaCOPT3D decreased the reactive oxygen species (ROS) levels and increased the active antioxidant enzymes under Cd conditions. Moreover, the transcription factor (TF) TaWRKY22, which targeted the TaCOPT3D promoter, was identified in the regulatory pathway of TaCOPT3D under Cd stress. Taken together, these results show that TaCOPT3D plays an important role in regulating plant adaptation to cadmium stress through bound by TaWRKY22. These findings suggest that TaCOPT3D is a potential candidate for decreasing Cd accumulation in wheat through genetic engineering.

WRKY74 regulates cadmium tolerance through glutathione-dependent pathway in wheat

Cadmium (Cd) is a toxic heavy metal to plants and human health. Ascorbate (ASA)-glutathione (GSH) synthesis pathway plays key roles in Cd detoxification, while its molecular regulatory mechanism remains largely unknown, especially in wheat. Here, we found a WRKY transcription factor-TaWRKY74, and its function in wheat Cd stress is not clear in previous studies. The expression levels of TaWRKY74 were significantly induced by Cd stress. Compared to control, the activities of GST, GR, or APX were significantly increased by 1.55-, 1.43-, or 1.75-fold and 1.63-, 2.65-, or 2.30-fold in shoots and roots of transiently TaWRKY74-silenced wheat plants under Cd stress. Similarly, the contents of hydrogen peroxide (H₂O₂), malondialdehyde (MDA), GSH, or Cd were also significantly increased by 2.39- or 1.25-fold, 1.54- or 1.20-fold, and 1.34- or 5.94-fold in shoots or roots in transiently TaWRKY74-silenced wheat plants, while ASA content was decreased by 47.4 or 43.3% in shoots, 10.7 or 6.5% in roots in these silenced wheat plants, respectively. Moreover, the expression levels of GSH, GPX, GR, DHAR, MDHAR, and APX genes, which are involved in ASA-GSH synthesis, were separately induced by 2.42-, 2.16-, 3.28-, 2.08-, 1.92-, and 2.23-fold in shoots, or by 10.69-, 3.33-, 3.26-, 1.81-, 16.53-, and 3.57-fold in roots of the BSMV-VIGS-TaWRKY74-inoculated wheat plants, respectively. However, the expression levels of TaNramp1, TaNramp5, TaHMA2, TaHMA3, TaLCT1, and TaIRT1 metal transporters genes were decreased by 21.2-76.3% (56.6%, 59.2%, 76.3%, 53.6%, 35.8%, and 21.2%) in roots of the BSMV-VIGS-TaWRKY74-inoculated wheat plants. Taken together, our results suggested that TaWRKY74 alleviated Cd toxicity in wheat by affecting the expression of ASA-GSH synthesis genes and suppressing the expression of Cd transporter genes, and further affecting Cd uptake and translocation in wheat plants.

Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors in Akebiatrifoliata: A Bioinformatics Study

WRKY transcription factors have been found in most plants and play an important role in regulating organ growth and disease response. Outlining the profile of WRKY genes is a very useful project for studying morphogenesis and resistance formation. In the present study, a total of 63 WRKY genes consisting of 13 class I, 41 class II, and 9 class III genes were identified from the newly published A. trifoliata genome, of which 62 were physically distributed on all 16 chromosomes. Structurally, two AkWRKY genes (AkWRKY6 and AkWRKY52) contained four domains, and AkWRKY17 lacked the typical heptapeptide structure. Evolutionarily, 42, 16, and 5 AkWRKY genes experienced whole genome duplication (WGD) or fragmentation, dispersed duplication, and tandem duplication, respectively; 28 Ka/Ks values of 30 pairs of homologous genes were far lower than 1, while those of orthologous gene pairs between AkWRKY41 and AkWRKY52 reached up to 2.07. Transcriptome analysis showed that many of the genes were generally expressed at a low level in 12 fruit samples consisting of three tissues, including rind, flesh, and seeds, at four developmental stages, and interaction analysis between AkWRKY and AkNBS genes containing W-boxes suggested that AkWRKY24 could play a role in plant disease resistance by positively regulating AkNBS18. In summary, the WRKY gene family of A. trifoliata was systemically characterized for the first time, and the data and information obtained regarding AkWRKY could be very useful in further theoretically elucidating the molecular mechanisms of plant development and response to pathogens and practically improving favorable traits such as disease resistance.

Lily WRKY factor LlWRKY22 promotes thermotolerance through autoactivation and activation of LlDREB2B

Most of WRKY transcription factors play important roles in plant development, protection against disease, and response to abiotic stress; however, their roles in lily are largely unknown. Transcriptome analysis in lily (Lilium longiflorum) led to the identification and isolation of a WRKY-IIe gene, LlWRKY22, which was found to be activated at high temperature and play a positive role in thermotolerance regulation. LlWRKY22 expression was continuously activated by heat stress. We further found that LlWRKY22 protein localized to the nucleus and exhibited transactivation activity in both yeast and plant cells, and that its C terminus contributed to its transactivation activity. Meanwhile, overexpression of LlWRKY22 in lily improved thermotolerance and activated the expression of heat-related LlDREB2B gene; however, silencing of LlWRKY22 exerted the opposite effects. Further analysis revealed that LlWRKY22 directly activated the expression of LlDREB2B by binding to two tandem W-box elements on its promoter. Simultaneously, we also found that LlWRKY22 can directly bind its own promoter, thereby activating its own expression and forming a positive regulatory loop. Combined, our findings demonstrated that LlWRKY22 may be a new regulator of heat stress response and positively participates in the establishment of thermotolerance by activating itself and LlDREB2B.

WRKY transcription factors: a promising way to deal with arsenic stress in rice

Arsenic (As) is a global carcinogenic contaminant, and is one of the significant environmental constraints that limits the development and yield of crop plants. It is always tagged along with rice as rice takes up As and tends to accumulate it in grains. This amassment makes a way for As to get into the food chain that leads to unforeseen human health risks. Being viewed as parallel with toxicity, As in rice is an important global risk that calls for an urgent solution. WRKY Transcription Factors (TFs) seems to be promising in this area. The classical and substantial progress in the molecular mechanism of WRKY TFs, strengthened the understanding of innovative solutions for dealing with As in rice. Here, we review the potential of WRKY TFs under As stressed rice as a genetic solution and also provide insights into As and rice. Further, we develop an understanding of WRKY TF gene family and its regulation in rice. To date, studies on the role of WRKY TFs under As stressed rice are lacking. This area needs to be explored more so that this gene family can be utilized as an effective genetic tool that can break the As cycle to develop low or As free rice cultivar.

A novel kinase subverts aluminium resistance by boosting ornithine decarboxylase-dependent putrescine biosynthesis

Rice, as one of the most aluminium (Al)-resistant cereal crops, has developed more complicated Al resistance mechanisms than others. By using forward genetic screening from a rice ethyl methanesulfonate mutant library, we obtained a mutant showing specifically high sensitivity to Al. Through MutMap analysis followed by a complementation test, we identified the causal gene, Al-related Protein Kinase (ArPK) for Al-sensitivity. ArPK expression was induced by a relatively longer exposure to high Al concentration in the roots. The result of RNA-sequencing indicated the functional disorder in arginine metabolism pathway with downregulation of N-acetylornithine deacetylase (NAOD) expression and upregulation of Ornithine decarboxylase1 (ODC1) expression in arpk mutant. Al specifically and rapidly upregulated ODC1 expression and causes overaccumulation of putrescine (Put), whereas the ODC inhibitor difluoromethylornithine reverted Al-sensitive phenotype of arpk, suggesting that overaccumulation of endogenous Put might be harmful for root growth, and that ArPK seems to act as an endogenous inhibitor of ODC1 action to maintain suitable endogenous Put level under Al treatment. Overall, we identified ArPK and its putative repressive role in controlling a novel ODC-dependent Put biosynthesis pathway specifically affecting rice Al resistance, thus enriching the fundamental understanding of plant Al resistance.

GmWRKY21, a Soybean WRKY Transcription Factor Gene, Enhances the Tolerance to Aluminum Stress in Arabidopsis thaliana

The WRKY transcription factors (TFs) are one of the largest families of TFs in plants and play multiple roles in plant growth and development and stress response. In this study, GmWRKY21 encoding a WRKY transcription factor was functionally characterized in Arabidopsis and soybean. The GmWRKY21 protein containing a highly conserved WRKY domain and a C₂H₂ zinc-finger structure is located in the nucleus and has the characteristics of transcriptional activation ability. The GmWRKY21 gene presented a constitutive expression pattern rich in the roots, leaves, and flowers of soybean with over 6-fold of relative expression levels and could be substantially induced by aluminum stress. As compared to the control, overexpression of GmWRKY21 in Arabidopsis increased the root growth of seedlings in transgenic lines under the AlCl₃ concentrations of 25, 50, and 100 μM with higher proline and lower MDA accumulation. The results of quantitative real-time polymerase chain reaction (qRT-PCR) showed that the marker genes relative to aluminum stress including ALMT, ALS3, MATE, and STOP1 were induced in GmWRKY21 transgenic plants under AlCl₃ treatment. The stress-related genes, such as KIN1, COR15A, COR15B, COR47, GLOS3, and RD29A, were also upregulated in GmWRKY21 transgenic Arabidopsis under aluminum stress. Similarly, stress-related genes, such as GmCOR47, GmDREB2A, GmMYB84, GmKIN1, GmGST1, and GmLEA, were upregulated in hair roots of GmWRKY21 transgenic plants. In summary, these results suggested that the GmWRKY21 transcription factor may promote the tolerance to aluminum stress mediated by the pathways regulating the expression of the acidic aluminum stress-responsive genes and abiotic stress-responsive genes.

Overexpression of MxbHLH18 Increased Iron and High Salinity Stress Tolerance in Arabidopsis thaliana

In the life cycle of apple, it will suffer a variety of abiotic stresses, such as iron stress and salt stress. bHLH transcription factors (TFs) play an indispensable role in the response of plants to stress. In this study, a new bHLH gene named MxbHLH18 was separated from Malus xiaojinensis. According to the results of subcellular localization, MxbHLH18 was localized in the nucleus. Salt stress and iron stress affected the expression of MxbHLH18 in Malus xiaojinensis seedlings to a large extent. Due to the introduction of MxbHLH18, the resistance of Arabidopsis thaliana to salt, high iron and low iron was significantly enhanced. Under the environmental conditions of high iron and low iron, the overexpression of MxbHLH18 increased many physiological indexes of transgenic Arabidopsis compared to wild type (WT), such as root length, fresh weight and iron content. The high level expression of MxbHLH18 in transformed Arabidopsis thaliana can not only increased the content of chlorophyll and proline, as well as increasing the activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT); it also reduced the content of malondialdehyde (MDA), which was more obvious under high salt conditions. In addition, the relative conductivity, H₂O₂ content and O²⁻ content in transgenic Arabidopsis decreased under salt stress. Meanwhile, MxbHLH18 can also regulate the expression of downstream genes associated with salt stress (AtCBF1/2/3, AtKIN1 and AtCOR15a/b) and iron stress (AtIRT1, AtFRO2, AtNAS2, ATACT2, AtZIF1 and AtOPT3). Therefore, MxbHLH18 can actively promote the adaptability of plants to the growth environment of salt and low and/or iron.

Metabolome Analysis under Aluminum Toxicity between Aluminum-Tolerant and -Sensitive Rice (Oryza sativa L.)

Aluminum (Al) solubilizes into trivalent ions (Al³⁺) on acidic soils, inhibiting root growth. Since about 13% of global rice cultivation is grown on acidic soils, improving Al tolerance in rice may significantly increase yields. In the present study, metabolome analysis under Al toxicity between the Al-tolerant variety Nipponbare and the Al-sensitive variety H570 were performed. There were 45 and 83 differential metabolites which were specifically detected in Nipponbare and H570 under Al toxicity, respectively. Furthermore, the results showed that 16 lipids out of 45 total metabolites were down-regulated, and 7 phenolic acids as well as 4 alkaloids of 45 metabolites were up-regulated in Nipponbare, while 12 amino acids and their derivatives were specifically detected in H570, of which 11 amino acids increased, including L-homoserine and L-methionine, which are involved in cysteine synthesis, L-ornithine and L-proline, which are associated with putrescine synthesis, and 1-aminocyclopropane-1-carboxylate, which is associated with ethylene synthesis. The contents of cysteine and s-(methyl) glutathione, which were reported to be related to Al detoxification in rice, decreased significantly. Meanwhile, putrescine was accumulated in H570, while there was no significant change in Nipponbare, so we speculated that it might be an intermediate product of Al detoxification in rice. The differential metabolites detected between Al-tolerant and -sensitive rice variants in the present study might play important roles in Al tolerance. These results provide new insights in the mechanisms of Al tolerance in rice.

GmWRKY81 Encoding a WRKY Transcription Factor Enhances Aluminum Tolerance in Soybean

Aluminum (Al) toxicity is an essential factor that adversely limits soybean (Glycine max (L.) Merr.) growth in acid soils. WRKY transcription factors play important roles in soybean responses to abiotic stresses. Here, GmWRKY81 was screened from genes that were differentially expressed under Al treatment in Al-tolerant soybean Baxi10 and Al-sensitive soybean Bendi2. We found that GmWRKY81 was significantly induced by 20 μM AlCl3 and upregulated by AlCl3 treatment for 2 h. In different tissues, the expression of GmWRKY81 was differentially induced. In 0-1 cm root tips, the expression of GmWRKY81 was induced to the highest level. The overexpression of GmWRKY81 in soybean resulted in higher relative root elongation, root weight, depth, root length, volume, number of root tips and peroxidase activity but lower root average diameter, malonaldehyde and H2O2 contents, indicating enhanced Al tolerance. Moreover, RNA-seq identified 205 upregulated and 108 downregulated genes in GmWRKY81 transgenic lines. Fifteen of these genes that were differentially expressed in both AlCl3-treated and GmWRKY81-overexpressing soybean had the W-box element, which can bind to the upstream-conserved WRKY domain. Overall, the combined functional analysis indicates that GmWRKY81 may improve soybean Al tolerance by regulating downstream genes participating in Al3+ transport, organic acid secretion and antioxidant reactions.

FvWRKY48 binds to the pectate lyase FvPLA promoter to control fruit softening in Fragaria vesca

The regulatory mechanisms that link WRKY gene expression to fruit ripening are largely unknown. Using transgenic approaches, we showed that a WRKY gene from wild strawberry (Fragaria vesca), FvWRKY48, may be involved in fruit softening and ripening. We showed that FvWRKY48 is localized to the nucleus and that degradation of the pectin cell wall polymer homogalacturonan, which is present in the middle lamella and tricellular junction zones of the fruit, was greater in FvWRKY48-OE (overexpressing) fruits than in empty vector (EV)-transformed fruits and less substantial in FvWRKY48-RNAi (RNA interference) fruits. Transcriptomic analysis indicated that the expression of pectate lyase A (FvPLA) was significantly downregulated in the FvWRKY48-RNAi receptacle. We determined that FvWRKY48 bound to the FvPLA promoter via a W-box element through yeast one-hybrid, electrophoretic mobility shift, and chromatin immunoprecipitation quantitative polymerase chain reaction experiments, and β-glucosidase activity assays suggested that this binding promotes pectate lyase activity. In addition, softening and pectin degradation were more intense in FvPLA-OE fruit than in EV fruit, and the middle lamella and tricellular junction zones were denser in FvPLA-RNAi fruit than in EV fruit. We speculated that FvWRKY48 maybe increase the expression of FvPLA, resulting in pectin degradation and fruit softening.

MdWRKY126 modulates malate accumulation in apple fruit by regulating cytosolic malate dehydrogenase (MdMDH5)

The content of organic acids greatly influences the taste and storage life of fleshy fruit. Our current understanding of the molecular mechanism of organic acid accumulation in apple (Malus domestica) fruit focuses on the aluminum-activated malate transporter 9/Ma1 gene. In this study, we identified a candidate gene, MdWRKY126, for controlling fruit acidity independent of Ma1 using homozygous recessive mutants of Ma1, namely Belle de Boskoop "BSKP" and Aifeng "AF." Analyses of transgenic apple calli and flesh and tomato (Solanum lycopersicum) fruit demonstrated that MdWRKY126 was substantially associated with malate content. MdWRKY126 was directly bound to the promoter of the cytoplasmic NAD-dependent malate dehydrogenase MdMDH5 and promoted its expression, thereby enhancing the malate content of apple fruit. In MdWRKY126 overexpressing calli, the mRNA levels of malate-associated transporters and proton pump genes also significantly increased, which contributed to the transport of malate accumulated in the cytoplasm to the vacuole. These findings demonstrated that MdWRKY126 regulates malate anabolism in the cytoplasm and coordinates the transport between cytoplasm and vacuole to regulate malate accumulation. Our study provides useful information to improve our understanding of the complex mechanism regulating apple fruit acidity.

The Tomato Transcription Factor SlNAC063 Is Required for Aluminum Tolerance by Regulating SlAAE3-1 Expression

Aluminum (Al) toxicity constitutes one of the major limiting factors of plant growth and development on acid soils, which comprises approximately 50% of potentially arable lands worldwide. When suffering Al toxicity, plants reprogram the transcription of genes, which activates physiological and metabolic pathways to deal with the toxicity. Here, we report the role of a NAM, ATAF1, 2 and CUC2 (NAC) transcription factor (TF) in tomato Al tolerance. Among 53 NAC TFs in tomatoes, SlNAC063 was most abundantly expressed in root apex and significantly induced by Al stress. Furthermore, the expression of SlNAC063 was not induced by other metals. Meanwhile, the SlNAC063 protein was localized at the nucleus and has transcriptional activation potentials in yeast. By constructing CRISPR/Cas9 knockout mutants, we found that slnac063 mutants displayed increased sensitivity to Al compared to wild-type plants. However, the mutants accumulated even less Al than wild-type (WT) plants, suggesting that internal tolerance mechanisms but not external exclusion mechanisms are implicated in SlNAC063-mediated Al tolerance in tomatoes. Further comparative RNA-sequencing analysis revealed that only 45 Al-responsive genes were positively regulated by SlNAC063, although the expression of thousands of genes (1,557 upregulated and 636 downregulated) was found to be affected in slnac063 mutants in the absence of Al stress. The kyoto encyclopedia of genes and genomes (KEGG) pathway analysis revealed that SlNAC063-mediated Al-responsive genes were enriched in "phenylpropanoid metabolism," "fatty acid metabolism," and "dicarboxylate metabolism," indicating that SlNAC063 regulates metabolisms in response to Al stress. Quantitative real-time (RT)-PCR analysis showed that the expression of SlAAE3-1 was repressed by SlNAC063 in the absence of Al. However, the expression of SlAAE3-1 was dependent on SlNAC063 in the presence of Al stress. Taken together, our results demonstrate that a NAC TF SlNAC063 is involved in tomato Al tolerance by regulating the expression of genes involved in metabolism, and SlNAC063 is required for Al-induced expression of SlAAE3-1.

A gain-of-function mutation of the MATE family transporter DTX6 confers paraquat resistance in Arabidopsis

Paraquat is one of the most widely used nonselective herbicides and has elicited the emergence of paraquat-resistant weeds. However, the molecular mechanisms of paraquat resistance are not completely understood. Here we report the Arabidopsis gain-of-function mutant pqt15-D with significantly enhanced resistance to paraquat and the corresponding gene PQT15, which encodes the Multidrug and Toxic Extrusion (MATE) transporter DTX6. A point mutation at +932 bp in DTX6 causes a G311E amino acid substitution, enhancing the paraquat resistance of pqt15-D, and overexpression of DTX6/PQT15 in the wild-type plants also results in strong paraquat resistance. Moreover, heterologous expression of DTX6 and DTX6-D in Escherichia coli significantly enhances bacterial resistance to paraquat. Importantly, overexpression of DTX6-D enables Arabidopsis plants to tolerate 4 mM paraquat, a near-commercial application level. DTX6/PQT15 is localized in the plasma membrane and endomembrane, and functions as a paraquat efflux transporter as demonstrated by paraquat efflux assays with isolated protoplasts and bacterial cells. Taken together, our results demonstrate that DTX6/PQT15 is an efflux transporter that confers paraquat resistance by exporting paraquat out of the cytosol. These findings reveal a molecular mechanism of paraquat resistance in higher plants and provide a promising candidate gene for engineering paraquat-resistant crops.

WRKY46 promotes ammonium tolerance in Arabidopsis by repressing NUDX9 and indole-3-acetic acid-conjugating genes and by inhibiting ammonium efflux in the root elongation zone

Ammonium (NH₄⁺ ) is toxic to root growth in most plants, even at moderate concentrations. Transcriptional regulation is one of the most important mechanisms in the response of plants to NH₄⁺ toxicity, but the nature of the involvement of transcription factors (TFs) in this regulation remains unclear. Here, RNA-seq analysis was performed on Arabidopsis roots to screen for ammonium-responsive TFs. WRKY46, the member of the WRKY transcription factor family most responsive to NH₄⁺ , was selected. We defined the role of WRKY46 using mutation and overexpression assays, and characterized the regulation of NUDX9 and indole-3-acetic acid (IAA)-conjugating genes by WRKY46 via yeast one-hybrid and electrophoretic mobility shift assays and chromatin immunoprecipitation-quantitative real-time polymerase chain reaction (ChIP-qPCR). Knockout of WRKY46 increased, while overexpression of WRKY46 decreased, NH₄⁺ -suppression of the primary root. WRKY46 is shown to directly bind to the promoters of the NUDX9 and IAA-conjugating genes (GH3.1, GH3.6, UGT75D1, UGT84B2) and to inhibit their transcription, thus positively regulating free IAA content and stabilizing protein N-glycosylation, leading to an inhibition of NH₄⁺ efflux in the root elongation zone (EZ). We identify TF involvement in the regulation of NH₄⁺ efflux in the EZ, and show that WRKY46 inhibits NH₄⁺ efflux by negative regulation of NUDX9 and IAA-conjugating genes.

TaWRKY74 participates copper tolerance through regulation of TaGST1 expression and GSH content in wheat

Glutathione S-transferase (GST) is the key enzyme in glutathione (GSH) synthesis, and plays a crucial role in copper (Cu) detoxification. Nonetheless, its regulatory mechanisms remain largely unclear. In this study, we identified a Cu-induced glutathione S-transferase 1 (TaGST1) gene in wheat. Yeast one-hybrid (Y1H) screened out TaWRKY74, which was one member from the WRKY transcription factor family. The bindings between TaGST1 promoter and TaWRKY74 were further verified by using another Y1H and luciferase assays. Expression of TaWRKY74 was induced more than 30-folds by Cu stress. Functions of TaWRKY74 were tested by using transiently silence methods. In transiently TaWRKY74-silenced wheat plants, TaWRKY74 and TaGST1 expression, GST activity, and GSH content was significantly inhibited by 25.68%, 19.88%, 27.66%, and 12.68% in shoots, and 53.81%, 52.11%, 23.47%, and 17.11% in roots, respectively. However, contents of hydrogen peroxide, malondialdehyde, or Cu were significantly increased by 2.58%, 12.45%, or 37.74% in shoots, and 25.24%, 53.84%, and 103.99% in roots, respectively. Notably, exogenous application of GSH reversed the adverse effects of transiently TaWRKY74-silenced wheat plants during Cu stress. Taken together, our results suggesting that TaWRKY74 regulated TaGST1 expression and affected GSH accumulation under Cu stress, and could be useful to ameliorate Cu toxicity for crop food safety.

Comparative Inter- and IntraSpecies Transcriptomics Revealed Key Differential Pathways Associated With Aluminium Stress Tolerance in Lentil

Aluminium stress causes plant growth retardation and engenders productivity loss under acidic soil conditions. This study accentuates morpho-physiological and molecular bases of aluminium (Al) tolerance within and between wild (ILWL-15) and cultivated (L-4602 and BM-4) lentil species. Morpho-physiological studies revealed better cyto-morphology of tolerant genotypes over sensitive under Al³⁺ stress conditions. Mitotic lesions were observed in root cells under these conditions. Transcriptome analysis under Al³⁺ stress revealed 30,158 specifically up-regulated genes in different comparison groups showing contigs between 15,305 and 18,861 bp. In tolerant genotypes, top up-regulated differentially expressed genes (DEGs) were found to be involved in organic acid synthesis and exudation, production of antioxidants, callose synthesis, protein degradation, and phytohormone- and calcium-mediated signalling under stress conditions. DEGs associated with epigenetic regulation and Al³⁺ sequestration inside vacuole were specifically upregulated in wild and cultivars, respectively. Based on assembled unigenes, an average of 6,645.7 simple sequence repeats (SSRs) and 14,953.7 high-quality single nucleotide polymorphisms (SNPs) were spotted. By quantitative real-time polymerase chain reaction (qRT-PCR), 12 selected genes were validated. Gene ontology (GO) annotation revealed a total of 8,757 GO terms in three categories, viz., molecular, biological, and cellular processes. Kyoto Encyclopaedia of Genes and Genomes pathway scanning also revealed another probable pathway pertaining to metacaspase-1,-4, and -9 for programmed cell death under Al-stress conditions. This investigation reveals key inter- and intraspecies metabolic pathways associated with Al-stress tolerance in lentil species that can be utilised in designing future breeding programmes to improve lentil and related species towards Al³⁺ stress.

CRISPR/Cas9-mediated mutagenesis of WRKY3 and WRKY4 function decreases salt and Me-JA stress tolerance in Arabidopsis thaliana

BACKGROUND

WRKY transcription factor is involved in regulation of plant growth and development, response to biotic and abiotic stresses, including homologous WRKY3 and WRKY4 genes which play a vital role in regulating plants defense response to pathogen and drought stress.

METHODS AND RESULTS

To investigate the function of AtWRKY3 and AtWRKY4 genes in regulating salt and Me-JA stresses, the loss-of-function mutations were generated by clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) system in Arabidopsis thaliana. Several independent transgenic lines with single or double mutations were obtained via Agrobacterium-mediated transformation. The knockout lines of AtWRKY3 and AtWRKY4 genes were successfully achieved and confirmed by qRT-PCR technology. Expression analysis showed that AtWRKY3 and AtWRKY4 genes had significantly up-regulated under salt and Me-JA stresses. The growth of double mutant plants under salt or Me-JA stresses were significantly inhibited compared with corresponding wild type (WT) plants, especially their root lengths. Moreover, the double mutant plants displayed salt and Me-JA sensitivity phenotypic characteristics, such as the increased relative electrolyte leakage (REL) and a substantial reduce in the activities of antioxidant enzymes, including superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities.

CONCLUSION

Taken together, these data suggested that the simultaneous modification of homologous gene copies of WRKY are established using CRISPR/Cas9 system in A. thaliana and the loss of AtWRKY3 and AtWRKY4 has an effect on ROS scavenging pathways to reduce stress tolerance.

Phytohormone signalling and cross-talk to alleviate aluminium toxicity in plants

Aluminium (Al) is one of the most abundant metals in earth crust, which becomes toxic to the plants growing in acidic soil. Phytohormones like ethylene, auxin, cytokinin, abscisic acid, jasmonic acid and gibberellic acid are known to play important role in regulating Al toxicity tolerance in plants. Exogenous applications of auxin, cytokinin and abscisic acid have shown significant effect on Al-induced root growth inhibition. Moreover, ethylene and cytokinin act synergistically with auxin in responding against Al toxicity. A number of studies showed that phytohormones play vital roles in controlling root responses to Al toxicity by modulating reactive oxygen species (ROS) signalling, cell wall modifications, organic acid exudation from roots and expression of Al responsive genes and transcription factors. This review provides a summary of recent studies related to involvement of phytohormone signalling and cross-talk with other pathways in regulating response against Al toxicity in plants.

Identification and characterization of 5 walnut MYB genes in response to drought stress involved in ABA signaling

Walnut is a popular nut tree species and usually suffers from drought stress. However, little information is available on the mechanism of walnut responding to drought stress, resulting in lack of basic understanding for its resistance. In order to excavate more functional genes that can respond to stressors, and enrich the theoretical basis for walnut resistance, in this study, 5 MYB genes with complete ORFs were identified from J. regia and the basic bio-information as well as expression patterns in different tissues and response to drought and ABA stresses were confirmed using qRT-PCR assay. The results showed that 2 JrMYB genes belong to R1-MYB subfamily and 3 JrMYBs belong to R2R3-MYB, encoding the proteins from 212 to 362 aa in length. The phylogenetic analysis categorized proteins of 5 JrMYBs and 40 Arabidopsis AtMYBs into 10 subgroups. JrMYBs in the same subgroup exhibited significant similarities in the composition of conserved domains and motifs in amino acid sequences and exon/intron organization in DNA sequences. The results of qRT-PCR analysis revealed that JrMYB genes diversely expressed in various tissues. Moreover, the expression values of JrMYBs were upregulated or downregulated significantly under drought and ABA stresses. Most attractively, in contrast with suffering from drought stress alone, the treatments with drought and additional ABA greatly enhanced the transcript levels of JrMYBs. All these results suggested that JrMYB genes play a vital role in plant biological processes and drought as well as ABA stress response, and possibly perform as ABA-dependent drought response transcription factors in plant.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01008-z.

Organic acids: versatile stress-response roles in plants

Organic acids (OAs) are central to cellular metabolism. Many plant stress responses involve the exudation of OAs at the root-soil interface, which can improve soil mineral acquisition and toxic metal tolerance. Because of their simple structure, the low-molecular-weight OAs are widely studied. We discuss the conventional roles of OAs, and some newly emerging roles in plant stress tolerance. OAs are more versatile in their role in plant stress tolerance and are more efficient chelating agents than other acids, such as amino acids. Root OA exudation is important in soil carbon sequestration. These functions are key processes in combating climate change and helping with more sustainable food production. We briefly review the mechanisms behind enhanced biosynthesis, secretion, and regulation of these activities under different stresses, and provide an outline of the transgenic approaches targeted towards the enhanced production and secretion of OAs. A recurring theme of OAs in plant biology is their role as 'acids' modifying pH, as 'chelators' binding metals, or as 'carbon sources' for microbes. We argue that these multiple functions are key factors for understanding these molecules' important roles in plant stress biology. Finally, we discuss how the functions of OAs in plant stress responses could be used, and identify the important unanswered questions.

Melatonin promotes potassium deficiency tolerance by regulating HAK1 transporter and its upstream transcription factor NAC71 in wheat

Melatonin (MT) is involved in various physiological processes and stress responses in animals and plants. However, little is known about the molecular mechanisms by which MT regulates potassium deficiency (DK) tolerance in crops. In this study, an appropriate concentration (50 μmol/L) was found to enhance the tolerance of wheat plants against DK. RNA-seq analysis showed that a total of 6253 and 5873 differentially expressed genes (DEGs) were separately identified in root and leaf tissues of the DK + MT-treated wheat plants. They functionally involved biological processes of secondary metabolite, signal transduction, and transport or catabolism. Of these, an upregulated high-affinity K transporter 1 (TaHAK1) gene was next characterized. TaHAK1 overexpression markedly enhanced the K absorption, while its transient silencing exhibited the opposite effect, suggesting its important role in MT-mediated DK tolerance. Moreover, yeast one-hybrid (Y1H) was used to screen the upstream regulators of TaHAK1 gene and the transcription factor TaNAC71 was identified. The binding between TaNAC71 and TaHAK1 promoter was evidenced by using Y1H, LUC, and EMSA assays. Transient overexpression of TaNAC71 in wheat protoplasts activated the TaHAK1 expression, whereas its transient silencing inhibited the TaHAK1 expression and aggravated the sensitivity to DK. Exogenous MT application greatly upregulated the expression of TaHAK1 in both transient overexpression and silencing systems. Our findings revealed some molecular mechanisms underlying MT-mediated DK tolerance and helped broaden its practical application in agriculture.

The role of solute transporters in aluminum toxicity and tolerance

The prevalence of aluminum ions (Al³⁺ ) under acidic soil conditions inhibits primary root elongation and hinders plant growth and productivity. Al³⁺ alters the membrane potential, displaces critical ions in the apoplast and disrupts intracellular ionic concentrations by targeting membrane-localized solute transporters. Here, we provide an overview of how Al³⁺ affects the activities of several solute transporters especially in the root. High Al³⁺ level impairs the functions of potassium (K⁺ ), calcium (Ca²⁺ ), magnesium (Mg²⁺ ), nitrate (NO₃ ^- ) and ammonium (NH₄ ⁺ ) transporters. We further discuss the role of some key transporters in mediating Al tolerance either by exclusion or sequestration. Anion channels responsible for organic acid efflux modulate the sensitivity to Al³⁺ . The ALUMINUM ACTIVATED MALATE TRANSPORTER (ALMT) and MULTIDRUG AND TOXIC COMPOUND EXTRUSION (MATE) family of transporters exude malate and citrate, respectively, to the rhizosphere to alleviate Al toxicity by Al exclusion. The ABC transporters, aquaporins and H⁺ -ATPases perform vacuolar sequestration of Al³⁺ , leading to aluminum tolerance in plants. Targeting these solute transporters in crop plants can help generating aluminum-tolerant crops in future.

Transcriptome analysis reveals significant difference in gene expression and pathways between two peanut cultivars under Al stress

Aluminum (Al) toxicity is an important factor in limiting peanut growth on acidic soil. The molecular mechanisms underlying peanut responses to Al stress are largely unknown. In this study, we performed transcriptome analysis of the root tips (0-1 cm) of peanut cultivar ZH2 (Al-sensitive) and 99-1507 (Al-tolerant) respectively. Root tips of peanuts that treated with 100 μM Al for 8 h and 24 h were analyzed by RNA-Seq, and a total of 8,587 differentially expressed genes (DEGs) were identified. GO and KEGG pathway analysis excavated a group of important Al-responsive genes related to organic acid transport, metal cation transport, transcription regulation and programmed cell death (PCD). These homologs were promising targets to modulate Al tolerance in peanuts. It was found that the rapid transcriptomic response to Al stress in 99-1507 helped to activate effective Al tolerance mechanisms. Protein and protein interaction analysis indicated that MAPK signal transduction played important roles in the early response to Al stress in peanuts. Moreover, weighted correlation network analysis (WGCNA) identified a predicted EIL (EIN3-like) gene with greatly increased expression as an Al-associated gene, and revealed a link between ethylene signaling transduction and Al resistance related genes in peanut, which suggested the enhanced signal transduction mediated the rapid transcriptomic responses. Our results revealed key pathways and genes associated with Al stress, and improved the understanding of Al response in peanut.

Recent Advances in Understanding Mechanisms of Plant Tolerance and Response to Aluminum Toxicity

Aluminum (Al) toxicity is a major environmental stress that inhibits plant growth and development. There has been impressive progress in recent years that has greatly increased our understanding of the nature of Al toxicity and its mechanisms of tolerance. This review describes the transcription factors (TFs) and plant hormones involved in the adaptation to Al stress. In particular, it discusses strategies to confer plant resistance to Al stress, such as transgenic breeding, as well as small molecules and plant growth-promoting rhizobacteria (PGPRs) to alleviate Al toxicity. This paper provides a theoretical basis for the enhancement of plant production in acidic soils.