Elevated levels of CYP94 family gene expression alleviate the jasmonate response and enhance salt tolerance in rice

Salinity-induced variations in wheat biomass are regulated by the Na+:K+ ratio, root exudates, and keystone species

Salt stress can limit crop productivity, and there are differences in salt tolerance among plant varieties; however, we lack a comprehensive understanding of how keystone species obtained from different plant varieties under salt stress change plant biomass by driving root exudate secretion and regulating the Na+:K+ ratio. We conducted a pot experiment for three wheat varieties (JiMai32 (JM32), XiaoYan60 (XY60), and ShanRong3 (SR3)) under saline/nonsaline soil conditions. Salt stress tended to significantly reduce wheat biomass, and the biomass reduction rates of the different varieties decreased in the order JM32 < XY60 < SR3. The compositions of the bacterial and fungal communities in the root endosphere, rhizosphere and bulk soil were measured, and salt-induced microbial taxa were isolated to identify keystone species from the co-occurrence networks and to study their effects on physiological responses to salinity in wheat varieties. We observed that root exudates participated in the regulation of the Na+:K+ ratio, thereby affecting wheat biomass, and this process was regulated by keystone species. JM32 was enriched in microorganisms that promote plant growth and resistance to salt stress, such as Burkholderiales, Sordariomycetes, Alteromonadaceae, Acremonium, and Dokdonella, and inhibited microorganisms that are sensitive to the environment (salt, nutrients) and plant pathogens, such as Nocardioidaceae, Nitrospira, Cytophagaceae, Syntrophobacteriaceae, and Striaticonidium. XY60 inhibited microorganisms with biological control and disease inhibition potential, such as Agromyces and Kaistobacter. SR3-enriched pathogens, such as Aurantimonadaceae and Pseudogymnoascus, as well as microorganisms with antagonistic pathogen potential and the ability to treat bacterial infections, such as RB41 and Saccharothrix, were inhibited. Our results confirmed the crucial function of salt-induced keystone species in enhancing plant adaptation to salt stress by driving root exudate secretion and regulating the Na+:K+ ratio, with implications for exploring reasonable measures to improve plant salt tolerance.

Gossypium arboreum PPD2 facilitates root architecture development to increase plant resilience to salt stress

The jasmonic acid (JA) signaling pathway plays an important role in plant responses to abiotic stresses. The PEAPOD (PPD) and jasmonate ZIM-domain (JAZ) protein in the JA signaling pathway belong to the same family, but their functions in regulating plant defense against salt stress remain to be elucidated. Here, Gossypium arboreum PPD2 was overexpressed in Arabidopsis thaliana and systematically silenced in cotton for exploring its function in regulating plant defense to salt stress. The GaPPD2-overexpressed Arabidopsis thaliana plants significantly increased the tolerance to salt stress compared to the wild type in both medium and soil, while the GaPPD2-silenced cotton plants showed higher sensitivity to salt stress than the control in pots. The antioxidant activities experiment showed that GaPPD2 may mitigate the accumulation of reactive oxygen species by promoting superoxide dismutase accumulation, consequently improving plant resilience to salt stress. Through the exogenous application of MeJA (methy jasmonate) and the protein degradation inhibitor MG132, it was found that GaPPD2 functions in plant defense against salt stress and is involved in the JA signaling pathway. The RNA-seq analysis of GaPPD2-overexpressed A. thaliana plants and receptor materials showed that the differentially expressed genes were mainly enriched in antioxidant activity, peroxidase activity, and plant hormone signaling pathways. qRT-PCR results demonstrated that GaPPD2 might positively regulate plant defense by inhibiting GH3.2/3.10/3.12 expression and activating JAZ7/8 expression. The findings highlight the potential of GaPPD2 as a JA signaling component gene for improving the cotton plant resistance to salt stress and provide insights into the mechanisms underlying plant responses to environmental stresses.

Understanding the role of boron in plant adaptation to soil salinity

Soil salinity is a major environmental constraint affecting the sustainability and profitability of agricultural production systems. Salinity stress tolerance has been present in wild crop relatives but then lost, or significantly weakened, during their domestication. Given the genetic and physiological complexity of salinity tolerance traits, agronomical solutions may be a suitable alternative to crop breeding for improved salinity stress tolerance. One of them is optimizing fertilization practices to assist plants in dealing with elevated salt levels in the soil. In this review, we analyse the causal relationship between the availability of boron (an essential metalloid micronutrient) and plant's adaptive responses to salinity stress at the whole-plant, cellular, and molecular levels, and a possibility of using boron for salt stress mitigation. The topics covered include the impact of salinity and the role of boron in cell wall remodelling, plasma membrane integrity, hormonal signalling, and operation of various membrane transporters mediating plant ionic and water homeostasis. Of specific interest is the role of boron in the regulation of H+-ATPase activity whose operation is essential for the control of a broad range of voltage-gated ion channels. The complex relationship between boron availability and expression patterns and the operation of aquaporins is also discussed.

Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice

BACKGROUND

Due to rising costs, water shortages, and labour shortages, farmers across the globe now prefer a direct seeding approach. However, submergence stress remains a major bottleneck limiting the success of this approach in rice cultivation. The merger of accumulated rice genetic resources provides an opportunity to detect key genomic loci and candidate genes that influence the flooding tolerance of rice.

RESULTS

In the present study, a whole-genome meta-analysis was conducted on 120 quantitative trait loci (QTL) obtained from 16 independent QTL studies reported from 2004 to 2023. These QTL were confined to 18 meta-QTL (MQTL), and ten MQTL were successfully validated by independent genome-wide association studies from diverse natural populations. The mean confidence interval (CI) of the identified MQTL was 3.44 times narrower than the mean CI of the initial QTL. Moreover, four core MQTL loci with genetic distance less than 2 cM were obtained. By combining differentially expressed genes (DEG) from two transcriptome datasets with 858 candidate genes identified in the core MQTL regions, we found 38 common differentially expressed candidate genes (DECGs). In silico expression analysis of these DECGs led to the identification of 21 genes with high expression in embryo and coleoptile under submerged conditions. These DECGs encode proteins with known functions involved in submergence tolerance including WRKY, F-box, zinc fingers, glycosyltransferase, protein kinase, cytochrome P450, PP2C, hypoxia-responsive family, and DUF domain. By haplotype analysis, the 21 DECGs demonstrated distinct genetic differentiation and substantial genetic distance mainly between indica and japonica subspecies. Further, the MQTL7.1 was successfully validated using flanked marker S2329 on a set of genotypes with phenotypic variation.

CONCLUSION

This study provides a new perspective on understanding the genetic basis of submergence tolerance in rice. The identified MQTL and novel candidate genes lay the foundation for marker-assisted breeding/engineering of flooding-tolerant cultivars conducive to direct seeding.

Characterization of a Novel Polysaccharide Derived from Rhizospheric Paecilomyces vaniformisi and Its Mechanism for Enhancing Salinity Resistance in Rice Seedlings

Soil salinity is an important limiting factor in agricultural production. Rhizospheric fungi can potentially enhance crop salinity tolerance, but the precise role of signaling substances is still to be systematically elucidated. A rhizospheric fungus identified as Paecilomyces vaniformisi was found to enhance the salinity tolerance of rice seedlings. In this study, a novel polysaccharide (PPL2b) was isolated from P. vaniformisi and identified as consisting of Manp, Glcp, GalpA, and Galp. In a further study, PPL2b showed significant activity in alleviating salinity stress-induced growth inhibition in rice seedlings. The results indicated that under salinity stress, PPL2b enhances seed germination, plant growth (height and biomass), and biochemical parameters (soluble sugar and protein contents). Additionally, PPL2b regulates genes such as SOS1 and SKOR to decrease K+ efflux and increase Na+ efflux. PPL2b increased the expression and activity of genes related to antioxidant enzymes and nonenzyme substances in salinity-induced oxidative stress. Further study indicated that PPL2b plays a crucial role in regulating osmotic substances, such as proline and betaine, in maintaining the osmotic balance. It also modulates plant hormones to promote rice seedling growth and enhance their tolerance to soil salinity. The variables interacted and were divided into two groups (PC1 77.39% and PC2 18.77%) based on their relative values. Therefore, these findings indicate that PPL2b from P. vaniformisi can alleviate the inhibitory effects of salinity stress on root development, osmotic adjustment, ion balance, oxidative stress balance, and growth of rice seedlings. Furthermore, it suggests that polysaccharides produced by rhizospheric fungi could be utilized to enhance crop tolerance to salinity.

Plant Metabolomics: Current Initiatives and Future Prospects

Plant metabolomics is a rapidly advancing field of plant sciences and systems biology. It involves comprehensive analyses of small molecules (metabolites) in plant tissues and cells. These metabolites include a wide range of compounds, such as sugars, amino acids, organic acids, secondary metabolites (e.g., alkaloids and flavonoids), lipids, and more. Metabolomics allows an understanding of the functional roles of specific metabolites in plants' physiology, development, and responses to biotic and abiotic stresses. It can lead to the identification of metabolites linked with specific traits or functions. Plant metabolic networks and pathways can be better understood with the help of metabolomics. Researchers can determine how plants react to environmental cues or genetic modifications by examining how metabolite profiles change under various crop stages. Metabolomics plays a major role in crop improvement and biotechnology. Integrating metabolomics data with other omics data (genomics, transcriptomics, and proteomics) provides a more comprehensive perspective of plant biology. This systems biology approach enables researchers to understand the complex interactions within organisms.

IAA and ACC deaminase producing-bacteria isolated from the rhizosphere of pineapple plants grown under different abiotic and biotic stresses

The roles of plant growth-promoting rhizobacteria in promoting plant growth and soil health, including alteration in plant metabolism and production of phytohormones such as indole-3-acetic acid (IAA) and the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, are indisputable. This study aimed to isolate and characterize beneficial bacteria isolated from the rhizosphere of pineapple from distinct stress-inducing habitats, including water excess-, herbicide-over-treated-, and pathogen-infected areas at PT Great Giant Foods located in Lampung, Indonesia. The isolated bacteria were screened based on IAA production and ACC deaminase activities. Six selected isolates produced IAA with concentrations of up to 36.93 mgL^-1. The highest value belongs to Bacillus sp. NCTB5I, followed by Brevundimonas sp. CHTB 2C (13.13 mgL^-1) and Pseudomonas sp. CHTB 5B (6.65 mgL^-1). All isolates were detected with ACC deaminase activities with Brevundimonas sp. CHTJ 5H consuming 88% of ACC over 24 h, the highest among all. Brevundimonas sp. CHTB 2C was detected with the highest ACC deaminase activity with the value of 13,370 nm α-ketobutyrate mg^-1h^-1. In another experiment, it was revealed that all selected isolates promote soybean growth. These bacteria are potential to be developed in the future as bioagents to promote plant growth, especially under stressful environmental conditions.

Jasmonate signaling controls negative and positive effectors of salt stress tolerance in rice

Plant responses to salt exposure involve large reconfigurations of hormonal pathways that orchestrate physiological changes towards tolerance. Jasmonate (JA) hormones are essential to withstand biotic and abiotic assaults, but their roles in salt tolerance remain unclear. Here we describe the dynamics of JA metabolism and signaling in root and leaf tissue of rice, a plant species that is highly exposed and sensitive to salt. Roots activate the JA pathway in an early pulse, while the second leaf displays a biphasic JA response with peaks at 1 h and 3 d post-exposure. Based on higher salt tolerance of a rice JA-deficient mutant (aoc), we examined, through kinetic transcriptome and physiological analysis, the salt-triggered processes that are under JA control. Profound genotype-differential features emerged that could underlie the observed phenotypes. Abscisic acid (ABA) content and ABA-dependent water deprivation responses were impaired in aoc shoots. Moreover, aoc accumulated more Na+ in roots, and less in leaves, with reduced ion translocation correlating with root derepression of the HAK4 Na+ transporter gene. Distinct reactive oxygen species scavengers were also stronger in aoc leaves, along with reduced senescence and chlorophyll catabolism markers. Collectively, our results identify contrasted contributions of JA signaling to different sectors of the salt stress response in rice.

Nitrogen application improves salt tolerance of grape seedlings via regulating hormone metabolism

Salt stress is a dominant environmental factor that restricts the growth and yield of crops. Nitrogen is an essential mineral element for plants, regulates various physiological and biochemical processes, and has been reported to enhance salt tolerance in plants. However, the crosstalk between salt and nitrogen in grapes is not well understood. In this study, we found that nitrogen supplementation (0.01 and 0.1 mol L-1 NH4 NO3 ) significantly increased the accumulation of proline, chlorophyll, Na+ , NH4 + , and NO3 - , while it reduced the malondialdehyde content and inhibited photosynthetic performance under salt stress conditions (200 mmol L-1 NaCl). Further transcriptome and metabolome analyses showed that a total of 4890 differentially expressed genes (DEGs) and 753 differently accumulated metabolites (DAMs) were identified. Joint omics results revealed that plant hormone signal transduction pathway connected the DEGs and DAMs. In-depth analysis revealed that nitrogen supplementation increased the levels of endogenous abscisic acid, salicylic acid, and jasmonic acid by inducing the expression of 11, 4, and 13 genes related to their respective biosynthesis pathway. In contrast, endogenous indoleacetic acid content was significantly reduced due to the remarkable regulation of seven genes of its biosynthetic pathway. The modulation in hormone contents subsequently activated the differential expression of 13, 10, 12, and 29 genes of the respective downstream hormone signaling transduction pathways. Overall, all results indicate that moderate nitrogen supplementation could improve salt tolerance by regulating grape physiology and endogenous hormone homeostasis, as well as the expression of key genes in signaling pathways, which provides new insights into the interactions between mineral elements and salt stress.

Formation of subcellular compartments by condensation-prone protein OsJAZ2 in Oryza sativa and Nicotiana benthamiana leaf cells

OsJAZ2 protein has a propensity to form condensates, possibly by multivalent interactions, and can be used to construct artificial compartments in plant cells. Eukaryotic cells contain various membraneless organelles, which are compartments consisting of proteinaceous condensates formed by phase separation. Such compartments are attractive for bioengineering and synthetic biology, because they can modify cellular function by the enrichment of molecules of interest and providing an orthogonal reaction system. This study reports that Oryza sativa JAZ2 protein (OsJAZ2) is an atypical jasmonate signalling regulator that can form large condensates in both the nucleus and cytosol of O. sativa cells. TIFY and Jas domains and low-complexity regions contribute to JAZ2 condensation, possibly by multivalent interaction. Fluorescence recovery after photobleaching (FRAP) analysis suggests that JAZ2 condensates form mostly gel-like or solid compartments, but can also be in a liquid-like state. Deletion of the N-terminal region or the TIFY domain of JAZ2 causes an increase in the mobile fraction of JAZ2 condensates, moderately. Moreover, JAZ2 can also form liquid-like condensates when expressed in Nicotiana benthamiana cells. The recombinant JAZ2 fused to the green fluorescent protein (GFP) forms condensate in vitro, suggesting that the intermolecular interaction of JAZ2 molecules is a driving force for condensation. These results suggest the potential use of JAZ2 condensates to construct artificial membraneless organelles in plant cells.

A meta-quantitative trait loci analysis identified consensus genomic regions and candidate genes associated with grain yield in rice

Improving grain yield potential in rice is an important step toward addressing global food security challenges. The meta-QTL analysis offers stable and robust QTLs irrespective of the genetic background of mapping populations and phenotype environment and effectively narrows confidence intervals (CI) for candidate gene (CG) mining and marker-assisted selection improvement. To achieve these aims, a comprehensive bibliographic search for grain yield traits (spikelet fertility, number of grains per panicle, panicles number per plant, and 1000-grain weight) QTLs was conducted, and 462 QTLs were retrieved from 47 independent QTL research published between 2002 and 2022. QTL projection was performed using a reference map with a cumulative length of 2,945.67 cM, and MQTL analysis was conducted on 313 QTLs. Consequently, a total of 62 MQTLs were identified with reduced mean CI (up to 3.40 fold) compared to the mean CI of original QTLs. However, 10 of these MQTLs harbored at least six of the initial QTLs from diverse genetic backgrounds and environments and were considered the most stable and robust MQTLs. Also, MQTLs were compared with GWAS studies and resulted in the identification of 16 common significant loci modulating the evaluated traits. Gene annotation, gene ontology (GO) enrichment, and RNA-seq analyses of chromosome regions of the stable MQTLs detected 52 potential CGs including those that have been cloned in previous studies. These genes encode proteins known to be involved in regulating grain yield including cytochrome P450, zinc fingers, MADs-box, AP2/ERF domain, F-box, ubiquitin ligase domain protein, homeobox domain, DEAD-box ATP domain, and U-box domain. This study provides the framework for molecular dissection of grain yield in rice. Moreover, the MQTLs and CGs identified could be useful for fine mapping, gene cloning, and marker-assisted selection to improve rice productivity.

Autotetraploidization Gives Rise to Differential Gene Expression in Response to Saline Stress in Rice

Plant polyploidization represents an effective means for plants to perpetuate their adaptive advantage in the face of environmental variation. Numerous studies have identified differential responsiveness to environmental cues between polyploids and their related diploids, and polyploids might better adapt to changing environments. However, the mechanism that underlies polyploidization contribution during abiotic stress remains hitherto obscure and needs more comprehensive assessment. In this study, we profile morphological and physiological characteristics, and genome-wide gene expression between an autotetraploid rice and its diploid donor plant following saline stress. The results show that the autotetraploid rice is more tolerant to saline stress than its diploid precursor. The physiological characteristics were rapidly responsive to saline stress in the first 24 h, during which the elevations in sodium ion, superoxide dismutase, peroxidase, and 1-aminocyclopropane-1-carboxylic acid were all significantly higher in the autotetraploid than in the diploid rice. Meanwhile, the genome-wide gene expression analysis revealed that the genes related to ionic transport, peroxidase activity, and phytohormone metabolism were differentially expressed in a significant manner between the autotetraploid and the diploid rice in response to saline stress. These findings support the hypothesis that diverse mechanisms exist between the autotetraploid rice and its diploid donor plant in response to saline stress, providing vital information for improving our understanding on the enhanced performance of polyploid plants in response to salt stress.

Insights into the Cytochrome P450 Monooxygenase Superfamily in Osmanthus fragrans and the Role of OfCYP142 in Linalool Synthesis

Osmanthus fragrans flowers have long been used as raw materials in food, tea, beverage, and perfume industries due to their attractive and strong fragrance. The P450 superfamily proteins have been reported to widely participate in the synthesis of plant floral volatile organic compounds (VOCs). To investigate the potential functions of P450 superfamily proteins in the fragrance synthesis of O. fragrans, we investigated the P450 superfamily genome wide. A total of 276 P450 genes were identified belonging to 40 families. The RNA-seq data suggested that many OfCYP genes were preferentially expressed in the flower or other organs, and some were also induced by multiple abiotic stresses. The expression patterns of seven flower-preferentially expressed OfCYPs during the five different flower aroma content stages were further explored using quantitative real-time PCR, showing that the CYP94C subfamily member OfCYP142 had the highest positive correlation with linalool synthesis gene OfTPS2. The transient expression of OfCYP142 in O. fragrans petals suggested that OfCYP142 can increase the content of linalool, an important VOC of the O. fragrans floral aroma, and a similar result was also obtained in flowers of OfCYP142 transgenic tobacco. Combined with RNA-seq data of the transiently transformed O. fragrans petals, we found that the biosynthesis pathway of secondary metabolites was significantly enriched, and many 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway genes were also upregulated. This evidence indicated that the OfCYP proteins may play critical roles in the flower development and abiotic response of O. fragrans, and that OfCYP142 can participate in linalool synthesis. This study provides valuable information about the functions of P450 genes and a valuable guide for studying further functions of OfCYPs in promoting fragrance biosynthesis of ornamental plants.

Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice

Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and histone modification, but the precise mechanism is as yet unclear. Here, we analysed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac with gene expression and transcript elongation. During flag leaf aging, we observed 1249 up-regulated differentially expressed genes (DEGs) and 996 down-regulated DEGs, showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac. We produced a landscape of H3K9 acetylation-modified gene expression targets that include known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis-related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac, and elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.

Multi-Omics and Integrative Approach towards Understanding Salinity Tolerance in Rice: A Review

Rice (Oryza sativa L.) plants are simultaneously encountered by environmental stressors, most importantly salinity stress. Salinity is the major hurdle that can negatively impact growth and crop yield. Understanding the salt stress and its associated complex trait mechanisms for enhancing salt tolerance in rice plants would ensure future food security. The main aim of this review is to provide insights and impacts of molecular-physiological responses, biochemical alterations, and plant hormonal signal transduction pathways in rice under saline stress. Furthermore, the review highlights the emerging breakthrough in multi-omics and computational biology in identifying the saline stress-responsive candidate genes and transcription factors (TFs). In addition, the review also summarizes the biotechnological tools, genetic engineering, breeding, and agricultural practicing factors that can be implemented to realize the bottlenecks and opportunities to enhance salt tolerance and develop salinity tolerant rice varieties. Future studies pinpointed the augmentation of powerful tools to dissect the salinity stress-related novel players, reveal in-depth mechanisms and ways to incorporate the available literature, and recent advancements to throw more light on salinity responsive transduction pathways in plants. Particularly, this review unravels the whole picture of salinity stress tolerance in rice by expanding knowledge that focuses on molecular aspects.

OsPP65 Negatively Regulates Osmotic and Salt Stress Responses Through Regulating Phytohormone and Raffinose Family Oligosaccharide Metabolic Pathways in Rice

Although type 2C protein phosphatases (PP2Cs) have been demonstrated to play important roles in regulating plant development and various stress responses, their specific roles in rice abiotic stress tolerance are still largely unknown. In this study, the functions of OsPP65 in rice osmotic and salt stress tolerance were investigated. Here, we report that OsPP65 is responsive to multiple stresses and is remarkably induced by osmotic and salt stress treatments. OsPP65 was highly expressed in rice seedlings and leaves and localized in the nucleus and cytoplasm. OsPP65 knockout rice plants showed enhanced tolerance to osmotic and salt stresses. Significantly higher induction of genes involved in jasmonic acid (JA) and abscisic acid (ABA) biosynthesis or signaling, as well as higher contents of endogenous JA and ABA, were observed in the OsPP65 knockout plants compared with the wild-type plants after osmotic stress treatment. Further analysis indicated that JA and ABA function independently in osmotic stress tolerance conferred by loss of OsPP65. Moreover, metabolomics analysis revealed higher endogenous levels of galactose and galactinol but a lower content of raffinose in the OsPP65 knockout plants than in the wild-type plants after osmotic stress treatment. These results together suggest that OsPP65 negatively regulates osmotic and salt stress tolerance through regulation of the JA and ABA signaling pathways and modulation of the raffinose family oligosaccharide metabolism pathway in rice. OsPP65 is a promising target for improvement of rice stress tolerance using gene editing.

Sulfenylation of ENOLASE2 facilitates H2O2-conferred freezing tolerance in Arabidopsis

H₂O₂ affects the expression of genes that are involved in plant responses to diverse environmental stresses; however, the underlying mechanisms remain elusive. Here, we demonstrate that H₂O₂ enhances plant freezing tolerance through its effect on a protein product of low expression of osmotically responsive genes2 (LOS2). LOS2 is translated into a major product, cytosolic enolase2 (ENO2), and sometimes an alternative product, the transcription repressor c-Myc-binding protein (MBP-1). ENO2, but not MBP-1, promotes cold tolerance by binding the promoter of C-repeat/DRE binding factor1 (CBF1), a central transcription factor in plant cold signaling, thus activating its expression. Overexpression of CBF1 restores freezing sensitivity of a LOS2 loss-of-function mutant. Furthermore, cold-induced H₂O₂ increases nuclear import and transcriptional binding activity of ENO2 by sulfenylating cysteine 408 and thereby promotes its oligomerization. Collectively, our results illustrate how H₂O₂ activates plant cold responses by sulfenylating ENO2 and promoting its oligomerization, leading to enhanced nuclear translocation and transcriptional activation of CBF1.

Whole-Genome Sequencing of KMR3 and Oryza rufipogon-Derived Introgression Line IL50-13 (Chinsurah Nona 2/Gosaba 6) Identifies Candidate Genes for High Yield and Salinity Tolerance in Rice

The genomes of an elite rice restorer line KMR3 (salinity-sensitive) and its salinity-tolerant introgression line IL50-13, a popular variety of coastal West Bengal, India, were sequenced. High-quality paired-end reads were obtained for KMR3 (147.6 million) and IL50-13 (131.4 million) with a sequencing coverage of 30X-39X. Scaffolds generated from the pre-assembled contigs of each sequenced genome were mapped separately onto the reference genome of Oryza sativa ssp. japonica cultivar Nipponbare to identify genomic variants in terms of SNPs and InDels. The SNPs and InDels identified for KMR3 and IL50-13 were then compared with each other to identify polymorphic SNPs and InDels unique and common to both the genomes. Functional enrichment analysis of the protein-coding genes with unique InDels identified GO terms involved in protein modification, ubiquitination, deubiquitination, peroxidase activity, and antioxidant activity in IL50-13. Linoleic acid metabolism, circadian rhythm, and alpha-linolenic acid metabolism pathways were enriched in IL50-13. These GO terms and pathways are involved in reducing oxidative damage, thus suggesting their role in stress responses. Sequence analysis of QTL markers or genes known to be associated with grain yield and salinity tolerance showed polymorphism in 20 genes, out of which nine were not previously reported. These candidate genes encoded Nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC) domain-containing protein, cyclase, receptor-like kinase, topoisomerase II-associated protein PAT1 domain-containing protein, ion channel regulatory protein, UNC-93 domain-containing protein, subunit A of the heteromeric ATP-citrate lyase, and three conserved hypothetical genes. Polymorphism was observed in the coding, intron, and untranslated regions of the genes on chromosomes 1, 2, 4, 7, 11, and 12. Genes showing polymorphism between the two genomes were considered as sequence-based new candidates derived from Oryza rufipogon for conferring high yield and salinity tolerance in IL50-13 for further functional studies.

Genome-wide transcriptome analysis and characterization of the cytochrome P450 flavonoid biosynthesis genes in pigeon pea (Cajanus cajan)

226 CcCYP450 genes were identified at the genomic level and were classified into 45 clades based on phylogenetic analysis. CcCYP75B165 gene was found that might play important roles in the biosynthesis of flavonoids in pigeon pea, and was significantly induced by methyl jasmonate (MeJA). The cytochrome P450 mono-oxygenase (CYP450) superfamily plays a key role in the flavonoid biosynthesis pathway and resists different kinds of stresses. Several CYP450 genes have been identified to be involved in the biosynthesis of crop protection agents. However, the CcCYP450 genes from pigeon pea have not been identified. Here, 226 CcCYP450 genes were identified at the genomic level by analysing the gene structure, distribution on chromosomes, gene duplication, and conserved motifs and were classified into 45 clades based on phylogenetic analysis. RNA-seq analysis revealed clear details of CcCYP450 genes that varied with time of MeJA (methyl jasmonate) induction. Among them, six CcCYP450 subfamily genes were found that might play important roles in the biosynthesis of flavonoids in pigeon pea. The overexpression of CcCYP75B165 in pigeon pea significantly induced the accumulation of genistin and downregulated the contents of cajaninstilbene acid, apigenin, isovitexin, and genistein and the expression of flavonoid synthase genes. This study provides theoretical guidance and plant genetic resources for cultivating new pigeon pea varieties with high flavonoid contents and exploring the molecular mechanisms of the biosynthesis of flavonoids under MeJA treatment.

Regulation and integration of plant jasmonate signaling: a comparative view of monocot and dicot

The phytohormone jasmonate plays a pivotal role in various aspects of plant life, including developmental programs and defense against pests and pathogens. A large body of knowledge on jasmonate biosynthesis, signal transduction as well as its functions in diverse plant processes has been gained in the past two decades. In addition, there exists extensive crosstalk between jasmonate pathway and other phytohormone pathways, such as salicylic acid (SA) and gibberellin (GA), in co-regulation of plant immune status, fine-tuning the balance of plant growth and defense, and so on, which were mostly learned from studies in the dicotyledonous model plants Arabidopsis thaliana and tomato but much less in monocot. Interestingly, existing evidence suggests both conservation and functional divergence in terms of core components of jasmonate pathway, its biological functions and signal integration with other phytohormones, between monocot and dicot. In this review, we summarize the current understanding on JA signal initiation, perception and regulation, and highlight the distinctive characteristics in different lineages of plants.

Impact of Nanomaterials on the Regulation of Gene Expression and Metabolomics of Plants under Salt Stress

Plant salinity resistance results from a combination of responses at the physiological, molecular, cellular, and metabolic levels. This article focuses on plant stress tolerance mechanisms for controlling ion homeostasis, stress signaling, hormone metabolism, anti-oxidative enzymes, and osmotic balance after nanoparticle applications. Nanoparticles are used as an emerging tool to stimulate specific biochemical reactions related to plant ecophysiological output because of their small size, increased surface area and absorption rate, efficient catalysis of reactions, and adequate reactive sites. Regulated ecophysiological control in saline environments could play a crucial role in plant growth promotion and survival of plants under suboptimal conditions. Plant biologists are seeking to develop a broad profile of genes and proteins that contribute to plant salt resistance. These plant metabolic profiles can be developed due to advancements in genomic, proteomic, metabolomic, and transcriptomic techniques. In order to quantify plant stress responses, transmembrane ion transport, sensors and receptors in signaling transduction, and metabolites involved in the energy supply require thorough study. In addition, more research is needed on the plant salinity stress response based on molecular interactions in response to nanoparticle treatment. The application of nanoparticles as an aspect of genetic engineering for the generation of salt-tolerant plants is a promising area of research. This review article addresses the use of nanoparticles in plant breeding and genetic engineering techniques to develop salt-tolerant crops.

The Effects of Exogenous Salicylic Acid on Endogenous Phytohormone Status in Hordeum vulgare L. under Salt Stress

Acclimation to salt stress in plants is regulated by complex signaling pathways involving endogenous phytohormones. The signaling role of salicylic acid (SA) in regulating crosstalk between endogenous plant growth regulators' levels was investigated in barley (Hordeum vulgare L. 'Ince'; 2n = 14) leaves and roots under salt stress. Salinity (150 and 300 mM NaCl) markedly reduced leaf relative water content (RWC), growth parameters, and leaf water potential (LWP), but increased proline levels in both vegetative organs. Exogenous SA treatment did not significantly affect salt-induced negative effects on RWC, LWP, and growth parameters but increased the leaf proline content of plants under 150 mM salt stress by 23.1%, suggesting that SA enhances the accumulation of proline, which acts as a compatible solute that helps preserve the leaf's water status under salt stress. Changes in endogenous phytohormone levels were also investigated to identify agents that may be involved in responses to increased salinity and exogenous SA. Salt stress strongly affected endogenous cytokinin (CK) levels in both vegetative organs, increasing the concentrations of CK free bases, ribosides, and nucleotides. Indole-3-acetic acid (IAA, auxin) levels were largely unaffected by salinity alone, especially in barley leaves, but SA strongly increased IAA levels in leaves at high salt concentration and suppressed salinity-induced reductions in IAA levels in roots. Salt stress also significantly increased abscisic acid (ABA) and ethylene levels; the magnitude of this increase was reduced by treatment with exogenous SA. Both salinity and SA treatment reduced jasmonic acid (JA) levels at 300 mM NaCl but had little effect at 150 mM NaCl, especially in leaves. These results indicate that under high salinity, SA has antagonistic effects on levels of ABA, JA, ethylene, and most CKs, as well as basic morphological and physiological parameters, but has a synergistic effect on IAA, which was well exhibited by principal component analysis (PCA).

Finding a breather for Oryza sativa: Understanding hormone signalling pathways involved in rice plants to submergence stress

During the course of evolution, different ecotypes of rice (Oryza sativa L.) have evolved distinct strategies to cope with submergence stress. Such contrasting responses are mediated by plant hormones that are principle regulators of growth, development and responses to various biotic and abiotic stresses. These hormones act cooperatively and show extensive crosstalk which is mediated by key regulatory genes that serve as nodes of molecular communication. The presence or absence of such genes leads to significant changes in hormone signalling pathways and hence, governs the type of response that the plant will exhibit. As flooding is one of the leading causes of crop loss across all the major rice-producing countries, it is crucial to deeply understand the molecular nexus governing the response to submergence to produce flood resilient varieties. This review focuses on the hormonal signalling pathways that mediate two contrasting responses of the rice plant to submergence stress namely, rapid internode elongation to escape flood waters and quiescence response that enables the plant to survive under complete submergence. The significance of several key genes such as Sub1A-1, SLR1, SD1 and SK1/SK2, in defining the ultimate response to submergence has also been discussed.

Plant salt response: Perception, signaling, and tolerance

Salt stress is one of the significant environmental stressors that severely affects plant growth and development. Plant responses to salt stress involve a series of biological mechanisms, including osmoregulation, redox and ionic homeostasis regulation, as well as hormone or light signaling-mediated growth adjustment, which are regulated by different functional components. Unraveling these adaptive mechanisms and identifying the critical genes involved in salt response and adaption are crucial for developing salt-tolerant cultivars. This review summarizes the current research progress in the regulatory networks for plant salt tolerance, highlighting the mechanisms of salt stress perception, signaling, and tolerance response. Finally, we also discuss the possible contribution of microbiota and nanobiotechnology to plant salt tolerance.

Combining GWAS, Genome-Wide Domestication and a Transcriptomic Analysis Reveals the Loci and Natural Alleles of Salt Tolerance in Rice (Oryza sativa L.)

Soil salinity poses a serious threat to the sustainable production of rice (Oryza sativa L.) throughout the world. Thus, the detection of loci and alleles responsible for salt tolerance is fundamental to accelerating the improvement of rice and producing the resilient varieties that will ensure future harvests. In this study, we collected a set of 191 mini-core rice populations from around the world, evaluated their salt tolerance based on plant growth and development phenotypes at the seedling stage, and divided a standard evaluation score (SES) of visual salt injury into five different grades. We used ∼3.82 million single nucleotide polymorphisms (SNPs) to identify 155 significant SNPs and 275 genes associated with salt sensitivity based on a genome-wide association study (GWAS) of SES. In particular, two candidate genes, ZFP179 and OsDSR2, were associated with salt tolerance, and OsHKT1;1 was co-detected in the entire GWAS of all the panels and indica. Additionally, we investigated the transcriptional changes in cultivars 93-11 and PA64s under normal and salinity stress conditions and found 517 co-upregulated and 223 co-downregulated genes. These differentially expressed genes (DEGs) were highly enriched in "response to chemical" and "stress" based on the gene ontology enrichment analysis. Notably, 30 candidate genes that were associated with the salt tolerance analysis were obtained by integrating GWAS and transcriptomic DEG analyses, including 13 cloned genes that had no reports of tolerance to salt and 17 candidate genes whose functions were unknown. To further explore these genes and their alleles, we performed haplotype analysis, genome-wide domestication detection, and transcriptome analysis to breed improved varieties. This data and the genetic resources provided will be valuable for the development of salt tolerant rice varieties.

Genome-wide identification and expression profiling of durian CYPome related to fruit ripening

Durian (Durio zibethinus L.) is a major economic crop native to Southeast Asian countries, including Thailand. Accordingly, understanding durian fruit ripening is an important factor in its market worldwide, owing to the fact that it is a climacteric fruit with a strikingly limited shelf life. However, knowledge regarding the molecular regulation of durian fruit ripening is still limited. Herein, we focused on cytochrome P450, a large enzyme family that regulates many biosynthetic pathways of plant metabolites and phytohormones. Deep mining of the durian genome and transcriptome libraries led to the identification of all P450s that are potentially involved in durian fruit ripening. Gene expression validation by RT-qPCR showed a high correlation with the transcriptome libraries at five fruit ripening stages. In addition to aril-specific and ripening-associated expression patterns, putative P450s that are potentially involved in phytohormone metabolism were selected for further study. Accordingly, the expression of CYP72, CYP83, CYP88, CYP94, CYP707, and CYP714 was significantly modulated by external treatment with ripening regulators, suggesting possible crosstalk between phytohormones during the regulation of fruit ripening. Interestingly, the expression levels of CYP88, CYP94, and CYP707, which are possibly involved in gibberellin, jasmonic acid, and abscisic acid biosynthesis, respectively, were significantly different between fast- and slow-post-harvest ripening cultivars, strongly implying important roles of these hormones in fruit ripening. Taken together, these phytohormone-associated P450s are potentially considered additional molecular regulators controlling ripening processes, besides ethylene and auxin, and are economically important biological traits.

Genome-Wide Characterization of Salt-Responsive miRNAs, circRNAs and Associated ceRNA Networks in Tomatoes

Soil salinization is a major environmental stress that causes crop yield reductions worldwide. Therefore, the cultivation of salt-tolerant crops is an effective way to sustain crop yield. Tomatoes are one of the vegetable crops that are moderately sensitive to salt stress. Global market demand for tomatoes is huge and growing. In recent years, the mechanisms of salt tolerance in tomatoes have been extensively investigated; however, the molecular mechanism through which non-coding RNAs (ncRNAs) respond to salt stress is not well understood. In this study, we utilized small RNA sequencing and whole transcriptome sequencing technology to identify salt-responsive microRNAs (miRNAs), messenger RNAs (mRNAs), and circular RNAs (circRNAs) in roots of M82 cultivated tomato and Solanum pennellii (S. pennellii) wild tomato under salt stress. Based on the theory of competitive endogenous RNA (ceRNA), we also established several salt-responsive ceRNA networks. The results showed that circRNAs could act as miRNA sponges in the regulation of target mRNAs of miRNAs, thus participating in the response to salt stress. This study provides insights into the mechanisms of salt tolerance in tomatoes and serves as an effective reference for improving the salt tolerance of salt-sensitive cultivars.

Genome-Wide Identification and Analyses of Drought/Salt-Responsive Cytochrome P450 Genes in Medicago truncatula

Cytochrome P450 monooxygenases (P450s) catalyze a great number of biochemical reactions and play vital roles in plant growth, development and secondary metabolism. As yet, the genome-scale investigation on P450s is still lacking in the model legume Medicago truncatula. In particular, whether and how many MtP450s are involved in drought and salt stresses for Medicago growth, development and yield remain unclear. In this study, a total of 346 MtP450 genes were identified and classified into 10 clans containing 48 families. Among them, sixty-one MtP450 genes pairs are tandem duplication events and 10 MtP450 genes are segmental duplication events. MtP450 genes within one family exhibit high conservation and specificity in intron–exon structure. Meanwhile, many Mt450 genes displayed tissue-specific expression pattern in various tissues. Specifically, the expression pattern of 204 Mt450 genes under drought/NaCl treatments were analyzed by using the weighted correlation network analysis (WGCNA). Among them, eight genes (CYP72A59v1, CYP74B4, CYP71AU56, CYP81E9, CYP71A31, CYP704G6, CYP76Y14, and CYP78A126), and six genes (CYP83D3, CYP76F70, CYP72A66, CYP76E1, CYP74C12, and CYP94A52) were found to be hub genes under drought/NaCl treatments, respectively. The expression levels of these selected hub genes could be induced, respectively, by drought/NaCl treatments, as validated by qPCR analyses, and most of these genes are involved in the secondary metabolism and fatty acid pathways. The genome-wide identification and co-expression analyses of M. truncatulaP450 superfamily genes established a gene atlas for a deep and systematic investigation of P450 genes in M. truncatula, and the selected drought-/salt-responsive genes could be utilized for further functional characterization and molecular breeding for resistance in legume crops.

WRKY9 transcription factor regulates cytochrome P450 genes CYP94B3 and CYP86B1, leading to increased root suberin and salt tolerance in Arabidopsis

Salinity affects crop productivity worldwide and mangroves growing under high salinity exhibit adaptations such as enhanced root apoplastic barrier to survive under such conditions. We have identified two cytochrome P450 family genes, AoCYP94B3 and AoCYP86B1 from the mangrove tree Avicennia officinalis and characterized them using atcyp94b3 and atcyp86b1, which are mutants of their putative Arabidopsis orthologs and the corresponding complemented lines with A. officinalis genes. CYP94B3 and CYP86B1 transcripts were induced upon salt treatment in the roots of both A. officinalis and Arabidopsis. Both AoCYP94B3 and AoCYP86B1 were localized to the endoplasmic reticulum. Heterologous expression of 35S::AoCYP94B3 and 35S::AoCYP86B1 in their respective Arabidopsis mutants (atcyp94b3 and atcyp86b1) increased the salt tolerance of the transgenic seedlings by reducing the amount of Na⁺ accumulation in the shoots. Moreover, the reduced root suberin phenotype of atcyp94b3 was rescued in the 35S::AoCYP94B3;atcyp94b3 transgenic Arabidopsis seedlings. Gas-chromatography and mass spectrometry analyses showed that the amount of suberin monomers (C-16 ω-hydroxy acids, C-16 α, ω-dicarboxylic acids and C-20 eicosanol) were increased in the roots of 35S::AoCYP94B3;atcyp94b3 Arabidopsis seedlings. Using chromatin immunoprecipitation and electrophoretic mobility shift assays, we identified AtWRKY9 as the upstream regulator of AtCYP94B3 and AtCYP86B1 in Arabidopsis. In addition, atwrky9 showed suppressed expression of AtCYP94B3 and AtCYP86B1 transcripts, and reduced suberin in the roots. These results show that AtWRKY9 controls suberin deposition by regulating AtCYP94B3 and AtCYP86B1, leading to salt tolerance. Our data can be used for generating salt-tolerant crop plants in the future.

Label-free quantitative proteomics analysis of Humulus scandens (Lour.) Merr. leaves treated by an odor compound of Periploca sepium Bunge

The odor compound from Periploca sepium Bunge, 2-hydroxy-4-methoxy-benzaldehyde (HMB), is an allelochemical agent and is one of the least investigated isomers of vanillin. In this study, we used label-free quantitative proteomics analysis technology to investigate the effect of HMB on the protein expression of Humulus scandens (Lour.) Merr. leaves in July 2019 on Guiyang. A total of 269 proteins of 624 identified proteins were differentially expressed, among which 21.18% of the proteins were up-regulated and 32.71% down-regulated. These proteins were classified into 11 cell components and more than 20% of differentially expressed proteins were located in cell membrane and chloroplast. Functional classification analysis showed that 12 molecular functions were altered upon HMB treatment, and the ratio of catalytic activity was the highest (19.53%). At least 12 biological functions were affected, which involved small molecule metabolic processes, organic substance metabolic processes, gene expression, and photosynthesis. Our data provide resources and insights into the biochemical mechanism by which HMB kills weeds.

Resveratrol Alleviates the KCl Salinity Stress of Malus hupehensis Rhed

Applying large amounts of potash fertilizer in apple orchards for high apple quality and yield aggravates KCl stress. As a phytoalexin, resveratrol (Res) participates in plant resistance to biotic stress. However, its role in relation to KCl stress has never been reported. Herein we investigated the role of Res in KCl stress response of Malus hupehensis Rehd., a widely used apple rootstock in China which is sensitive to KCl stress. KCl-stressed apple seedlings showed significant wilting phenotype and decline in photosynthetic rate, and the application of 100 μmol Res alleviated KCl stress and maintained photosynthetic capacity. Exogenous Res can strengthen the activities of peroxidase and catalase, thus eliminating reactive oxygen species production induced by KCl stress. Moreover, exogenous Res can decrease the electrolyte leakage by accumulating proline for osmotic balance under KCl stress. Furthermore, exogenous Res application can affect K+/Na+ homeostasis in cytoplasm by enhancing K+ efflux outside the cells, inhibiting Na+ efflux and K+ absorption, and compartmentalizing K+ into vacuoles through regulating the expression of K+ and Na+ transporter genes. These findings provide a theoretical basis for the application of exogenous Res to relieve the KCl stress of apples.

Evolution and identification of DREB transcription factors in the wheat genome: modeling, docking and simulation of DREB proteins associated with salt stress

Soil salinity and the resulting salt stress it imposes on crop plants is a major problem for modern agriculture. Understanding how salt tolerance mechanisms in plants are regulated is therefore important. One regulatory mechanism is the APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factor family, including dehydration responsive element binding (DREB) transcription factors. By binding to DNA, specifically upstream of genes that play roles in salt tolerance pathways, DREB proteins upregulate expression of these genes. DREB in Triticum aestivum (wheat) cluster in sub-groups and in this study by scanning the recently extended predicted proteome of wheat for DREB, we increased the number of members of this sub-family. Using the wheat genome, we identified 576 genes coding for the AP2 domain of which 508 were identified to have one AP2 domain, a characteristic of the DREB/ERF subfamily. We confirmed the existing four sub-groups by sequence-based phylogenetic analyses but also identified 32 new DREB subfamily members, not belonging to any known sub-group. Transcription factor profile inference analysis identified two genes, TraesCS2B02G002700 and TraesCS2D02G015200, being homologous to DREB1A of Arabidopsis thaliana. Based on molecular simulation (25 ns) analysis, TraesCS2B02G002700 with a CCGAC motif was observed to interact very stably with DNA. In silico mutational analysis at the 19^th position in the DREB domain of TraesCS2B02G002700-DNA complex indicated this as a stable part for recognizing and forming interaction with DNA. Moreover, six target genes were predicted having an upstream CCGAC motif regulated by TraesCS2B02G002700. Our study provides an overall framework for exploring the transcription factors in plants and identifying e.g. potential salt stress target genes.Communicated by Ramaswamy H. Sarma.

Jasmonates and Plant Salt Stress: Molecular Players, Physiological Effects, and Improving Tolerance by Using Genome-Associated Tools

Soil salinity is one of the most limiting stresses for crop productivity and quality worldwide. In this sense, jasmonates (JAs) have emerged as phytohormones that play essential roles in mediating plant response to abiotic stresses, including salt stress. Here, we reviewed the mechanisms underlying the activation and response of the JA-biosynthesis and JA-signaling pathways under saline conditions in Arabidopsis and several crops. In this sense, molecular components of JA-signaling such as MYC2 transcription factor and JASMONATE ZIM-DOMAIN (JAZ) repressors are key players for the JA-associated response. Moreover, we review the antagonist and synergistic effects between JA and other hormones such as abscisic acid (ABA). From an applied point of view, several reports have shown that exogenous JA applications increase the antioxidant response in plants to alleviate salt stress. Finally, we discuss the latest advances in genomic techniques for the improvement of crop tolerance to salt stress with a focus on jasmonates.

Jasmonic Acid Signaling and Molecular Crosstalk with Other Phytohormones

Plants continually monitor their innate developmental status and external environment and make adjustments to balance growth, differentiation and stress responses using a complex and highly interconnected regulatory network composed of various signaling molecules and regulatory proteins. Phytohormones are an essential group of signaling molecules that work through a variety of different pathways conferring plasticity to adapt to the everchanging developmental and environmental cues. Of these, jasmonic acid (JA), a lipid-derived molecule, plays an essential function in controlling many different plant developmental and stress responses. In the past decades, significant progress has been made in our understanding of the molecular mechanisms that underlie JA metabolism, perception, signal transduction and its crosstalk with other phytohormone signaling pathways. In this review, we discuss the JA signaling pathways starting from its biosynthesis to JA-responsive gene expression, highlighting recent advances made in defining the key transcription factors and transcriptional regulatory proteins involved. We also discuss the nature and degree of crosstalk between JA and other phytohormone signaling pathways, highlighting recent breakthroughs that broaden our knowledge of the molecular bases underlying JA-regulated processes during plant development and biotic stress responses.

Identification of QTLs for Salt Tolerance at the Germination and Seedling Stages in Rice

Rice is highly sensitive to salinity stress during the seedling establishment phase. Salt stress is widely occurring in cultivated areas and severely affects seed germination ability and seedling establishment, which may result in a complete crop failure. The objective of the present study is to identify quantitative trait loci (QTLs) related to salt tolerance of the germination and seedling stages in a rice backcross inbred line (BIL) population that was derived from a backcross of an Africa rice ACC9 as donor and indica cultivar Zhenshan97 (ZS97) as the recurrent parent. Under salt stress, ACC9 exhibited a higher germination percentage, but more repressed seedling growth than ZS97. Using the BIL population, 23 loci for germination parameters were detected at the germination stage and 46 loci were identified for several morphological and physiological parameters at the seedling stage. Among them, nine and 33 loci with the ACC9 alleles increased salt tolerance at the germination and seedling stages, respectively. Moreover, several major QTLs were found to be co-localized in the same or overlapping regions of previously reported genes for salt stress. These major loci will facilitate improving salt-tolerance rice in genome-breeding programs.

Jasmonic Acid Impairs Arabidopsis Seedling Salt Stress Tolerance Through MYC2-Mediated Repression of CAT2 Expression

High salinity causes ionic, osmotic, and oxidative stresses to plants, and the antioxidant enzyme Catalase2 (CAT2) plays a vital role in this process, while how CAT2 expression is regulated during plant response to high salinity remains elusive. Here, we report that phytohormone jasmonic acid (JA) impairs plant salt stress tolerance by repressing CAT2 expression in an MYC2-dependent manner. Exogenous JA application decreased plant salt stress tolerance while the jar1 mutant with reduced bioactive JA-Ile accumulation showed enhanced salt stress tolerance. JA enhanced salt-induced hydrogen peroxide (H₂O₂) accumulation, while treatment with H₂O₂-scavenger glutathione compromised such effects of JA on plant H₂O₂ accumulation and salt stress tolerance. In addition, JA repressed CAT2 expression in salt-stressed wild-type plant but not in myc2, a mutant of the master transcriptional factor MYC2 in JA signaling, therefore, the myc2 mutant exhibited increased salt stress tolerance. Further study showed that mutation of CAT2 largely reverted lower reactive oxygen species (ROS) accumulation, higher CAT activity, and enhanced salt stress tolerance of the myc2 mutant in myc2 cat2-1 double mutant, revealing that CAT2 functions downstream JA-MYC2 module in plant response to high salinity. Together, our study reveals that JA impairs Arabidopsis seedling salt stress tolerance through MYC2-mediated repression of CAT2 expression.

Comparative transcriptome analysis of two rice genotypes differing in their tolerance to saline-alkaline stress

Saline-alkaline stress is an abiotic stress that suppresses rice plant growth and reduces yield. However, few studies have investigated the mechanism by which rice plants respond to saline-alkaline stress at a global transcriptional level. Dongdao-4 and Jigeng-88, which differ in their tolerance to saline-alkaline stress, were used to explore gene expression differences under saline-alkaline stress by RNA-seq technology. In seedlings of Dongdao-4 and Jigeng-88, 3523 and 4066 genes with differential levels of expression were detected, respectively. A total of 799 genes were upregulated in the shoots of both Dongdao-4 and Jigeng-88, while 411 genes were upregulated in the roots of both genotypes. Among the downregulated genes in Dongdao-4 and Jigeng-88, a total of 453 and 372 genes were found in shoots and roots, respectively. Gene ontology (GO) analysis showed that upregulated genes were enriched in several GO terms such as response to stress, response to jasmonic acid, organic acid metabolic process, nicotianamine biosynthetic process, and iron homeostasis. The downregulated genes were enriched in several GO terms, such as photosynthesis and response to reactive oxygen species. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that Dongdao-4 seedlings were specifically enriched in the biosynthesis of secondary metabolites such as diterpenoids and phenylpropanoids. The upregulated genes that were involved in secondary metabolite biosynthesis, amino acid biosynthesis, betalain biosynthesis, organic acid metabolic process, and iron homeostasis pathways may be central to saline-alkaline tolerance in both rice genotypes. In contrast, the genes involved in the diterpenoid and phenylpropanoid biosynthesis pathways may contribute to the greater tolerance to saline-alkaline stress in Dongdao-4 seedlings than in Jigeng-88. These results suggest that Dongdao-4 was equipped with a more efficient mechanism involved in multiple biological processes to adapt to saline-alkaline stress.

How Plant Hormones Mediate Salt Stress Responses

Salt stress is one of the major environmental stresses limiting plant growth and productivity. To adapt to salt stress, plants have developed various strategies to integrate exogenous salinity stress signals with endogenous developmental cues to optimize the balance of growth and stress responses. Accumulating evidence indicates that phytohormones, besides controlling plant growth and development under normal conditions, also mediate various environmental stresses, including salt stress, and thus regulate plant growth adaptation. In this review, we mainly discuss and summarize how plant hormones mediate salinity signals to regulate plant growth adaptation. We also highlight how, in response to salt stress, plants build a defense system by orchestrating the synthesis, signaling, and metabolism of various hormones via multiple crosstalks.

Understanding salt tolerance mechanism using transcriptome profiling and de novo assembly of wild tomato Solanum chilense

Soil salinity affects the plant growth and productivity detrimentally, but Solanum chilense, a wild relative of cultivated tomato (Solanum lycopersicum L.), is known to have exceptional salt tolerance. It has precise adaptations against direct exposure to salt stress conditions. Hence, a better understanding of the mechanism to salinity stress tolerance by S. chilense can be accomplished by comprehensive gene expression studies. In this study 1-month-old seedlings of S. chilense and S. lycopersicum were subjected to salinity stress through application of sodium chloride (NaCl) solution. Through RNA-sequencing here we have studied the differences in the gene expression patterns. A total of 386 million clean reads were obtained through RNAseq analysis using the Illumina HiSeq 2000 platform. Clean reads were further assembled de novo into a transcriptome dataset comprising of 514,747 unigenes with N50 length of 578 bp and were further aligned to the public databases. Genebank non-redundant (Nr), Viridiplantae, Gene Ontology (GO), KOG, and KEGG databases classification suggested enrichment of these unigenes in 30 GO categories, 26 KOG, and 127 pathways, respectively. Out of 265,158 genes that were differentially expressed in response to salt treatment, 134,566 and 130,592 genes were significantly up and down-regulated, respectively. Upon placing all the differentially expressed genes (DEG) in known signaling pathways, it was evident that most of the DEGs involved in cytokinin, ethylene, auxin, abscisic acid, gibberellin, and Ca²⁺ mediated signaling pathways were up-regulated. Furthermore, GO enrichment analysis was performed using REVIGO and up-regulation of multiple genes involved in various biological processes in chilense under salinity were identified. Through pathway analysis of DEGs, “Wnt signaling pathway” was identified as a novel pathway for the response to the salinity stress. Moreover, key genes for salinity tolerance, such as genes encoding proline and arginine metabolism, ROS scavenging system, transporters, osmotic regulation, defense and stress response, homeostasis and transcription factors were not only salt-induced but also showed higher expression in S. chilense as compared to S. lycopersicum. Thus indicating that these genes may have an important role in salinity tolerance in S. chilense. Overall, the results of this study improve our understanding on possible molecular mechanisms underlying salt tolerance in plants in general and tomato in particular.

Gossypium hirsutum Salt Tolerance Is Enhanced by Overexpression of G. arboreum JAZ1

Gossypium arboreum possesses many favorable traits including robust defense against biotic and abiotic stress although it has been withdrawn from the market because of lower yield and fiber quality compared to G. hirsutum (upland cotton). It is therefore important to explore and utilize the beneficial genes of G. arboretum for G. hirsutum cultivar breeding. Here, the function of G. arboreum JAZ1 in tolerance to salt stress was determined through loss-of-function analysis. GaJAZ1can interact with GaMYC2 to repress expression of downstream genes whose promoters contain a G-box cis element, affecting plant tolerance to salinity stress. The experimental data from NaCl treatments and a 2 year continuous field trial with natural saline-alkaline soil showed that the ectopically overexpressed GaJAZ1 significantly increased salt tolerance in upland cotton compared to the wild type, showing higher growth vigor with taller plants, increased fresh weight, and more bolls, which is due to reprogrammed expression of tolerance-related genes and promotion of root development. High-throughput RNA sequencing of GaJAZ1 transgenic and wild-type plants showed many differentially expressed genes involved in JA signaling and biosynthesis, salt stress-related genes, and hormone-related genes, suggesting that overexpressing GaJAZ1 can reprogram the expression of defense-related genes in G. hirsutum plants to increase tolerance to salt stress. The research provides a foundation to explore and utilize favorable genes from Gossypium species for upland cotton cultivar breeding.

Metabolomics: A Way Forward for Crop Improvement

Metabolomics is an emerging branch of "omics" and it involves identification and quantification of metabolites and chemical footprints of cellular regulatory processes in different biological species. The metabolome is the total metabolite pool in an organism, which can be measured to characterize genetic or environmental variations. Metabolomics plays a significant role in exploring environment-gene interactions, mutant characterization, phenotyping, identification of biomarkers, and drug discovery. Metabolomics is a promising approach to decipher various metabolic networks that are linked with biotic and abiotic stress tolerance in plants. In this context, metabolomics-assisted breeding enables efficient screening for yield and stress tolerance of crops at the metabolic level. Advanced metabolomics analytical tools, like non-destructive nuclear magnetic resonance spectroscopy (NMR), liquid chromatography mass-spectroscopy (LC-MS), gas chromatography-mass spectrometry (GC-MS), high performance liquid chromatography (HPLC), and direct flow injection (DFI) mass spectrometry, have sped up metabolic profiling. Presently, integrating metabolomics with post-genomics tools has enabled efficient dissection of genetic and phenotypic association in crop plants. This review provides insight into the state-of-the-art plant metabolomics tools for crop improvement. Here, we describe the workflow of plant metabolomics research focusing on the elucidation of biotic and abiotic stress tolerance mechanisms in plants. Furthermore, the potential of metabolomics-assisted breeding for crop improvement and its future applications in speed breeding are also discussed. Mention has also been made of possible bottlenecks and future prospects of plant metabolomics.

Interruption of Jasmonic Acid Biosynthesis Causes Differential Responses in the Roots and Shoots of Maize Seedlings against Salt Stress

Jasmonates (JAs) together with jasmonic acid and its offshoots are lipid-derived endogenous hormones that play key roles in both developmental processes and different defense responses in plants. JAs have been studied intensively in the past decades for their substantial roles in plant defense comebacks against diverse environmental stresses among model plants. However, the role of this phytohormone has been poorly investigated in the monocotyledonous species against abiotic stresses. In this study, a JA biosynthesis mutant opr7opr8 was used for the investigation of JA roles in the salt stress responses of maize seedlings, whose roots were exposed to 0 to 300 mM NaCl. Foliar stomatal observation showed that opr7opr8 had a larger stomatal aperture than wild type (WT) (B73) under salinity stress, indicating that JA positively regulates guard cell movement under salt stress. The results regarding chlorophyll content and leaf senescence showed that opr7opr8 exhibited delayed leaf senescence under salt stress as compared to WT, indicating that JA plays a role in salt-inducing cell death and subsequent leaf senescence. Moreover, the morphological parameters, including the length of the shoots and roots, and the fresh and dry weights of the shoots and roots, showed that after 7 days of salt treatment, opr7opr8 had heavier and longer shoots than WT but slighter and shorter roots than WT. In addition, ion analysis showed that opr7opr8 accumulated less sodium but more potassium in the leaves than WT but more sodium and less potassium in the roots than WT, suggesting that JA deficiency causes higher salt stress to the roots but less stress to the leaves of the seedlings. Reactive oxygen species (ROS) analysis showed that opr7opr8 produced less H₂O₂ than WT in the leaves but more H₂O₂ in the roots under salt treatment, and correspondingly, ROS-scavenging enzymes superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) showed a similar variation, i.e., opr7opr8 has lower enzymatic activities in the shoots but higher activities in the roots than WT under salt treatment. For osmotic adjustment, opr7opr8 produced less proline in the shoots at 100 and 300 mM NaCl treatments but more in the roots than the WT roots under all salt treatments. In addition, the gene expression for abscisic acid (ABA) biosynthesis under salt stress was investigated. Results showed that the expression levels of four key enzymes of ABA biosynthesis, ZEP1, NCED5, AO1, and VP10, were significantly downregulated in the shoots as compared to WT under salt treatment. Putting all the data together, we concluded that JA-deficiency in maize seedlings reduced the salt-stress responses in the shoots but exaggerated the responses in the roots. In addition, endogenous JA acted as a positive regulator for the transportation of sodium ions from the roots to the shoots because the mutant opr7opr8 had a higher level of sodium in the roots but a significantly lower level in the shoots than WT. Furthermore, JA may act as a positive regulator for ABA biosynthesis in the leaves under salt stress.

Metabolic Control within the Jasmonate Biochemical Pathway

Regulation of defense and developmental responses by jasmonates (JAs) has been intensively investigated at genetic and transcriptional levels. Plasticity in the jasmonic acid (JA) metabolic pathway as a means to control signal output has received less attention. Although the amplitude of JA responses generally follows the accumulation dynamics of the active hormone jasmonoyl-isoleucine (JA-Ile), emerging evidence has identified cases where this relationship is distorted and that we discuss in this review. JA-Ile is turned over in Arabidopsis by two inducible, intertwined catabolic pathways; one is oxidative and mediated by cytochrome P450 enzymes of the subfamily 94 (CYP94), and the other proceeds via deconjugation by amidohydrolases. Their genetic inactivation has profound effects on JAs homeostasis, including strong JA-Ile overaccumulation, but this correlates with enhanced defense and tolerance to microbial or insect attacks only in the absence of overinduction of negative signaling regulators. By contrast, the impairment of JA oxidation in the jasmonic acid oxidase 2 (jao2) mutant turns on constitutive defense responses without elevating JA-Ile levels in naive leaves and enhances resistance to subsequent biotic stress. This latter and other recent cases of JA signaling are associated with JA-Ile catabolites accumulation rather than more abundant hormone, reflecting increased metabolic flux through the pathway. Therefore, manipulating upstream and downstream JA-Ile homeostatic steps reveals distinct metabolic nodes controlling defense signaling output.

A Meta-Analysis of Comparative Transcriptomic Data Reveals a Set of Key Genes Involved in the Tolerance to Abiotic Stresses in Rice

Several environmental factors, such as drought, salinity, and extreme temperatures, negatively affect plant growth and development, which leads to yield losses. The tolerance or sensitivity to abiotic stressors are the expression of a complex machinery involving molecular, biochemical, and physiological mechanisms. Here, a meta-analysis on previously published RNA-Seq data was performed to identify the genes conferring tolerance to chilling, osmotic, and salt stresses, by comparing the transcriptomic changes between tolerant and susceptible rice genotypes. Several genes encoding transcription factors (TFs) were identified, suggesting that abiotic stress tolerance involves upstream regulatory pathways. A gene co-expression network defined the metabolic and signalling pathways with a prominent role in the differentiation between tolerance and susceptibility: (i) the regulation of endogenous abscisic acid (ABA) levels, through the modulation of genes that are related to its biosynthesis/catabolism, (ii) the signalling pathways mediated by ABA and jasmonic acid, (iii) the activity of the "Drought and Salt Tolerance" TF, involved in the negative regulation of stomatal closure, and (iv) the regulation of flavonoid biosynthesis by specific MYB TFs. The identified genes represent putative key players for conferring tolerance to a broad range of abiotic stresses in rice; a fine-tuning of their expression seems to be crucial for rice plants to cope with environmental cues.

Jasmonates-the Master Regulator of Rice Development, Adaptation and Defense

Rice is one of the most important food crops worldwide, as well as the model plant in molecular studies on the cereals group. Many different biotic and abiotic agents often limit rice production and threaten food security. Understanding the molecular mechanism, by which the rice plant reacts and resists these constraints, is the key to improving rice production to meet the demand of an increasing population. The phytohormone jasmonic acid (JA) and related compounds, collectively called jasmonates, are key regulators in plant growth and development. They are also one of the central players in plant immunity against biotic attacks and adaptation to unfavorable environmental conditions. Here, we review the most recent knowledge about jasmonates signaling in the rice crop model. We highlight the functions of jasmonates signaling in many adaptive responses, and also in rice growth and development processes. We also draw special attention to different signaling modules that are controlled by jasmonates in rice.

Characterization of Jasmonoyl-Isoleucine (JA-Ile) Hormonal Catabolic Pathways in Rice upon Wounding and Salt Stress

BACKGROUND

Jasmonate (JA) signaling and functions have been established in rice development and response to a range of biotic or abiotic stress conditions. However, information on the molecular actors and mechanisms underlying turnover of the bioactive jasmonoyl-isoleucine (JA-Ile) is very limited in this plant species.

RESULTS

Here we explored two gene families in rice in which some members were described previously in Arabidopsis to encode enzymes metabolizing JA-Ile hormone, namely cytochrome P450 of the CYP94 subfamily (CYP94, 20 members) and amidohydrolases (AH, 9 members). The CYP94D subclade, of unknown function, was most represented in the rice genome with about 10 genes. We used phylogeny and gene expression analysis to narrow the study to candidate members that could mediate JA-Ile catabolism upon leaf wounding used as mimic of insect chewing or seedling exposure to salt, two stresses triggering jasmonate metabolism and signaling. Both treatments induced specific transcriptional changes, along with accumulation of JA-Ile and a complex array of oxidized jasmonate catabolites, with some of these responses being abolished in the JASMONATE RESISTANT 1 (jar1) mutant. However, upon response to salt, a lower dependence on JAR1 was evidenced. Dynamics of CYP94B5, CYP94C2, CYP94C4 and AH7 transcripts matched best the accumulation of JA-Ile catabolites. To gain direct insight into JA-Ile metabolizing activities, recombinant expression of some selected genes was undertaken in yeast and bacteria. CYP94B5 was demonstrated to catalyze C12-hydroxylation of JA-Ile, whereas similarly to its Arabidopsis bi-functional homolog IAR3, AH8 performed cleavage of JA-Ile and auxin-alanine conjugates.

CONCLUSIONS

Our data shed light on two rice gene families encoding enzymes related to hormone homeostasis. Expression data along with JA profiling and functional analysis identifies likely actors of JA-Ile catabolism in rice seedlings. This knowledge will now enable to better understand the metabolic fate of JA-Ile and engineer optimized JA signaling under stress conditions.

Gene Expression analysis associated with salt stress in a reciprocally crossed rice population

The rice landrace Horkuch, endemic to the southern saline coast of Bangladesh, is known to have salt tolerance traits and can therefore contribute to a high yielding recipient for breeding purposes. In this study, we reciprocally crossed Horkuch with high yielding but salt sensitive IR29 to detect the complement of genes that were responsible for conferring salt tolerance versus sensitivity at the seedling developmental stage. We looked at tolerant and sensitive F3 families from individual F2 segregating plants and analyzed them for differential gene expressions using RNAseq. In general, we observed higher numbers of genes differentially expressed in leaves compared to root tissues. This included both upregulation and downregulation of gene expression across our experimental factors. Gene expression decreased in sensitive leaf after stress exposure where tolerant plants showed the opposite trend. In root, tolerant plants expression decreased at higher time points of stress exposure. We also observed a strong maternal cytoplasmic effect on gene expression and this was most evident in roots where there was upregulation in functional enrichments related to phosphorylation, electron carriers, transporter and cation transmembrane activities. Stress groups (tolerant and sensitive) response in F3 families were distinctive in both cytoplasmic backgrounds and involved uniquely upregulated genes in tolerant progenies including membrane sensor proteins, enzymes involved with signaling pathways, such as those producing trehalose and G-protein coupled receptor proteins, photosynthesis-related enzymes and golgi body recycling as well as prolamin precursor proteins involved in refolding of proteins. On the other hand, sensitivity was found to be associated with differential upregulation of only a few redox proteins and higher number of apoptosis related genes compared to the tolerant response. Overall, our highly replicated experimental design was powerful and allowed the detection of relatively subtle differential expression. Our future goal is to correlate these expression differences with QTLs in this population, which would help identify the relative importance of specific genetic loci and provide a direct avenue for combining higher levels of salt tolerance with better agronomic traits in rice.

Comparative transcriptomic analysis reveal the regulation mechanism underlying MeJA-induced accumulation of alkaloids in Dendrobium officinale

Dendrobium officinale is a traditional medicinal herb with a variety of bioactive components. Alkaloid is one of the major active ingredients of Dendrobium plants, and its immune regulatory effects have been well-studied. Although a number of genes involved in the biosynthetic pathway of alkaloids have been elucidated, the regulation mechanism underlying the methyl-jasmonate (MeJA)-induced accumulation of alkaloids in D. officinale is largely unknown. In our study, a total of 4,857 DEGs, including 2,943 up- and 1,932 down-regulated genes, were identified between the control and MeJA-treated groups. Kyoto Encyclopedia of Genes and Genomes annotation showed that a number of DEGs were associated with the putative alkaloid biosynthetic pathway in D. officinale. The main group of Dendrobium alkaloids are sesquiterpene alkaloids, which are the downstream products of mevalonate (MVA) and methylerythritol 4-phosphate (MEP) pathway. Several MVA and MEP pathway genes were significantly up-regulated by the MeJA treatment, suggesting an active precursor supply for the alkaloid biosynthesis under MeJA treatment. A number of MeJA-induced P450 family genes, aminotransferase genes and methyltransferase genes were identified, providing several important candidates to further elucidate the sesquiterpene alkaloid biosynthetic pathway of D. officinale. Furthermore, a large number of MeJA-induced transcript factor encoding genes were identified, suggesting a complex genetic network affecting the sesquiterpene alkaloid metabolism in D. officinale. Our data aids to reveal the regulation mechanism underlying the MeJA-induced accumulation of sesquiterpene alkaloids in D. officinale.