Recent advances in dissecting stress-regulatory crosstalk in rice

Unveiling the power of MYB transcription factors: Master regulators of multi-stress responses and development in cotton

Plants, being immobile, are subject to environmental stresses more than other creatures, necessitating highly effective stress tolerance systems. Transcription factors (TFs) play a crucial role in the adaptation mechanism as they can be activated by diverse signals and ultimately control the expression of stress-responsive genes. One of the most prominent plant TFs family is MYB (myeloblastosis), which is involved in secondary metabolites, developmental mechanisms, biological processes, cellular architecture, metabolic pathways, and stress responses. Extensive research has been conducted on the involvement of MYB TFs in crops, while their role in cotton remains largely unexplored. We also utilized genome-wide data to discover potential 440 MYB genes and investigated their plausible roles in abiotic and biotic stress conditions, as well as in different tissues across diverse transcriptome databases. This review primarily summarized the structure and classification of MYB TFs biotic and abiotic stress tolerance and their role in secondary metabolism in different crops, especially in cotton. However, it intends to identify gaps in current knowledge and emphasize the need for further research to enhance our understanding of MYB roles in plants.

A natural variation in OsDSK2a modulates plant growth and salt tolerance through phosphorylation by SnRK1A in rice

Plants grow rapidly for maximal production under optimal conditions; however, they adopt a slower growth strategy to maintain survival when facing environmental stresses. As salt stress restricts crop architecture and grain yield, identifying genetic variations associated with growth and yield responses to salinity is critical for breeding optimal crop varieties. OsDSK2a is a pivotal modulator of plant growth and salt tolerance via the modulation of gibberellic acid (GA) metabolism; however, its regulation remains unclear. Here, we showed that OsDSK2a can be phosphorylated at the second amino acid (S2) to maintain its stability. The gene-edited mutant osdsk2aS2G showed decreased plant height and enhanced salt tolerance. SnRK1A modulated OsDSK2a-S2 phosphorylation and played a substantial role in GA metabolism. Genetic analysis indicated that SnRK1A functions upstream of OsDSK2a and affects plant growth and salt tolerance. Moreover, SnRK1A activity was suppressed under salt stress, resulting in decreased phosphorylation and abundance of OsDSK2a. Thus, SnRK1A preserves the stability of OsDSK2a to maintain plant growth under normal conditions, and reduces the abundance of OsDSK2a to limit growth under salt stress. Haplotype analysis using 3 K-RG data identified a natural variation in OsDSK2a-S2. The allele of OsDSK2a-G downregulates plant height and improves salt-inhibited grain yield. Thus, our findings revealed a new mechanism for OsDSK2a stability and provided a valuable target for crop breeding to overcome yield limitations under salinity stress.

Screening for brown-spot disease and drought stress response and identification of dual-stress responsive genes in rice cultivars of Northeast India

Rice cultivation in Northeast India (NEI) primarily relies on rainfed conditions, making it susceptible to severe drought spells that promote the onset of brown spot disease (BSD) caused by Bipolaris oryzae. This study investigates the response of prevalent rice cultivars of NEI to the combined stress of drought and B. oryzae infection. Morphological, physiological, biochemical, and molecular changes were recorded post-stress imposition. Qualitative assessment of reactive oxygen species through DAB (3,3-diaminobenzidine) assay confirmed the elicitation of plant defense responses. Based on drought scoring system and biochemical analyses, the cultivars were categorized into susceptible (Shasharang and Bahadur), moderately susceptible (Gitesh and Ranjit), and moderately tolerant (Kapilee and Mahsuri) groups. Antioxidant enzyme accumulation (catalase, guaiacol peroxidase) and osmolyte (proline) levels increased in all stressed plants, with drought-tolerant cultivars exhibiting higher enzyme activities, indicating stress mitigation efforts. Nevertheless, electrolyte leakage and lipid peroxidation rates increased in all stressed conditions, though variations were observed among stress types. Based on findings from a previous transcriptomic study, a total of nine genes were chosen for quantitative real-time PCR analysis. Among these, OsEBP89 appeared as a potential negative regulatory gene, demonstrating substantial upregulation in the susceptible cultivars at both 48 and 72 h post-treatment (hpt). This finding suggests that OsEBP89 may play a role in conferring drought-induced susceptibility to BSD in the rice cultivars being investigated.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01447-4.

Life-Cycle Multiomics of Rice Shoots Reveals Growth Stage-Specific Effects of Drought Stress and Time-Lag Drought Responses

Field-grown rice plants are exposed to various stresses at different stages of their life cycle, but little is known about the effects of stage-specific stresses on phenomes and transcriptomes. In this study, we performed integrated time-course multiomics on rice at 3-d intervals from seedling to heading stage under six drought conditions in a well-controlled growth chamber. Drought stress at seedling and reproductive stages reduced yield performance by reducing seed number and setting rate, respectively. High temporal resolution analysis revealed that drought response occurred in two steps: a rapid response via the abscisic acid (ABA) signaling pathway and a slightly delayed DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN (DREB) pathway, allowing plants to respond flexibly to deteriorating soil water conditions. Our long-term time-course multiomics showed that temporary drought stress delayed flowering due to prolonged expression of the flowering repressor gene GRAIN NUMBER, PLANT HEIGHT AND HEADING DATE 7 (Ghd7) and delayed expression of the florigen genes HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1). Our life-cycle multiomics dataset on rice shoots under drought conditions provides a valuable resource for further functional genomic studies to improve crop resilience to drought stress.

Transcriptome-Wide Analysis of Core Transcription Factors Associated with Defense Responses in Autotetraploid versus Diploid Rice under Saline Stress and Recovery

Saline stress is a major abiotic stress that inhibits plant growth and yields worldwide. The plant transcription factor (TF) family plays an important role in converting abiotic stress signals into gene expression changes. In this study, a transcriptome-based comparative analysis was performed to investigate the global gene expression of all the TFs in diploid and autotetraploid rice during the early stage of NaCl stress and recovery period. The phenotypic data indicated that the tetraploid rice exhibited a superior salt-tolerant ability compared to the diploid rice. A total of 55 TF families were co-expressed in the tetraploid and diploid rice, and the cumulative number of TF-expressed genes was relatively higher in the diploid rice than in the tetraploid rice at all time points. Unlike the diploid rice, the overall gene expression levels of the tetraploid rice were comparable to the control during recovery. The number of differentially expressed TFs (DE-TFs) in the tetraploid rice decreased after recovery, whereas it increased to a large extent in the diploid rice. GO and KEGG pathway enrichment analysis of the DE-TFs discovered the early switching of the ABA-activated signaling pathway and specific circadian rhythm in the tetraploid rice. Combining the PPI network and heatmap analysis, some core DE-TFs were found that may have potential roles to play in tetraploid salt tolerance. This study will pave the way for elucidating the complex network regulatory mechanisms of salt tolerance in tetraploid rice.

Role of Bacillus spp. Plant Growth Promoting Properties in Mitigating Biotic and Abiotic Stresses in Lowland Rice (Oryza sativa L.)

The ability of microorganisms to promote plant growth and mitigate abiotic and biotic stresses makes them an interesting tool for sustainable agriculture. Numerous studies aim to identify new, promising bacteria isolates. Traditional culture-based methods, which focus on selecting microorganisms with plant-growth-promoting traits, such as hormone production, nutrient solubilization, and antifungal properties, are widely used. This study aims to investigate the role of plant-growth-promoting properties in bacteria-mediated stress mitigation and the suitability of traditional culture-based methods as a screening tool for the identification of beneficial bacteria. To this end, we tested three endophytic Bacillus isolates, which have previously been shown to affect tolerance against iron toxicity in lowland rice, (a) for their effect on the resistance against brown spot disease, and (b) for plant-growth-promoting traits using common culture-based methods. Both B. pumilus isolates inhibited fungal growth in vitro and reduced brown spot disease in two of three rice cultivars in planta, although they tested negative for all plant-growth-promoting traits. While B. megaterium was negative for ACC deaminase activity and nutrient solubilization, it exhibited auxin production. Nevertheless, B. megaterium did not suppress brown spot disease in any of the three rice cultivars. This study shows that bacteria do not necessarily have to possess classical plant-growth-promoting properties in order to be beneficial to plants, and it emphasizes the limitation of common culture-based methods in effectively identifying beneficial bacteria. Moreover, our results highlight the significance of the interaction between bacteria and plant cultivars in determining the beneficial effects of Bacillus spp. on plants under biotic or abiotic stresses.

Identification and characterization of TMV-induced volatile signals in Nicotiana benthamiana: evidence for JA/ET defense pathway priming in congeneric neighbors via airborne (E)-2-octenal

Plants release a mixture of volatile compounds when subjects to environmental stress, allowing them to transmit information to neighboring plants. Here, we find that Nicotiana benthamiana plants infected with tobacco mosaic virus (TMV) induces defense responses in neighboring congeners. Analytical screening of volatiles from N. benthamiana at 7 days post inoculation (dpi) using an optimized SPME-GC-MS method showed that TMV triggers the release of several volatiles, such as (E)-2-octenal, 6-methyl-5-hepten-2-one, and geranylacetone. Exposure to (E)-2-octenal enhances the resistance of N. benthamiana plants to TMV and triggers the immune system with upregulation of pathogenesis-related genes, such as NbPR1a, NbPR1b, NbPR2, and NbNPR1, which are related to TMV resistance. Furthermore, (E)-2-octenal upregulates jasmonic acid (JA) that levels up to 400-fold in recipient N. benthamiana plants and significantly affects the expression pattern of key genes in the JA/ET signaling pathway, such as NbMYC2, NbERF1, and NbPDF1.2, while the salicylic acid (SA) level is not significantly affected. Our results show for the first time that the volatile (E)-2-octenal primes the JA/ET pathway and then activates immune responses, ultimately leading to enhanced TMV resistance in adjacent N. benthamiana plants. These findings provide new insights into the role of airborne compounds in virus-induced interplant interactions.

Climate change challenges, plant science solutions

Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.

Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.

Genome-wide identification of MAPK family genes and their response to abiotic stresses in tea plant (Camellia sinensis)

Mitogen-activated protein kinase (MAPK) cascades are conserved and universal signal transduction modules that play important roles in regulating stress responses in plants. Although MAP3K, MP2K, and MPK family in tea plant (Camellia sinensis) have been investigated, little is known about MPK family genes responding to various abiotic stresses in tea plant. In this study, we performed a comprehensive genome-wide analysis of the tea plant MAPKs (CsMPKs) family gene based on the genomic data of tea plants by bioinformatics-based methods. Here, 21 putative CsMPK genes were identified in the tea plant and divided into 4 subfamilies according to the homologous to Arabidopsis and their phylogenetic relationships. The gene structure and conserved motifs of these CsMPKs in the same group showed high similarity, suggesting that they were highly conserved and might have a similar function. The expression profiles of the CsMPK genes were further investigated by quantitative real-time reverse transcription PCR, indicating that many CsMPK genes were involved in response to cold, drought, heat, or heat combined with drought treatment, suggesting their potential roles in abiotic stress responses in tea plant. These results would provide valuable information for further exploring the functional characterization of CsMPK genes in tea plants.

Transcriptomic and physiological responses of contrasting maize genotypes to drought stress

Drought is a significant environmental stress factor that adversely affects maize productivity. However, many details regarding the molecular mechanisms of maize against drought are still unclear. In this study, leaf transcriptomics and physiological traits of two maize genotypes with differing drought resistance were analyzed. Transcriptome sequencing identified 8985 and 7305 differentially expressed genes (DEGs) in SD902 and SD609, respectively. Functional analysis suggested that numerous genes are highly involved in oxidative defense, protein modification, photosynthesis, phytohormone response, MAPK signaling, and transcription factors (TFs). Compared to SD902, SD609 had a higher expression of DEGs related to antioxidant enzymes, photosynthetic electron transport, heat shock proteins, and indole-3-acetic acid (IAA) signaling under drought conditions, which might contribute to its tolerance mechanisms to drought. Stress-induced TFs may play a crucial regulatory role in genotypic differences. Moreover, the physiological changes and gene expression abundance determined using quantitative reverse transcription polymerase chain reaction were consistent with the RNA sequencing data. The study results suggest that the higher drought tolerance of SD609 than SD902 can be attributed to stronger stress defense capabilities, IAA signal transduction, and more stable photosynthesis. Our findings provide new insights into the molecular mechanisms of maize against drought stress, and the candidate genes identified may be used in breeding drought-tolerant maize cultivars.

Transcriptomic responses under combined bacterial blight and drought stress in rice reveal potential genes to improve multi-stress tolerance

BACKGROUND

The unprecedented drought and frequent occurrence of pathogen infection in rice is becoming more due to climate change. Simultaneous occurrence of stresses lead to more crop loss. To cope up multiple stresses, the durable resistant cultivars needs to be developed, by identifying relevant genes from combined biotic and abiotic stress exposed plants.

RESULTS

We studied the effect of drought stress, bacterial leaf blight disease causing Xanthomonas oryzae pv. oryzae (Xoo) pathogen infection and combined stress in contrasting BPT5204 and TN1 rice genotypes. Mild drought stress increased Xoo infection irrespective of the genotype. To identify relevant genes that could be used to develop multi-stress tolerant rice, RNA sequencing from individual drought, pathogen and combined stresses in contrasting genotypes has been developed. Many important genes are identified from resistant genotype and diverse group of genes are differentially expressed in contrasting genotypes under combined stress. Further, a meta-analysis from individual drought and Xoo pathogen stress from public domain data sets narrowed- down candidate differentially expressed genes. Many translation associated genes are differentially expressed suggesting their extra-ribosomal function in multi-stress adaptation. Overexpression of many of these genes showed their relevance in improving stress tolerance in rice by different scientific groups. In combined stress, many downregulated genes also showed their relevance in stress adaptation when they were over-expressed.

CONCLUSIONS

Our study identifies many important genes, which can be used as molecular markers and targets for genetic manipulation to develop durable resistant rice cultivars. Strategies should be developed to activate downregulated genes, to improve multi-stress tolerance in plants.

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.

Physiological and Transcriptome Analysis on Diploid and Polyploid Populus ussuriensis Kom. under Salt Stress

Populus ussuriensis Kom. is a valuable forest regeneration tree species in the eastern mountainous region of Northeast China. It is known that diploid P. ussuriensis (CK) performed barely satisfactorily under salt stress, but the salt stress tolerance of polyploid (i.e., triploid (T12) and tetraploid (F20)) P. ussuriensis is still unknown. In order to compare the salt stress tolerance and salt stress response mechanism between diploid and polyploid P. ussuriensis, phenotypic observation, biological and biochemistry index detections, and transcriptome sequencing (RNA-seq) were performed on CK, T12, and F20. Phenotypic observation and leaf salt injury index analysis indicated CK suffered more severe salt injury than T12 and F20. SOD and POD activity detections indicated the salt stress response capacity of T12 was stronger than that of CK and F20. MDA content, proline content and relative electric conductivity detections indicated CK suffered the most severe cell-membrane damage, and T12 exhibited the strongest osmoprotective capacity under salt stress. Transcriptome analysis indicated the DEGs of CK, T12, and F20 under salt stress were different in category and change trend, and there were abundant WRKY, NAM, MYB and AP2/ERF genes among the DEGs in CK, T12, and F20 under salt stress. GO term enrichment indicated the basic growth progresses of CK, and F20 was obviously influenced, while T12 immediately launched more salt stress response processes in 36 h after salt stress. KEGG enrichment indicated the DEGs of CK mainly involved in plant−pathogen interaction, ribosome biogenesis in eukaryotes, protein processing in endoplasmic reticulum, degradation of aromatic compounds, plant hormone signal transduction, photosynthesis, and carbon metabolism pathways. The DEGs of T12 were mainly involved in plant−pathogen interaction, cysteine and methionine metabolism, phagosomes, biosynthesis of amino acids, phenylalanine, tyrosine and tryptophan biosynthesis, plant hormone signal transduction, and starch and sucrose metabolism pathways. The DEGs of F20 were mainly involved in plant hormone signal transduction, plant−pathogen interaction, zeatin biosynthesis, and glutathione metabolism pathways. In conclusion, triploid exhibited stronger salt stress tolerance than tetraploid and diploid P. ussuriensis (i.e., T12 > F20 > CK). The differences between the DEGs of CK, T12, and F20 probably are the key clues for discovering the salt stress response signal transduction network in P. Ussuriensis.

Overexpression of OsGF14f Enhances Quantitative Leaf Blast and Bacterial Blight Resistance in Rice

Although it is known that rice 14-3-3 family genes are involved in various defense responses, the functions of OsGF14f in response to diseases have not been reported. Here, we showed that the transcription of OsGF14f was significantly induced by leaf blast infection, and the overexpression of OsGF14f quantitatively enhanced resistance to leaf blast and bacterial blight in rice. Further analysis showed that the expression levels of salicylic acid (SA) pathway-associated genes (PAL1, NH1, PR1a and PR10) in the OsGF14f-overexpressing plants, were higher than those in wild-type plants after inoculation with the blast isolate (Magnaporthe oryzae Barr). In addition, the expression level of OsGF14f was significantly induced after SA treatment, and higher endogenous SA levels were observed in the OsGF14f-overexpressing plants compared with that in wild-type plants, especially after blast challenge. Taken together, these results suggest that OsGF14f positively regulates leaf blast and bacterial blight resistance in rice via the SA-dependent signaling pathway.

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.

Identification of major candidate genes for multiple abiotic stress tolerance at seedling stage by network analysis and their validation by expression profiling in rice (Oryza sativa L.)

A wealth of microarray and RNA-seq data for studying abiotic stress tolerance in rice exists but only limited studies have been carried out on multiple stress-tolerance responses and mechanisms. In this study, we identified 6657 abiotic stress-responsive genes pertaining to drought, salinity and heat stresses from the seedling stage microarray data of 83 samples and used them to perform unweighted network analysis and to identify key hub genes or master regulators for multiple abiotic stress tolerance. Of the total 55 modules identified from the analysis, the top 10 modules with 8-61 nodes comprised 239 genes. From these 10 modules, 10 genes common to all the three stresses were selected. Further, based on the centrality properties and highly dense interactions, we identified 7 intra-modular hub genes leading to a total of 17 potential candidate genes. Out of these 17 genes, 15 were validated by expression analysis using a panel of 4 test genotypes and a pair of standard check genotypes for each abiotic stress response. Interestingly, all the 15 genes showed upregulation under all stresses and in all the genotypes, suggesting that they could be representing some of the core abiotic stress-responsive genes. More pertinently, eight of the genes were found to be co-localized with the stress-tolerance QTL regions. Thus, in conclusion, our study not only provided an effective approach for studying abiotic stress tolerance in rice, but also identified major candidate genes which could be further validated by functional genomics for abiotic stress tolerance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03182-7.

Transcriptome Meta-Analysis Associated Targeting Hub Genes and Pathways of Drought and Salt Stress Responses in Cotton (Gossypium hirsutum): A Network Biology Approach

Abiotic stress tolerance is an intricate feature controlled through several genes and networks in the plant system. In abiotic stress, salt, and drought are well known to limit cotton productivity. Transcriptomics meta-analysis has arisen as a robust method to unravel the stress-responsive molecular network in crops. In order to understand drought and salt stress tolerance mechanisms, a meta-analysis of transcriptome studies is crucial. To confront these issues, here, we have given details of genes and networks associated with significant differential expression in response to salt and drought stress. The key regulatory hub genes of drought and salt stress conditions have notable associations with functional drought and salt stress-responsive (DSSR) genes. In the network study, nodulation signaling pathways 2 (NSP2), Dehydration-responsive element1 D (DRE1D), ethylene response factor (ERF61), cycling DOF factor 1 (CDF1), and tubby like protein 3 (TLP3) genes in drought and tubby like protein 1 (TLP1), thaumatin-like proteins (TLP), ethylene-responsive transcription factor ERF109 (EF109), ETS-Related transcription Factor (ELF4), and Arabidopsis thaliana homeodomain leucine-zipper gene (ATHB7) genes in salt showed the significant putative functions and pathways related to providing tolerance against drought and salt stress conditions along with the significant expression values. These outcomes provide potential candidate genes for further in-depth functional studies in cotton, which could be useful for the selection of an improved genotype of Gossypium hirsutum against drought and salt stress conditions.

Signal Transduction in Cereal Plants Struggling with Environmental Stresses: From Perception to Response

Cereal plants under abiotic or biotic stressors to survive unfavourable conditions and continue growth and development, rapidly and precisely identify external stimuli and activate complex molecular, biochemical, and physiological responses. To elicit a response to the stress factors, interactions between reactive oxygen and nitrogen species, calcium ions, mitogen-activated protein kinases, calcium-dependent protein kinases, calcineurin B-like interacting protein kinase, phytohormones and transcription factors occur. The integration of all these elements enables the change of gene expression, and the release of the antioxidant defence and protein repair systems. There are still numerous gaps in knowledge on these subjects in the literature caused by the multitude of signalling cascade components, simultaneous activation of multiple pathways and the intersection of their individual elements in response to both single and multiple stresses. Here, signal transduction pathways in cereal plants under drought, salinity, heavy metal stress, pathogen, and pest attack, as well as the crosstalk between the reactions during double stress responses are discussed. This article is a summary of the latest discoveries on signal transduction pathways and it integrates the available information to better outline the whole research problem for future research challenges as well as for the creative breeding of stress-tolerant cultivars of cereals.

Sugar conundrum in plant-pathogen interactions: roles of invertase and sugar transporters depend on pathosystems

It has been increasingly recognized that CWIN (cell wall invertase) and sugar transporters including STP (sugar transport protein) and SWEET (sugar will eventually be exported transporters) play important roles in plant-pathogen interactions. However, the information available in the literature comes from diverse systems and often yields contradictory findings and conclusions. To solve this puzzle, we provide here a comprehensive assessment of the topic. Our analyses revealed that the regulation of plant-microbe interactions by CWIN, SWEET, and STP is conditioned by the specific pathosystems involved. The roles of CWINs in plant resistance are largely determined by the lifestyle of pathogens (biotrophs versus necrotrophs or hemibiotrophs), possibly through CWIN-mediated salicylic acid or jasmonic acid signaling and programmed cell death pathways. The up-regulation of SWEETs and STPs may enhance or reduce plant resistance, depending on the cellular sites from which pathogens acquire sugars from the host cells. Finally, plants employ unique mechanisms to defend against viral infection, in part through a sugar-based regulation of plasmodesmatal development or aperture. Our appraisal further calls for attention to be paid to the involvement of microbial sugar metabolism and transport in plant-pathogen interactions, which is an integrated but overlooked component of such interactions.

Unravelling the physiological basis of salinity stress tolerance in cultivated and wild rice species

Wild rice species provide a rich source of genetic diversity for possible introgression of salinity stress tolerance in cultivated rice. We investigated the physiological basis of salinity stress tolerance in Oryza species by using six rice genotypes (Oryza sativa L.) and four wild rice species. Three weeks of salinity treatment significantly (P <0.05) reduced physiological and growth indices of all cultivated and wild rice lines. However, the impact of salinity-induced growth reduction differed substantially among accessions. Salt tolerant accessions showed better control over gas exchange properties, exhibited higher tissue tolerance, and retained higher potassium ion content despite higher sodium ion accumulation in leaves. Wild rice species showed relatively lower and steadier xylem sap sodium ion content over the period of 3weeks analysed, suggesting better control over ionic sodium xylem loading and its delivery to shoots with efficient vacuolar sodium ion sequestration. Contrary to this, saline sensitive genotypes managed to avoid initial Na+ loading but failed to accomplish this in the long term and showed higher sap sodium ion content. Conclusively, our results suggest that wild rice genotypes have more efficient control over xylem sodium ion loading, rely on tissue tolerance mechanisms and allow for a rapid osmotic adjustment by using sodium ions as cheap osmoticum for osmoregulation.

Overexpression of Rice OsS1Fa1 Gene Confers Drought Tolerance in Arabidopsis

Small peptides and proteins play critical regulatory roles in plant development and environmental stress responses; however, only a few of these molecules have been identified and characterized to date because of their poor annotation and other experimental challenges. Here, we present that rice (Oryza sativa L.) OsS1Fa1, a small 76-amino acid protein, confers drought stress tolerance in Arabidopsis thaliana. OsS1Fa1 was highly expressed in leaf, culm, and root tissues of rice seedlings during vegetative growth and was significantly induced under drought stress. OsS1Fa1 overexpression in Arabidopsis induced the expression of selected drought-responsive genes and enhanced the survival rate of transgenic lines under drought. The proteasome inhibitor MG132 protected the OsS1Fa1 protein from degradation. Together, our data indicate that the small protein OsS1Fa1 is induced by drought and is post-translationally regulated, and the ectopic expression of OsS1Fa1 protects plants from drought stress.

Characterization of the Function of Two S1Fa-Like Family Genes From Populus trichocarpa

S1Fa-like transcription factors (TFs) are small molecular weight proteins that contain both nuclear localization and DNA binding domains. However, the functions of S1Fa-like TFs are poorly understood. In the present study, we identified the S1Fa-like TFs from the Populus trichocarpa genome, which revealed two S1Fa-like TF genes, PtS1Fa1 and PtS1Fa2. PtS1Fa1 and PtS1Fa2 expression was suppressed by drought and salt stress, and was also significantly altered by ABA, MeJA, or SA treatment. Both PtS1Fa1 and PtS1Fa2 are nuclear proteins. Transgenic P. trichocarpa plants overexpressing PtS1Fa1 and PtS1Fa2, respectively, were generated. The plants overexpressing PtS1Fa2 showed increased fresh weight, chlorophyll content, and root length and weight compared with those in wild-type (WT) P. trichocarpa under drought conditions. Meanwhile, these phenotype traits of plants overexpressing PtS1Fa1 were similar to those of WT plants. Furthermore, overexpression of PtS1Fa2 reduced the malondialdehyde (MDA) content, electrolyte leakage, H₂O₂ and O₂- contents, and increased superoxide dismutase (SOD) and peroxidase (POD) activities. The expression of SOD and POD was also induced by PtS1Fa2. However, overexpression of PtS1Fa1 failed to affect any of these physiological parameters or SOD and POD gene expression. These results suggested that PtS1Fa2 plays a role in drought tolerance, and confers drought tolerance by increase antioxidant activity to reduce reactive oxygen species (ROS) accumulation.

Pepper NAC-type transcription factor NAC2c balances the trade-off between growth and defense responses

Plant responses to pathogen attacks and high-temperature stress (HTS) are distinct in nature but generally share several signaling components. How plants produce specific responses through these common signaling intermediates remains elusive. With the help of reverse-genetics approaches, we describe here the mechanism underlying trade-offs in pepper (Capsicum annuum) between growth, immunity, and thermotolerance. The NAC-type transcription factor CaNAC2c was induced by HTS and Ralstonia solanacearum infection (RSI). CaNAC2c-inhibited pepper growth, promoted immunity against RSI by activating jasmonate-mediated immunity and H2O2 accumulation, and promoted HTS responses by activating Heat shock factor A5 (CaHSFA5) transcription and blocking H2O2 accumulation. We show that CaNAC2c physically interacts with CaHSP70 and CaNAC029 in a context-specific manner. Upon HTS, CaNAC2c-CaHSP70 interaction in the nucleus protected CaNAC2c from degradation and resulted in the activation of thermotolerance by increasing CaNAC2c binding and transcriptional activation of its target promoters. CaNAC2c did not induce immunity-related genes under HTS, likely due to the degradation of CaNAC029 by the 26S proteasome. Upon RSI, CaNAC2c interacted with CaNAC029 in the nucleus and activated jasmonate-mediated immunity but was prevented from activating thermotolerance-related genes. In non-stressed plants, CaNAC2c was tethered outside the nucleus by interaction with CaHSP70, and thus was unable to activate either immunity or thermotolerance. Our results indicate that pepper growth, immunity, and thermotolerance are coordinately and tightly regulated by CaNAC2c via its inducible expression and differential interaction with CaHSP70 and CaNAC029.

Transcriptional activation of SUGAR TRANSPORT PROTEIN 13 mediates biotic and abiotic stress signaling

Plants have evolved elaborate physiological and molecular responses to diverse environmental challenges, including biotic and abiotic stresses. Accumulating evidence suggests that biotic and abiotic stress signaling pathways are intricately intertwined, and factors involved in molecular crosstalk between these pathways have been identified. The R2R3-type MYB96 transcription factor is a key player that mediates plant response to drought and osmotic stresses as well as to microbial pathogens, acting as a molecular signaling integrator. Here, we report that MYB96 is required for the transcriptional regulation of SUGAR TRANSPORT PROTEIN 13 (STP13) that lies at the intersection of abscisic acid (ABA) and defense signaling pathways. MYB96 directly binds to the STP13 promoter and activates gene expression upon exogenous application of ABA and bacterial flagellin peptide flg22. Our findings indicate that MYB96 integrates biotic and abiotic stress signals and possibly induces sugar uptake to confer tolerance to a wide range of adverse environmental challenges.

Role of Jasmonates, Calcium, and Glutathione in Plants to Combat Abiotic Stresses Through Precise Signaling Cascade

Plant growth regulators have an important role in various developmental processes during the life cycle of plants. They are involved in abiotic stress responses and tolerance. They have very well-developed capabilities to sense the changes in their external milieu and initiate an appropriate signaling cascade that leads to the activation of plant defense mechanisms. The plant defense system activation causes build-up of plant defense hormones like jasmonic acid (JA) and antioxidant systems like glutathione (GSH). Moreover, calcium (Ca2+) transients are also seen during abiotic stress conditions depicting the role of Ca2+ in alleviating abiotic stress as well. Therefore, these growth regulators tend to control plant growth under varying abiotic stresses by regulating its oxidative defense and detoxification system. This review highlights the role of Jasmonates, Calcium, and glutathione in abiotic stress tolerance and activation of possible novel interlinked signaling cascade between them. Further, phyto-hormone crosstalk with jasmonates, calcium and glutathione under abiotic stress conditions followed by brief insights on omics approaches is also elucidated.

Down-Regulation of SlGRAS10 in Tomato Confers Abiotic Stress Tolerance

Adverse environmental factors like salt stress, drought, and extreme temperatures, cause damage to plant growth, development, and crop yield. GRAS transcription factors (TFs) have numerous functions in biological processes. Some studies have reported that the GRAS protein family plays significant functions in plant growth and development under abiotic stresses. In this study, we demonstrated the functional characterization of a tomato SlGRAS10 gene under abiotic stresses such as salt stress and drought. Down-regulation of SlGRAS10 by RNA interference (RNAi) produced dwarf plants with smaller leaves, internode lengths, and enhanced flavonoid accumulation. We studied the effects of abiotic stresses on RNAi and wild-type (WT) plants. Moreover, SlGRAS10-RNAi plants were more tolerant to abiotic stresses (salt, drought, and Abscisic acid) than the WT plants. Down-regulation of SlGRAS10 significantly enhanced the expressions of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) to reduce the effects of reactive oxygen species (ROS) such as O²⁻ and H₂O₂. Malondialdehyde (MDA) and proline contents were remarkably high in SlGRAS10-RNAi plants. Furthermore, the expression levels of chlorophyll biosynthesis, flavonoid biosynthesis, and stress-related genes were also enhanced under abiotic stress conditions. Collectively, our conclusions emphasized the significant function of SlGRAS10 as a stress tolerate transcription factor in a certain variety of abiotic stress tolerance by enhancing osmotic potential, flavonoid biosynthesis, and ROS scavenging system in the tomato plant.

Priming by High Temperature Stress Induces MicroRNA Regulated Heat Shock Modules Indicating Their Involvement in Thermopriming Response in Rice

Rice plants often encounter high temperature stress, but the associated coping strategies are poorly understood. It is known that a prior shorter exposure to high temperature, called thermo-priming, generally results in better adaptation of the plants to subsequent exposure to high temperature stress. High throughput sequencing of transcript and small RNA libraries of rice seedlings primed with short exposure to high temperature followed by high temperature stress and from plants exposed to high temperature without priming was performed. This identified a number of transcripts and microRNAs (miRs) that are induced or down regulated. Among them osa-miR531b, osa-miR5149, osa-miR168a-5p, osa-miR1846d-5p, osa-miR5077, osa-miR156b-3p, osa-miR167e-3p and their respective targets, coding for heat shock activators and repressors, showed differential expression between primed and non-primed plants. These findings were further validated by qRT-PCR. The results indicate that the miR-regulated heat shock proteins (HSPs)/heat shock transcription factors (HSFs) may serve as important regulatory nodes which are induced during thermo-priming for plant survival and development under high temperatures.

Acetic-acid-induced jasmonate signaling in root enhances drought avoidance in rice

Conferring drought resistant traits to crops is one of the major aims of current breeding programs in response to global climate changes. We previously showed that exogenous application of acetic acid to roots of various plants could induce increased survivability under subsequent drought stress conditions, but details of the metabolism of exogenously applied acetic acid, and the nature of signals induced by its application, have not been unveiled. In this study, we show that rice rapidly induces jasmonate signaling upon application of acetic acid, resulting in physiological changes similar to those seen under drought. The major metabolite of the exogenously applied acetic acid in xylem sap was determined as glutamine-a common and abundant component of xylem sap-indicating that acetic acid is not the direct agent inducing the observed physiological responses in shoots. Expression of drought-responsive genes in shoot under subsequent drought conditions was attenuated by acetic acid treatment. These data suggest that acetic acid activates root-to-shoot jasmonate signals that partially overlap with those induced by drought, thereby conferring an acclimated state on shoots prior to subsequent drought.

Systemic propagation of immunity in plants

Systemic immunity triggered by local plant-microbe interactions is studied as systemic acquired resistance (SAR) or induced systemic resistance (ISR) depending on the site of induction and the lifestyle of the inducing microorganism. SAR is induced by pathogens interacting with leaves, whereas ISR is induced by beneficial microbes interacting with roots. Although salicylic acid (SA) is a central component of SAR, additional signals exclusively promote systemic and not local immunity. These signals cooperate in SAR- and possibly also ISR-associated signaling networks that regulate systemic immunity. The non-SA SAR pathway is driven by pipecolic acid or its presumed bioactive derivative N-hydroxy-pipecolic acid. This pathway further regulates inter-plant defense propagation through volatile organic compounds that are emitted by SAR-induced plants and recognized as defense cues by neighboring plants. Both SAR and ISR influence phytohormone crosstalk towards enhanced defense against pathogens, which at the same time affects the composition of the plant microbiome. This potentially leads to further changes in plant defense, plant-microbe, and plant-plant interactions. Therefore, we propose that such inter-organismic interactions could be combined in potentially highly effective plant protection strategies.

Microarray analysis of Arabidopsis thaliana exposed to single and mixed infections with Cucumber mosaic virus and turnip viruses

Cucumber mosaic virus (CMV), Turnip mosaic virus (TuMV) and Turnip crinkle virus (TCV) are important plant infecting viruses. In the present study, whole transcriptome alteration of Arabidopsis thaliana in response to CMV, TuMV and TCV, individual as well as mixed infections of CMV and TuMV/CMV and TCV were investigated using microarray data. In response to CMV, TuMV and TCV infections, a total of 2517, 3985 and 277 specific differentially expressed genes (DEGs) were up-regulated, while 2615, 3620 and 243 specific DEGs were down-regulated, respectively. The number of 1222 and 30 common DEGs were up-regulated during CMV and TuMV as well as CMV and TCV infections, while 914 and 24 common DEGs were respectively down-regulated. Genes encoding immune response mediators, signal transducer activity, signaling and stress response functions were among the most significantly upregulated genes during CMV and TuMV or CMV and TCV mixed infections. The NAC, C3H, C2H2, WRKY and bZIP were the most commonly presented transcription factor (TF) families in CMV and TuMV infection, while AP2-EREBP and C3H were the TF families involved in CMV and TCV infections. Moreover, analysis of miRNAs during CMV and TuMV and CMV and TCV infections have demonstrated the role of miRNAs in the down regulation of host genes in response to viral infections. These results identified the commonly expressed virus-responsive genes and pathways during plant-virus interaction which might develop novel antiviral strategies for improving plant resistance to mixed viral infections.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-00925-3.

NPR1 is required for root colonization and the establishment of a mutualistic symbiosis between the beneficial bacterium Rhizobium radiobacter and barley

Non-expressor of pathogenesis-related genes 1 (NPR1) is a key regulator of plant innate immunity and systemic disease resistance. The model for NPR1 function is based on experimental evidence obtained largely from dicots; however, this model does not fit all aspects of Poaceae family, which includes major crops such as wheat, rice and barley. In addition, there is little scientific data on NPR1's role in mutualistic symbioses. We assessed barley (Hordeum vulgare) HvNPR1 requirement during the establishment of mutualistic symbiosis between barley and beneficial Alphaproteobacterium Rhizobium radiobacter F4 (RrF4). Upon RrF4 root-inoculation, barley NPR1-knockdown (KD-hvnpr1) plants lost the typical spatiotemporal colonization pattern and supported less bacterial multiplication. Following RrF4 colonization, expression of salicylic acid marker genes were strongly enhanced in wild-type roots; whereas in comparison, KD-hvnpr1 roots exhibited little to no induction. Both basal and RrF4-induced root-initiated systemic resistance against virulent Blumeria graminis were impaired in leaves of KD-hvnpr1. Besides these immune-related differences, KD-hvnpr1 plants displayed higher root and shoot biomass than WT. However, RrF4-mediated growth promotion was largely compromised in KD-hvnpr1. Our results demonstrate a critical role for HvNPR1 in establishing a mutualistic symbiosis between a beneficial bacterium and a cereal crop.

ζ-Carotene Isomerase Suppresses Tillering in Rice through the Coordinated Biosynthesis of Strigolactone and Abscisic Acid

Rice tillering is an important agronomic trait affecting grain yield. Here, we identified a high-tillering mutant tillering20 (t20), which could be restored to the wild type by treatment with the strigolactone (SL) analog rac-GR24. T20 encodes a chloroplast ζ-carotene isomerase (Z-ISO), which is involved in the biosynthesis of carotenoids and their metabolites, SL and abscisic acid (ABA). The t20 mutant has reduced SL and ABA, raising the question of how SL and ABA biosynthesis is coordinated, and whether they have overlapping functions in tillering. We discovered that rac-GR24 stimulated T20 expression and enhanced all-trans-β-carotene biosynthesis. Importantly, rac-GR24 also stimulated expression of Oryza sativa 9-CIS-EPOXYCAROTENOID DIOXYGENASE 1 (OsNCED1) through induction of Oryza sativa HOMEOBOX12 (OsHOX12), promoting ABA biosynthesis in shoot base. On the other hand, ABA treatment significantly repressed SL biosynthesis and the ABA biosynthetic mutants displayed elevated SL biosynthesis. ABA treatment reduced the number of basal tillers in both t20 and wild-type plants. Furthermore, while ABA-deficient mutants aba1 and aba2 had the same number of basal tillers as wild type, they had more unproductive upper tillers at maturity. This work demonstrates complex interactions in the biosynthesis of carotenoid, SLs and ABA, and reveals a role for ABA in the regulation of rice tillering.

Functional characterization of the Glyoxalase-I (PdGLX1) gene family in date palm under abiotic stresses

Methylglyoxal (MG), a cytotoxic oxygenated short aldehyde, is a by-product of various metabolic reactions in plants, including glycolysis. The basal level of MG in plants is low, whereby it acts as an essential signaling molecule regulating multiple cellular processes. However, hyperaccumulation of MG under stress conditions is detrimental for plants as it inhibits multiple developmental processes, including seed germination, photosynthesis, and root growth. The evolutionarily conserved glyoxalase system is critical for MG detoxification, and it comprises of two-enzymes, the glyoxalase-I and glyoxalase-II. Here, we report the functional characterization of six putative glyoxalase-I genes from date palm (Phoenix dactylifera L.) (PdGLX1), by studying their gene expression under various environmental stress conditions and investigating their function in bacteria (Escherichia coli) and yeast (Saccharomyces cerevisiae) mutant cells. The putative PdGLX1 genes were initially identified using computational methods and cloned using molecular tools. The PdGLX1 gene expression analysis using quantitative PCR (qPCR) revealed differential expression under various stress conditions such as salinity, oxidative stress, and exogenous MG stress in a tissue-specific manner. Further, in vivo functional characterization indicated that overexpression of the putative PdGLX1 genes in E. coli enhanced their growth and MG detoxification ability. The putative PdGLX1 genes were also able to complement the loss-of-function MG hypersensitive GLO1 (YML004C) yeast mutants and promote growth by enhancing MG detoxification and reducing the accumulation of reactive oxygen species (ROS) under stress conditions as indicated by flow cytometry. These findings denote the potential importance of PdGLX1 genes in MG detoxification under stress conditions in the date palm.

SnRK1 Phosphorylates and Destabilizes WRKY3 to Enhance Barley Immunity to Powdery Mildew

Plants recognize pathogens and activate immune responses, which usually involve massive transcriptional reprogramming. The evolutionarily conserved kinase, Sucrose non-fermenting-related kinase 1 (SnRK1), functions as a metabolic regulator that is essential for plant growth and stress responses. Here, we identify barley SnRK1 and a WRKY3 transcription factor by screening a cDNA library. SnRK1 interacts with WRKY3 in yeast, as confirmed by pull-down and luciferase complementation assays. Förster resonance energy transfer combined with noninvasive fluorescence lifetime imaging analysis indicates that the interaction occurs in the barley nucleus. Transient expression and virus-induced gene silencing analyses indicate that WRKY3 acts as a repressor of disease resistance to the Bgh fungus. Barley plants overexpressing WRKY3 have enhanced fungal microcolony formation and sporulation. Phosphorylation assays show that SnRK1 phosphorylates WRKY3 mainly at Ser83 and Ser112 to destabilize the repressor, and WRKY3 non-phosphorylation-null mutants at these two sites are more stable than the wild-type protein. SnRK1-overexpressing barley plants display enhanced disease resistance to Bgh. Transient expression of SnRK1 reduces fungal haustorium formation in barley cells, which probably requires SnRK1 nuclear localization and kinase activity. Together, these findings suggest that SnRK1 is directly involved in plant immunity through phosphorylation and destabilization of the WRKY3 repressor, revealing a new regulatory mechanism of immune derepression in plants.

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

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

Lead Toxicity in Cereals: Mechanistic Insight Into Toxicity, Mode of Action, and Management

Cereals are the major contributors to global food supply, accounting for more than half of the total human calorie requirements. Sustainable availability of quality cereal grains is an important step to address the high-priority issue of food security. High concentrations of heavy metals specifically lead (Pb) in the soil negatively affect biochemical and physiological processes regulating grain quality in cereals. The dietary intake of Pb more than desirable quantity via food chain is a major concern for humans, as it can predispose individuals to chronic health issues. In plant systems, high Pb concentrations can disrupt several key metabolic processes such as electron transport chain, cellular organelles integrity, membrane stability index, PSII connectivity, mineral metabolism, oxygen-evolving complex, and enzymatic activity. Plant growth-promoting rhizobacteria (PGPR) has been recommended as an inexpensive strategy for remediating Pb-contaminated soils. A diverse group of Ascomycetes fungi, i.e., dark septate endophytes is successfully used for this purpose. A symbiotic relationship between endophytes and host cereal induces Pb tolerance by immobilizing Pb ions. Molecular and cellular modifications in plants under Pb-stressed environments are explained by transcription factor families such as bZIP, ERF, and GARP as a regulator. The role of metal tolerance protein (MTP), natural resistance-associated macrophage protein (NRAMP), and heavy metal ATPase in decreasing Pb toxicity is well known. In the present review, we provided the contemporary synthesis of existing data regarding the effects of Pb toxicity on morpho-physiological and biochemical responses of major cereal crops. We also highlighted the mechanism/s of Pb uptake and translocation in plants, critically discussed the possible management strategies and way forward to overcome the menace of Pb toxicity in cereals.

Stress-Activated Protein Kinase OsSAPK9 Regulates Tolerance to Salt Stress and Resistance to Bacterial Blight in Rice

BACKGROUND

Salt stress and bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) are key limiting factors of rice (Oryza sativa L.) yields. Members of sucrose non-fermenting 1 (SNF1)-related protein kinase 2 (SnRK2), which is a family of plant-specific Ser/Thr kinases, are important components of signaling pathways involved in plant developmental processes and responses to stresses. There are 10 members of the SnRK2 family in rice; however, their functions are poorly understood, as are the underlying molecular mechanisms.

RESULTS

In this study, we found that OsSAPK9, which belongs to the SnRK2 family, positively regulated salt-stress tolerance and strain-specific resistance to bacterial blight in rice. RNA sequencing revealed that there were 404 and 1324 genes differentially expressed in OsSAPK9-RNAi in comparison with wild-type plants under salt-stress conditions and after Xoo inoculation, respectively, which participate in basic metabolic processes. In total, 65 common differentially expressed genes involved mainly in defense responses were detected both under salt-stress conditions and after Xoo inoculation. Moreover, in vivo and in vitro experiments demonstrated that OsSAPK9 forms a protein complex with the molecular chaperones OsSGT1 and OsHsp90, and transgenic plants overexpressing OsSGT1 exhibited decreased tolerances to salt stress and significantly increased resistance levels to bacterial blight. Thus, OsSAPK9 may function as a center node regulator of salt-stress responses and disease-resistance pathways through its interaction with OsSGT1 in rice.

CONCLUSION

This study confirms that OsSAPK9 functions as a positive regulator of salt-stress responses and disease resistance through its interaction with OsSGT1 in rice.

Molecular Effects of Xylella fastidiosa and Drought Combined Stress in Olive Trees

Due to global climate change, complex combinations of stresses are expected to occur, among which the interaction between pathogens and drought stress may have a significant effect on growth and yield. In this study, the Xylella fastidiosa (Xf)-resistant cultivar Leccino and the susceptible one Cellina di Nardò were subjected to (a) individual drought stress, (b) Xf infection and (c) combination of both stress conditions. Here we report the physiological response to stresses in water content in leaves and the modulation in the expression level of seven genes responsive to plant water status and pathogen infection. In Xf-resistant plants, higher expression levels are reported for genes belonging to ROS-scavenging systems and for genes involved in pathogen stress (pathogenesis-related, PR, and leucine-rich repeat genes, LRR-RLK). However, PR and LRR-RLK were not further induced by water deficit. Interestingly, the genes related to drought response (aquaporin, PIP2.1, dehydration responsive element binding, DREB, and dehydrin, DHN), which induction was higher in Cellina di Nardò compared to Leccino during drought stress, was poorly induced in Xf-susceptible plants when Xf occur. Conversely, DHN was induced by Xf presence in Leccino. These results were consistent with observations on water content. Indeed, response was similar in Leccino regardless kind of stress or combination, whereas a strong reduction was observed in Xf-susceptible plants infected by Xf or in presence of combined stresses. Thus, the reported findings indicate that resistance of Leccino to Xf could be linked to its lower resistance to water stress, probably leading to the activation of alternative defense pathways that support the plant in Xf response.

Pipecolic Acid Is Induced in Barley upon Infection and Triggers Immune Responses Associated with Elevated Nitric Oxide Accumulation

Pipecolic acid (Pip) is an essential component of systemic acquired resistance, priming resistance in Arabidopsis thaliana against (hemi)biotrophic pathogens. Here, we studied the potential role of Pip in bacteria-induced systemic immunity in barley. Exudates of barley leaves infected with the systemic immunity-inducing pathogen Pseudomonas syringae pv. japonica induced immune responses in A. thaliana. The same leaf exudates contained elevated Pip levels compared with those of mock-treated barley leaves. Exogenous application of Pip induced resistance in barley against the hemibiotrophic bacterial pathogen Xanthomonas translucens pv. cerealis. Furthermore, both a systemic immunity-inducing infection and exogenous application of Pip enhanced the resistance of barley against the biotrophic powdery mildew pathogen Blumeria graminis f. sp. hordei. In contrast to a systemic immunity-inducing infection, Pip application did not influence lesion formation by a systemically applied inoculum of the necrotrophic fungus Pyrenophora teres. Nitric oxide (NO) levels in barley leaves increased after Pip application. Furthermore, X. translucens pv. cerealis induced the accumulation of superoxide anion radicals and this response was stronger in Pip-pretreated compared with mock-pretreated plants. Thus, the data suggest that Pip induces barley innate immune responses by triggering NO and priming reactive oxygen species accumulation.

Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis

Abiotic stress tolerance is a complex trait regulated by multiple genes and gene networks in plants. A range of abiotic stresses are known to limit rice productivity. Meta-transcriptomics has emerged as a powerful approach to decipher stress-associated molecular network in model crops. However, retaining specificity of gene expression in tolerant and susceptible genotypes during meta-transcriptome analysis is important for understanding genotype-dependent stress tolerance mechanisms. Addressing this aspect, we describe here "abiotic stress tolerant" (ASTR) genes and networks specifically and differentially expressing in tolerant rice genotypes in response to different abiotic stress conditions. We identified 6,956 ASTR genes, key hub regulatory genes, transcription factors, and functional modules having significant association with abiotic stress-related ontologies and cis-motifs. Out of the 6956 ASTR genes, 73 were co-located within the boundary of previously identified abiotic stress trait-related quantitative trait loci. Functional annotation of 14 uncharacterized ASTR genes is proposed using multiple computational methods. Around 65% of the top ASTR genes were found to be differentially expressed in at least one of the tolerant genotypes under different stress conditions (cold, salt, drought, or heat) from publicly available RNAseq data comparison. The candidate ASTR genes specifically associated with tolerance could be utilized for engineering rice and possibly other crops for broad-spectrum tolerance to abiotic stresses.

OsANN3, a calcium-dependent lipid binding annexin is a positive regulator of ABA-dependent stress tolerance in rice

Annexin is a multigene family that plays critical roles in plant stress responses and various cellular processes. Here, we reported the cloning and functional characterization of a novel rice annexin protein, OsANN3. We found that expression of OsANN3 was induced by polyethylene glycol (PEG) and abscisic acid (ABA) treatments. Overexpression of OsANN3 in rice significantly increased survival rates under drought stress, while knocking down OsANN3 resulted in sensitivity to drought. Meanwhile, OsANN3 overexpression showed enhanced sensitivity to exogenous ABA. Together with its Ca²⁺ and phospholipid binding activity, we proposed that when plants were subjected to drought stress, OsANN3 might mediate Ca²⁺ influx by binding to phospholipid to activate ABA signaling pathways. In addition, overexpression OsANN3 showed better growth under drought stress comparing to wild type, such as longer root length and more stomata closure for reducing water loss by regulating ABA-dependent stress response pathways.

Integrative meta-analysis of transcriptomic responses to abiotic stress in cotton

Abiotic environmental stresses are important factors that limit the growth, fiber yield, and quality of cotton. In this study, an integrative meta-analysis and a system-biology analysis were performed to explore the underlying transcriptomic mechanisms that are critical for response to stresses. From the meta-analysis, it was observed that a total of 1465 differentially expressed genes (DEGs) between normal and stress conditions. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that DEGs were significantly enriched in the ubiquitin-dependent process, biosynthesis of secondary metabolites, plant hormone, and signaled transduction. The results also indicated that some of DEGs were assigned to transcription factors (TFs). A total of 148 TFs belonged to 25 conserved families were identified that among them S1Fa-like, ERF, NAC, bZIP families, were the most abundant groups. Moreover, we searched in upstream regions of DEGs for over-represented DNA motifs and were able to identify 11 conserved sequence motifs. The functional analysis of these motifs revealed that they were involved in regulation of transcription, DNA replication, cytoskeleton organization, and translation. Weighted gene co-expression network analysis (WGCNA) uncovered 12 distinct co-expression modules. Four modules were significantly associated with genes involved in response to stress and cell wall organization. The network analysis also identified hub genes such as RTNLB5 and PRA1, which may be involved in regulating stress response. The findings could help to understand the mechanisms of response to abiotic stress and introduce candidate genes that may be beneficial to cotton plant breeding programs.

Exploring the protein-protein interaction landscape in plants

Protein-protein interactions (PPIs) represent an essential aspect of plant systems biology. Identification of key protein players and their interaction networks provide crucial insights into the regulation of plant developmental processes and into interactions of plants with their environment. Despite the great advance in the methods for the discovery and validation of PPIs, still several challenges remain. First, the PPI networks are usually highly dynamic, and the in vivo interactions are often transient and difficult to detect. Therefore, the properties of the PPIs under study need to be considered to select the most suitable technique, because each has its own advantages and limitations. Second, besides knowledge on the interacting partners of a protein of interest, characteristics of the interaction, such as the spatial or temporal dynamics, are highly important. Hence, multiple approaches have to be combined to obtain a comprehensive view on the PPI network present in a cell. Here, we present the progress in commonly used methods to detect and validate PPIs in plants with a special emphasis on the PPI features assessed in each approach and how they were or can be used for the study of plant interactions with their environment.

Analysis of ambient temperature-responsive transcriptome in shoot apical meristem of heat-tolerant and heat-sensitive broccoli inbred lines during floral head formation

BACKGROUND

Head formation of broccoli (Brassica oleracea var. italica) is greatly reduced under high temperature (22 °C and 27 °C). Broccoli inbred lines that are capable of producing heads at high temperatures in summer are varieties that are unique to Taiwan. However, knowledge of the early-activated pathways of broccoli head formation under high temperature is limited.

RESULTS

We compared heat-tolerant (HT) and heat-sensitive (HS) transcriptome of broccoli under different temperatures. Weighted gene correlation network analysis (WGCNA) revealed that genes involved in calcium signaling pathways, mitogen-activated protein kinase (MAPK) cascades, leucine-rich repeat receptor-like kinases (LRR-RLKs), and genes coding for heat-shock proteins and reactive oxygen species homeostasis shared a similar expression pattern to BoFLC1, which was highly expressed at high temperature (27 °C). Of note, these genes were less expressed in HT than HS broccoli at 22 °C. Co-expression analysis identified a model for LRR-RLKs in survival-reproduction tradeoffs by modulating MAPK- versus phytohormones-signaling during head formation. The difference in head-forming ability in response to heat stress between HT and HS broccoli may result from their differential transcriptome profiles of LRR-RLK genes. High temperature induced JA- as well as suppressed auxin- and cytokinin-related pathways may facilitate a balancing act to ensure fitness at 27 °C. BoFLC1 was less expressed in HT than HS at 22 °C, whereas other FLC homologues were not. Promoter analysis of BoFLC1 showed fewer AT dinucleotide repeats in HT broccoli. These results provide insight into the early activation of stress- or development-related pathways during head formation in broccoli. The identification of the BoFLC1 DNA biomarker may facilitate breeding of HT broccoli.

CONCLUSIONS

In this study, HT and HS broccoli genotypes were used to determine the effect of temperature on head formation by transcriptome profiling. On the basis of the expression pattern of high temperature-associated signaling genes, the HS transcriptome may be involved in stress defense instead of transition to the reproductive phase in response to heat stress. Transcriptome profiling of HT and HS broccoli helps in understanding the molecular mechanisms underlying head-forming capacity and in promoting functional marker-assisted breeding.

Cross-Talk Signaling in Rice During Combined Drought and Bacterial Blight Stress

Due to climatic changes, rice crop is affected by moisture deficit stress and pathogens. Tissue water limitation besides reducing growth rates, also renders the crop susceptible to the infection by Xanthomonas oryzae pv. oryzae (Xoo) that causes bacterial leaf blight. Independently, both drought adaptation and Xoo resistance have been extensively studied. Though the cross-talk between drought and Xoo stress responses have been explored from individual stress studies, examining the combinatorial stress response is limited in rice. Recently published combined stress studies showed that under the combined stress, maintenance of carbon assimilation is hindered and such response is regulated by overlapping cellular mechanisms that are different from either of the individual stresses. Several receptors, MAP kinases, transcription factors, and ribosomal proteins, are predicted for playing a role in cellular homeostasis and protects cells from combined stress effects. Here we provide a critical analysis of these aspects using information from the recently published combined stress literature. This review is useful for researchers to comprehend combinatorial stress response of rice plants to drought and Xoo.

Dissecting the Role of a Basic Helix-Loop-Helix Transcription Factor, SlbHLH22, Under Salt and Drought Stresses in Transgenic Solanum lycopersicum L

Environmental stresses, such as temperature, heavy metals, drought, cold, and microbial infections adversely damage various aspects of plant growth and development. Salinity and drought are among major hazardous factors, which adversity affects plant growth and productivity. Transcription factors, such as basic helix-loop-helix play critical roles in regulating plant physiological processes under abiotic stresses. In this study, we presented the characterization of a tomato SlbHLH22 gene under abiotic stresses such as drought and salinity. Plants overexpressing SlbHLH22 showed short height with small leaves and enhanced flavonoid accumulation. In wild type (WT) plant, the elevated levels of SlbHLH22 were detected under salt and D-mannitol stresses. Subcellular localization analysis revealed that SlbHLH22 protein was targeted to the nucleus in onion epidermal cells. Transactivation assay in yeast demonstrated that SlbHLH22 had transcriptional activation ability. The transgenic plants overexpressing SlbHLH22 displayed enhanced vigor and more tolerant to drought and salinity than WT. Overexpression of SlbHLH22 significantly peaked the activities of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) to minimize the impacts of reactive oxygen species such as H₂O₂, which was reduced significantly in transgenic plants along with Malondialdehyde (MDA). Moreover, the expression levels of ROS defense genes (SlPOD, SlCAT, SlSOD), ABA biosynthesis genes, proline biosynthesis, and flavonoids synthesis genes were also activated under salinity and drought. Taken together, our study implies that the overexpression of SlbHLH22 improved tomato plant stress resistance by improving ROS scavenging system, increasing osmotic potential and enhanced accumulation of secondary metabolites in tomato plants.

The Crosstalks Between Jasmonic Acid and Other Plant Hormone Signaling Highlight the Involvement of Jasmonic Acid as a Core Component in Plant Response to Biotic and Abiotic Stresses

Plant hormones play central roles in plant growth, developmental processes, and plant response to biotic and abiotic stresses. On the one hand, plant hormones may allocate limited resources to the most serious stresses; on the other hand, the crosstalks among multiple plant hormone signaling regulate the balance between plant growth and defense. Many studies have reported the mechanism of crosstalks between jasmonic acid (JA) and other plant hormones in plant growth and stress responses. Based on these studies, this paper mainly reviews the crosstalks between JA and other plant hormone signaling in regulating the balance between plant growth and defense response. The suppressor proteins JASMONATE ZIM DOMAIN PROTEIN (JAZ) and MYC2 as the key components in the crosstalks are also highlighted in the review. We conclude that JA interacts with other hormone signaling pathways [such as auxin, ethylene (ET), abscisic acid (ABA), salicylic acid (SA), brassinosteroids (BRs), and gibberellin (GA)] to regulate plant growth, abiotic stress tolerance, and defense resistance against hemibiotrophic pathogens such as Magnaporthe oryzae and Pseudomonas syringae. Notably, JA may act as a core signal in the phytohormone signaling network.

Biological Roles of Ornithine Aminotransferase (OAT) in Plant Stress Tolerance: Present Progress and Future Perspectives

Plant tolerance to biotic and abiotic stresses is complicated by interactions between different stresses. Maintaining crop yield under abiotic stresses is the most daunting challenge for breeding resilient crop varieties. In response to environmental stresses, plants produce several metabolites, such as proline (Pro), polyamines (PAs), asparagine, serine, carbohydrates including glucose and fructose, and pools of antioxidant reactive oxygen species. Among these metabolites, Pro has long been known to accumulate in cells and to be closely related to drought, salt, and pathogen resistance. Pyrroline-5-carboxylate (P5C) is a common intermediate of Pro synthesis and metabolism that is produced by ornithine aminotransferase (OAT), an enzyme that functions in an alternative Pro metabolic pathway in the mitochondria under stress conditions. OAT is highly conserved and, to date, has been found in all prokaryotic and eukaryotic organisms. In addition, ornithine (Orn) and arginine (Arg) are both precursors of PAs, which confer plant resistance to drought and salt stresses. OAT is localized in the cytosol in prokaryotes and fungi, while OAT is localized in the mitochondria in higher plants. We have comprehensively reviewed the research on Orn, Arg, and Pro metabolism in plants, as all these compounds allow plants to tolerate different kinds of stresses.