Enhancing blast disease resistance by overexpression of the calcium-dependent protein kinase OsCPK4 in rice

Rice breeding for low input agriculture

A low-input-based farming system can reduce the adverse effects of modern agriculture through proper utilization of natural resources. Modern varieties often need to improve in low-input settings since they are not adapted to these systems. In addition, rice is one of the most widely cultivated crops worldwide. Enhancing rice performance under a low input system will significantly reduce the environmental concerns related to rice cultivation. Traits that help rice to maintain yield performance under minimum inputs like seedling vigor, appropriate root architecture for nutrient use efficiency should be incorporated into varieties for low input systems through integrated breeding approaches. Genes or QTLs controlling nutrient uptake, nutrient assimilation, nutrient remobilization, and root morphology need to be properly incorporated into the rice breeding pipeline. Also, genes/QTLs controlling suitable rice cultivars for sustainable farming. Since several variables influence performance under low input conditions, conventional breeding techniques make it challenging to work on many traits. However, recent advances in omics technologies have created enormous opportunities for rapidly improving multiple characteristics. This review highlights current research on features pertinent to low-input agriculture and provides an overview of alternative genomics-based breeding strategies for enhancing genetic gain in rice suitable for low-input farming practices.

The role of priming and memory in rice environmental stress adaptation: Current knowledge and perspectives

Plant responses to abiotic stresses are dynamic, following the unpredictable changes of physical environmental parameters such as temperature, water and nutrients. Physiological and phenotypical responses to stress are intercalated by periods of recovery. An earlier stress can be remembered as 'stress memory' to mount a response within a generation or transgenerationally. The 'stress priming' phenomenon allows plants to respond quickly and more robustly to stressors to increase survival, and therefore has significant implications for agriculture. Although evidence for stress memory in various plant species is accumulating, understanding of the mechanisms implicated, especially for crops of agricultural interest, is in its infancy. Rice is a major food crop which is susceptible to abiotic stresses causing constraints on its cultivation and yield globally. Advancing the understanding of the stress response network will thus have a significant impact on rice sustainable production and global food security in the face of climate change. Therefore, this review highlights the effects of priming on rice abiotic stress tolerance and focuses on specific aspects of stress memory, its perpetuation and its regulation at epigenetic, transcriptional, metabolic as well as physiological levels. The open questions and future directions in this exciting research field are also laid out.

A pattern for the early, middle, and late phase of tea chrysanthemum response to Fusarium oxysporum

Chrysanthemum morifolium is cultivated worldwide and has high ornamental, tea, and medicinal value. With the increasing area of chrysanthemum cultivation and years of continuous cropping, Fusarium wilt disease frequently occurs in various production areas, seriously affecting the quality and yield and causing huge economic losses. However, the molecular response mechanism of Fusarium wilt infection remains unclear, which limits the molecular breeding process for disease resistance in chrysanthemums. In the present study, we analyzed the molecular response mechanisms of 'Huangju,' one of the tea chrysanthemum cultivars severely infested with Fusarium wilt in the field at the early, middle, and late phases of F. oxysporum infestation. 'Huangju' responded to the infestation mainly through galactose metabolism, plant-pathogen interaction, auxin, abscisic acid, and ethylene signalling in the early phase; galactose metabolism, plant-pathogen interaction, auxin, salicylic acid signal, and certain transcription factors (e.g., CmWRKY48) in the middle phase; and galactose metabolism in the late phase. Notably, the galactose metabolism was important in the early, middle, and late phases of 'Huangju' response to F. oxysporum. Meanwhile, the phytohormone auxin was involved in the early and middle responses. Furthermore, silencing of CmWRKY48 in 'Huangju' resulted in resistance to F. oxysporum. Our results revealed a new molecular pattern for chrysanthemum in response to Fusarium wilt in the early, middle, and late phases, providing a foundation for the molecular breeding of chrysanthemum for disease resistance.

The Calcium-Dependent Protein Kinase TaCDPK7 Positively Regulates Wheat Resistance to Puccinia striiformis f. sp. tritici

Ca2+ plays a crucial role as a secondary messenger in plant development and response to abiotic/biotic stressors. Calcium-dependent protein kinases (CDPKs/CPKs) are essential Ca2+ sensors that can convert Ca2+ signals into downstream phosphorylation signals. However, there is limited research on the function of CDPKs in the context of wheat-Puccinia striiformis f. sp. tritici (Pst) interaction. In this study, we aimed to address this gap by identifying putative CDPK genes from the wheat reference genome and organizing them into four phylogenetic clusters (I-IV). To investigate the expression patterns of the TaCDPK family during the wheat-Pst interaction, we analyzed time series RNA-seq data and further validated the results through qRT-PCR assays. Among the TaCDPK genes, TaCDPK7 exhibited a significant induction during the wheat-Pst interaction, suggesting that it has a potential role in wheat resistance to Pst. To gain further insights into the function of TaCDPK7, we employed virus-induced gene silencing (VIGS) to knock down its expression which resulted in impaired wheat resistance to Pst, accompanied by decreased accumulation of hydrogen peroxide (H2O2), increased fungal biomass ratio, reduced expression of defense-related genes, and enhanced pathogen hyphal growth. These findings collectively suggest that TaCDPK7 plays an important role in wheat resistance to Pst. In summary, this study expands our understanding of wheat CDPKs and provides novel insights into their involvement in the wheat-Pst interaction.

The calcium connection: exploring the intricacies of calcium signaling in plant-microbe interactions

The process of plant immune response is orchestrated by intracellular signaling molecules. Since plants are devoid of a humoral system, they develop extensive mechanism of pathogen recognition, signal perception, and intricate cell signaling for their protection from biotic and abiotic stresses. The pathogenic attack induces calcium ion accumulation in the plant cells, resulting in calcium signatures that regulate the synthesis of proteins of defense system. These calcium signatures induct different calcium dependent proteins such as calmodulins (CaMs), calcineurin B-like proteins (CBLs), calcium-dependent protein kinases (CDPKs) and other signaling molecules to orchestrate the complex defense signaling. Using advanced biotechnological tools, the role of Ca2+ signaling during plant-microbe interactions and the role of CaM/CMLs and CDPKs in plant defense mechanism has been revealed to some extent. The Emerging perspectives on calcium signaling in plant-microbe interactions suggest that this complex interplay could be harnessed to improve plant resistance against pathogenic microbes. We present here an overview of current understanding in calcium signatures during plant-microbe interaction so as to imbibe a future direction of research.

Multiomics analysis reveals the molecular mechanisms underlying virulence in Rhizoctonia and jasmonic acid-mediated resistance in Tartary buckwheat (Fagopyrum tataricum)

Rhizoctonia solani is a devastating soil-borne pathogen that seriously threatens the cultivation of economically important crops. Multiple strains with a very broad host range have been identified, but only 1 (AG1-IA, which causes rice sheath blight disease) has been examined in detail. Here, we analyzed AG4-HGI 3 originally isolated from Tartary buckwheat (Fagopyrum tataricum), but with a host range comparable to AG1-IA. Genome comparison reveals abundant pathogenicity genes in this strain. We used multiomic approaches to improve the efficiency of screening for disease resistance genes. Transcriptomes of the plant-fungi interaction identified differentially expressed genes associated with virulence in Rhizoctonia and resistance in Tartary buckwheat. Integration with jasmonate-mediated transcriptome and metabolome changes revealed a negative regulator of jasmonate signaling, cytochrome P450 (FtCYP94C1), as increasing disease resistance probably via accumulation of resistance-related flavonoids. The integration of resistance data for 320 Tartary buckwheat accessions identified a gene homolog to aspartic proteinase (FtASP), with peak expression following R. solani inoculation. FtASP exhibits no proteinase activity but functions as an antibacterial peptide that slows fungal growth. This work reveals a potential mechanism behind pathogen virulence and host resistance, which should accelerate the molecular breeding of resistant varieties in economically essential crops.

Constitutive expression of nucleotide-binding and leucine-rich repeat gene AtRPS2 enhanced drought and salt tolerance in rice

Drought and salt are major abiotic stresses that severely restricts plant growth and development, leading to serious losses in agricultural production. Therefore, improving crop tolerance to drought and salt stresses is an urgent issue. A previous study showed that overexpression of Arabidopsis NLR gene AtRPS2 conferred broad-spectrum disease resistance in rice. In this study, we demonstrated that constitutive expression of AtRPS2 increased abscisic acid (ABA) sensitivity during seedling stage, the shoot length of transgenic plants were shorter than wild type plants. Exogenous application of ABA markedly induced the expression of stress-related genes and promoted stomatal close in transgenic plants. Overexpression of AtRPS2 also enhanced drought and salt tolerance in rice, transgenic plants exhibited higher survival rates under drought and salt conditions than wild type plants. The activities of catalase (CAT) and superoxide dismutase (SOD) were higher in AtRPS2 transgenic rice than wild type plants. In addition, the expression of stress-related genes and ABA-responsive genes were significantly upregulated in AtRPS2 transgenic plants than wild type plants under drought and salt treatments. Besides, exogenous application of ABA could facilitate drought and salt tolerance in AtRPS2 transgenic plants. Taken together, this study indicated that AtRPS2 could improve drought and salt tolerance in rice, and this phenomenon is likely to be regulated through ABA signaling pathways.

Calcium-dependent protein kinase GhCDPK4 plays a role in drought and abscisic acid stress responses

Drought is an important factor limiting the yield and quality of cotton. In the present study, the gene encoding the cotton calcium-dependent protein kinase GhCDPK4 was identified and characterized in the transcriptome of cotton under PEG-induced drought stress. In RT-qPCR experiments, GhCDPK4 expression was found to be up-regulated under drought and abscisic acid (ABA) stress. Under drought conditions, heterologous overexpression of GhCDPK4 in tobacco showed a better phenotypic status, higher antioxidant enzyme activity, and lower relative electrolyte leakage (REL) and malondialdehyde (MDA) content. Meanwhile, ghcdpk4-silenced cotton plants, which were extremely sensitive to drought, exhibited higher levels of O^2-，H₂O₂, and MDA contents compared to the control. Meanwhile, silenced lines showed impaired stomatal closure under drought stress, resulting in increased water loss from transpiration in silenced lines. GhCDPK4 expression was induced by ABA, and there are five ABA-responsive elements in its promoter. and C2-DOMAIN ABA-RELATED 4(CAR4, Gh_D09G1653) were found to interact and be co-expressed in the GhCDPK4 interaction network. Therefore, GhCDPK4 may reduce the extent of water loss and oxidative damage in cotton under drought by positively regulating ABA-controlled stomatal closure and reactive oxygen species (ROS) scavenging systems. This study demonstrates the great potential of GhCDPK4 in improving drought resistance in crops.

Immune Mechanism of Ethylicin-Induced Resistance to Xanthomonas oryzae pv. oryzae in Rice

Ethylicin (ET) was reported to be promising in the control of rice bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo). The detailed mechanism for this process remains unknown. Disclosed here is an in-depth study on the action mode of ET to Xoo. Through plant physiological and biochemical analysis, it was found that ET could inhibit the proliferation of Xoo by increasing the content of defense enzymes and chlorophyll in rice (Oryza sativa ssp. Japonica cv. Nipponbare). Label-free quantitative proteomic analysis showed that ET affected the rice abscisic acid (ABA) signal pathway and made the critical differential calcium-dependent protein kinase 24 (OsCPK24) more active. In addition, the biological function of OsCPK24 as a mediator for rice resistance to Xoo was determined through the anti-Xoo phenotypic test of OsCPK24 transgenic rice and the affinity analysis of the OsCPK24 recombinant protein in vitro and ET. This study revealed the molecular mechanism of ET-induced resistance to Xoo in rice via OsCPK24, which provided a basis for the development of new bactericides based on the OsCPK24 protein.

Fine-tuning OsCPK18/OsCPK4 activity via genome editing of phosphorylation motif improves rice yield and immunity

Plants have evolved complex signalling networks to regulate growth and defence responses under an ever-changing environment. However, the molecular mechanisms underlying the growth-defence tradeoff are largely unclear. We previously reported that rice CALCIUM-DEPENDENT PROTEIN KINASE 18 (OsCPK18) and MITOGEN-ACTIVATED PROTEIN KINASE 5 (OsMPK5) mutually phosphorylate each other and that OsCPK18 phosphorylates and positively regulates OsMPK5 to suppress rice immunity. In this study, we found that OsCPK18 and its paralog OsCPK4 positively regulate plant height and yield-related traits. Further analysis reveals that OsCPK18 and OsMPK5 synergistically regulate defence-related genes but differentially regulate development-related genes. In vitro and in vivo kinase assays demonstrated that OsMPK5 phosphorylates C-terminal threonine (T505) and serine (S512) residues of OsCPK18 and OsCPK4, respectively. The kinase activity of OsCPK18^T505D , in which T505 was replaced by aspartic acid to mimic T505 phosphorylation, displayed less calcium sensitivity than that of wild-type OsCPK18. Interestingly, editing the MAPK phosphorylation motif in OsCPK18 and its paralog OsCPK4, which deprives OsMPK5-mediated phosphorylation but retains calcium-dependent activation of kinase activity, simultaneously increases rice yields and immunity. This editing event also changed the last seven amino acid residues of OsCPK18 and attenuated its binding with OsMPK5. This study presents a new regulatory circuit that fine tunes the growth-defence tradeoff by modulating OsCPK18/4 activity and suggests that CRISPR/Cas9-mediated engineering phosphorylation pathways could simultaneously improve crop yield and immunity.

Exogenous 5-aminolevulinic acid alleviates low-temperature damage by modulating the xanthophyll cycle and nutrient uptake in tomato seedlings

5-Aminolevulinic acid (ALA), an antioxidant existing in plants, has been widely reported to participate in the process of coping with cold stress of plants. In this study, exogenous ALA promoted the growth of tomato plants and alleviated the appearance of purple tomato leaves under low-temperature stress. At the same time, exogenous ALA improved antioxidant enzyme activities, SlSOD gene expression, Fv/Fm, and proline contents and reduced H₂O₂ contents, SlRBOH gene expression, relative electrical conductivity, and malondialdehyde contents to alleviate the damage caused by low temperature to tomato seedlings. Compared with low-temperature stress, spraying exogenous ALA before low-temperature stress could restore the indicators of photochemical quenching, actual photochemical efficiency, electron transport rate, and nonphotochemical quenching to normal. Exogenous ALA could increase the total contents of the xanthophyll cycle pool, the positive de-epoxidation rate of the xanthophyll cycle and improved the expression levels of key genes in the xanthophyll cycle under low-temperature stress. In addition, we found that exogenous ALA significantly enhanced the absorption of mineral nutrients, promoted the transfer and distribution of mineral nutrients to the leaves, and improved the expression levels of mineral nutrient absorption-related genes, which were all conducive to the improved adaptation of tomato seedlings under low-temperature stress. In summary, the application of exogenous ALA can increase tomato seedlings' tolerance to low-temperature stress by improving the xanthophyll cycle and the ability of the absorption of mineral nutrients in tomato seedlings.

Rice CIRCADIAN CLOCK ASSOCIATED 1 transcriptionally regulates ABA signaling to confer multiple abiotic stress tolerance

The circadian clock facilitates the survival and reproduction of crop plants under harsh environmental conditions such as drought and osmotic and salinity stresses, mainly by reprogramming the endogenous transcriptional landscape. Nevertheless, the genome-wide roles of core clock components in rice (Oryza sativa L.) abiotic stress tolerance are largely uncharacterized. Here, we report that CIRCADIAN CLOCK ASSOCIATED1 (OsCCA1), a vital clock component in rice, is required for tolerance to salinity, osmotic, and drought stresses. DNA affinity purification sequencing coupled with transcriptome analysis identified 692 direct transcriptional target genes of OsCCA1. Among them, the genes involved in abscisic acid (ABA) signaling, including group A protein phosphatase 2C genes and basic region and leucine zipper 46 (OsbZIP46), were substantially enriched. Moreover, OsCCA1 could directly bind the promoters of OsPP108 and OsbZIP46 to activate their expression. Consistently, oscca1 null mutants generated via genome editing displayed enhanced sensitivities to ABA signaling. Together, our findings illustrate that OsCCA1 confers multiple abiotic stress tolerance likely by orchestrating ABA signaling, which links the circadian clock with ABA signaling in rice.

Deep learning uncovers distinct behavior of rice network to pathogens response

Rice, apart from abiotic stress, is prone to attack from multiple pathogens. Predominantly, the two rice pathogens, bacterial Xanthomonas oryzae (Xoo) and hemibiotrophic fungus, Magnaporthe oryzae, are extensively well explored for more than the last decade. However, because of lack of holistic studies, we design a deep learning-based rice network model (DLNet) that has explored the quantitative differences resulting in the distinct rice network architecture. Validation studies on rice in response to biotic stresses show that DLNet outperforms other machine learning methods. The current finding indicates the compactness of the rice PTI network and the rise of independent modules in the rice ETI network, resulting in similar patterns of the plant immune response. The results also show more independent network modules and minimum structural disorderness in rice-M. oryzae as compared to the rice-Xoo model revealing the different adaptation strategies of the rice plant to evade pathogen effectors.

Activation and turnover of the plant immune signaling kinase BIK1: a fine balance

Mechanisms to sense and respond to pathogens have evolved in all species. The plant immune pathway is initiated by the activation of transmembrane receptor kinases that trigger phosphorylation relays resulting in cellular reprogramming. BOTRYTIS-INDUCED KINASE 1 (BIK1) is a direct substrate of multiple immune receptors in Arabidopsis thaliana and is a central regulator of plant immunity. Here, we review how BIK1 activity and protein stability are regulated by a dynamic interplay between phosphorylation and ubiquitination.

Transcriptome-wide analysis of North-East Indian rice cultivars in response to Bipolaris oryzae infection revealed the importance of early response to the pathogen in suppressing the disease progression

Brown spot disease (BSD) of rice (Oryza sativa L.) caused by Bipolaris oryzae is one of the major and neglected fungal diseases worldwide affecting rice production. Despite its significance, very limited knowledge on genetics and genomics of rice in response to B. oryzae available. Our study firstly identified moderately resistant (Gitesh) and susceptible (Shahsarang) North-East Indian rice cultivars in response to a native Bipolaris oryzae isolate BO1. Secondly, a systematic comparative RNA seq was performed for both cultivars at four different time points viz. 12, 24, 48, and 72 hours post infestation (hpi). Differential gene expression analysis revealed the importance of early response to the pathogen in suppressing disease progression. The pathogen negatively regulates the expression of photosynthetic-related genes at early stages in both cultivars. Of the cell wall modification enzymes, cellulose synthase and callose synthase are important for signal transduction and defense. Cell wall receptors OsLYP6, OsWAK80 might positively and OsWAK25 negatively regulate disease resistance. Jasmonic acid and/or abscisic acid signaling pathways are presumably involved in disease resistance, whereas salicylic acid pathway, and an ethylene response gene OsEBP-89 in promoting disease. Surprisingly, pathogenesis-related proteins showed no antimicrobial impact on the pathogen. Additionally, transcription factors OsWRKY62 and OsWRKY45 together might negatively regulate resistance to the pathogen. Taken together, our study has identified and provide key regulatory genes involved in response to B. oryzae which serve as potential resources for functional genetic analysis to develop genetic tolerance to BSD of rice.

Visualization of a curated Oryza sativa L. CDPKs Protein-Protein Interaction Network (CDPK-OsPPIN)

Calcium-Dependent Protein Kinases (CDPKs) translate calcium ion (Ca²⁺) signals into direct phosphorylation of proteins involved in stress response and plant growth. To get a clear picture of CDPKs functions, we must identify and explore the CDPKs targets and their respective roles in plant physiology. Here, we present a manually curated Oryza sativa L. CDPK Protein-Protein Interaction Network (CDPK-OsPPIN). The CDPK-OsPPIN provides an interactive graphical tool to assist hypothesis generation by researchers investigating CDPK roles and functional diversity.

Regulatory Mechanisms of the Resistance to Common Bacterial Blight Revealed by Transcriptomic Analysis in Common Bean (Phaseolus vulgaris L.)

Common bean blight (CBB), primarily caused by Xanthomonas axonopodis pv. phaseoli (Xap), is one of the most destructive diseases of common bean (Phaseolus vulgaris L.). The tepary bean genotype PI 319443 displays high resistance to Xap, and the common bean genotypes HR45 and Bilu display high resistance and susceptibility to Xap, respectively. To identify candidate genes related to Xap resistance, transcriptomic analysis was performed to compare gene expression levels with Xap inoculation at 0, 24, and 48 h post inoculation (hpi) among the three genotypes. A total of 1,146,009,876 high-quality clean reads were obtained. Differentially expressed gene (DEG) analysis showed that 1,688 DEGs responded to pathogen infection in the three genotypes. Weighted gene coexpression network analysis (WGCNA) was also performed to identify three modules highly correlated with Xap resistance, in which 334 DEGs were likely involved in Xap resistance. By combining differential expression analysis and WGCNA, 139 DEGs were identified as core resistance-responsive genes, including 18 genes encoding resistance (R) proteins, 19 genes belonging to transcription factor families, 63 genes encoding proteins with oxidoreductase activity, and 33 plant hormone signal transduction-related genes, which play important roles in the resistance to pathogen infection. The expression patterns of 20 DEGs were determined by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-seq results.

Quantitative proteome analysis reveals changes of membrane transport proteins in Sedum plumbizincicola under cadmium stress

Sedum plumbizincicola is an herbaceous species tolerant of excessive cadmium accumulation in above-ground tissues. The implications of membrane proteins, especially integrative membrane proteins, in Cd detoxification of plants have received attention in recent years, but a comprehensive profiling of Cd-responsive membrane proteins from Cd hyperaccumulator plants is lacking. In this study, the membrane proteins of root, stem, and leaf tissues of S. plumbizincicola seedlings treated with Cd solution for 0, 1 or 4 days were analyzed by Tandem Mass Tag (TMT) labeling-based proteome quantification (Data are available via ProteomeXchange with identifier PXD025302). Total 3353 proteins with predicted transmembrane helices were identified and quantified in at least one tissue group. 1667 proteins were defined as DAPs (differentially abundant proteins) using fold change >1.5 with p-values <0.05. The number of DAPs involved in metabolism, transport protein, and signal transduction was significantly increased after exposure to Cd, suggesting that the synthesis and decomposition of organic compounds and the transport of ions were actively involved in the Cd tolerance process. The number of up-regulated transport proteins increased significantly from 1-day exposure to 4-day exposure, from 5 to 112, 16 to 42, 18 to 44, in root, stem, and leaf, respectively. Total 352 Cd-regulated transport proteins were identified, including ABC transporters, ion transport proteins, aquaporins, proton pumps, and organic transport proteins. Heterologous expression of SpABCB28, SpMTP5, SpNRAMP5, and SpHMA2 in yeast and subcellular localization showed the Cd-specific transport activity. The results will enhance our understanding of the molecular mechanism of Cd hypertolerance and hyperaccumulation in S. plumbizincicola and will be benefit for future genetic engineering in phytoremediation.

Effects of Laccaria bicolor on Gene Expression of Populus trichocarpa Root under Poplar Canker Stress

Poplars can be harmed by poplar canker. Inoculation with mycorrhizal fungi can improve the resistance of poplars to canker, but the molecular mechanism is still unclear. In this study, an aseptic inoculation system of L. bicolor-P. trichocarpa-B. dothidea was constructed, and transcriptome analysis was performed to investigate regulation by L. bicolor of the expression of genes in the roots of P. trichocarpa during the onset of B. dothidea infection, and a total of 3022 differentially expressed genes (DEGs) were identified. Weighted correlation network analysis (WGCNA) was performed on these DEGs, and 661 genes' expressions were considered to be affected by inoculation with L. bicolor and B. dothidea. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that these 661 DEGs were involved in multiple pathways such as signal transduction, reactive oxygen metabolism, and plant-pathogen interaction. Inoculation with L. bicolor changed the gene expression pattern of the roots, evidencing its involvement in the disease resistance response of P. trichocarpa. This research reveals the mechanism of L. bicolor in inducing resistance to canker of P. trichocarpa at the molecular level and provides a theoretical basis for the practical application of mycorrhizal fungi to improve plant disease resistance.

TypiCal but DeliCate Ca++re: Dissecting the Essence of Calcium Signaling Network as a Robust Response Coordinator of Versatile Abiotic and Biotic Stimuli in Plants

Plant growth, development, and ultimately crop productivity are largely impacted by the interaction of plants with different abiotic and biotic factors throughout their life cycle. Perception of different abiotic stresses, such as salt, cold, drought, heat, and heavy metals, and interaction with beneficial and harmful biotic agents by plants lead to transient, sustained, or oscillatory changes of [calcium ion, Ca²⁺]_cyt within the cell. Significant progress has been made in the decoding of Ca²⁺ signatures into downstream responses to modulate differential developmental and physiological responses in the whole plant. Ca²⁺ sensor proteins, mainly calmodulins (CaMs), calmodulin-like proteins (CMLs), and others, such as Ca²⁺-dependent protein kinases (CDPKs), calcineurin B-like proteins (CBLs), and calmodulin-binding transcription activators (CAMTAs) have played critical roles in coupling the specific stress stimulus with an appropriate response. This review summarizes the current understanding of the Ca²⁺ influx and efflux system in plant cells and various Ca²⁺ binding protein-mediated signal transduction pathways that are delicately orchestrated to mitigate abiotic and biotic stresses. The probable interactions of different components of Ca²⁺ sensor relays and Ca²⁺ sensor responders in response to various external stimuli have been described diagrammatically focusing on established pathways and latest developments. Present comprehensive insight into key components of the Ca²⁺ signaling toolkit in plants can provide an innovative framework for biotechnological manipulations toward crop improvability in near future.

The resistance of peanut to soil-borne pathogens improved by rhizosphere probiotics under calcium treatment

Background

Peanut (Arachis hypogaea L.) is an important oil and economic crop. Calcium modulates plants in response to abiotic stresses and improves plant resistance to pathogens. Enrichment of beneficial microorganisms in the rhizosphere is associated with plant disease resistance and soil development. The purpose of this study was to analyze the differences in peanut rhizosphere microbial community structure between the calcium treatment and the control during two growth stages and to explain why calcium application could improve the resistance of peanuts to soil-borne pathogens.

Results

The 16S rDNA amplicon sequencing of rhizosphere microbiome showed that calcium application significantly enriched Serratia marcescens and other three dominant strains at the seedling stage. At the pod filling stage, ten dominant stains such as Sphingomonas changbaiensis and Novosphingobium panipatense were enriched by calcium. Serratia marcescens aseptic fermentation filtrate was mixed with PDA medium and inoculated with the main soil-borne pathogens in the seedling stage, which could inhibit the growth of Fusarium solani and Aspergillus flavus. The aseptic fermentation filtrate of Novosphingobium panipatense was mixed with PDA medium and inoculated with the main soil-borne pathogens in the pod filling stage, which could inhibit the growth of Sclerotium rolfsii and Leptosphaerulina arachidicola.

Conclusions

Calcium application increases the resistance of peanuts to soil-borne pathogens by enriching them with specific dominant bacteria.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02355-3.

Progressive Genomic Approaches to Explore Drought- and Salt-Induced Oxidative Stress Responses in Plants under Changing Climate

Drought and salinity are the major environmental abiotic stresses that negatively impact crop development and yield. To improve yields under abiotic stress conditions, drought- and salinity-tolerant crops are key to support world crop production and mitigate the demand of the growing world population. Nevertheless, plant responses to abiotic stresses are highly complex and controlled by networks of genetic and ecological factors that are the main targets of crop breeding programs. Several genomics strategies are employed to improve crop productivity under abiotic stress conditions, but traditional techniques are not sufficient to prevent stress-related losses in productivity. Within the last decade, modern genomics studies have advanced our capabilities of improving crop genetics, especially those traits relevant to abiotic stress management. This review provided updated and comprehensive knowledge concerning all possible combinations of advanced genomics tools and the gene regulatory network of reactive oxygen species homeostasis for the appropriate planning of future breeding programs, which will assist sustainable crop production under salinity and drought conditions.

Overexpression of two CDPKs from wild Chinese grapevine enhances powdery mildew resistance in Vitis vinifera and Arabidopsis

Calcium-dependent protein kinases (CDPKs) play vital roles in metabolic regulations and stimuli responses in plants. However, little is known about their function in grapevine. Here, we report that VpCDPK9 and VpCDPK13, two paralogous CDPKs from Vitis pseudoreticulata accession Baihe-35-1, appear to positively regulate powdery mildew resistance. The transcription of them in leaves of 'Baihe-35-1' were differentially induced upon powdery mildew infection. Overexpression of VpCDPK9-YFP or VpCDPK13-YFP in the V. vinifera susceptible cultivar Thompson Seedless resulted in enhanced resistance to powdery mildew (YFP, yellow fluorescent protein). This might be due to elevation of SA and ethylene production, and excess accumulation of H₂ O₂ and callose in penetrated epidermal cells and/or the mesophyll cells underneath. Ectopic expression of VpCDPK9-YFP in Arabidopsis resulted in varied degrees of reduced stature, pre-mature senescence and enhanced powdery mildew resistance. However, these phenotypes were abolished in VpCDPK9-YFP transgenic lines impaired in SA signaling (pad4sid2) or ethylene signaling (ein2). Moreover, both of VpCDPK9 and VpCDPK13 were found to interact with and potentially phosphorylate VpMAPK3, VpMAPK6, VpACS1 and VpACS2 in vivo (ACS, 1-aminocyclopropane-1-carboxylic acid (ACC) synthase; MAPK, mitogen-activated protein kinase). These results suggest that VpCDPK9 and VpCDPK13 contribute to powdery mildew resistance via positively regulating SA and ethylene signaling in grapevine.

Ca2+-Dependent Protein Kinase 6 Enhances KAT2 Shaker Channel Activity in Arabidopsis thaliana

Post-translational regulations of Shaker-like voltage-gated K⁺ channels were reported to be essential for rapid responses to environmental stresses in plants. In particular, it has been shown that calcium-dependent protein kinases (CPKs) regulate Shaker channels in plants. Here, the focus was on KAT2, a Shaker channel cloned in the model plant Arabidopsis thaliana, where is it expressed namely in the vascular tissues of leaves. After co-expression of KAT2 with AtCPK6 in Xenopuslaevis oocytes, voltage-clamp recordings demonstrated that AtCPK6 stimulates the activity of KAT2 in a calcium-dependent manner. A physical interaction between these two proteins has also been shown by Förster resonance energy transfer by fluorescence lifetime imaging (FRET-FLIM). Peptide array assays support that AtCPK6 phosphorylates KAT2 at several positions, also in a calcium-dependent manner. Finally, K⁺ fluorescence imaging in planta suggests that K⁺ distribution is impaired in kat2 knock-out mutant leaves. We propose that the AtCPK6/KAT2 couple plays a role in the homeostasis of K⁺ distribution in leaves.

Extracellular Fragmented Self-DNA Is Involved in Plant Responses to Biotic Stress

A growing body of evidence indicates that extracellular fragmented self-DNA (eDNA), by acting as a signaling molecule, triggers inhibitory effects on conspecific plants and functions as a damage-associated molecular pattern (DAMP). To evaluate early and late events in DAMP-dependent responses to eDNA, we extracted, fragmented, and applied the tomato (Solanum lycopersicum) eDNA to tomato leaves. Non-sonicated, intact self-DNA (intact DNA) was used as control. Early event analyses included the evaluation of plasma transmembrane potentials (Vm), cytosolic calcium variations (Ca²⁺ _{cy t}), the activity and subcellular localization of both voltage-gated and ligand-gated rectified K⁺ channels, and the reactive oxygen species (ROS) subcellular localization and quantification. Late events included RNA-Seq transcriptomic analysis and qPCR validation of gene expression of tomato leaves exposed to tomato eDNA. Application of eDNA induced a concentration-dependent Vm depolarization which was correlated to an increase in (Ca²⁺)_cyt; this event was associated to the opening of K⁺ channels, with particular action on ligand-gated rectified K⁺ channels. Both eDNA-dependent (Ca²⁺)_cyt and K⁺ increases were correlated to ROS production. In contrast, application of intact DNA produced no effects. The plant response to eDNA was the modulation of the expression of genes involved in plant-biotic interactions including pathogenesis-related proteins (PRPs), calcium-dependent protein kinases (CPK1), heat shock transcription factors (Hsf), heat shock proteins (Hsp), receptor-like kinases (RLKs), and ethylene-responsive factors (ERFs). Several genes involved in calcium signaling, ROS scavenging and ion homeostasis were also modulated by application of eDNA. Shared elements among the transcriptional response to eDNA and to biotic stress indicate that eDNA might be a common DAMP that triggers plant responses to pathogens and herbivores, particularly to those that intensive plant cell disruption or cell death. Our results suggest the intriguing hypothesis that some of the plant reactions to pathogens and herbivores might be due to DNA degradation, especially when associated to the plant cell disruption. Fragmented DNA would then become an important and powerful elicitor able to trigger early and late responses to biotic stress.

NDW, encoding a receptor-like protein kinase, regulates plant growth, cold tolerance and susceptibility to Botrytis cinerea in tomato

Plants utilize different mechanisms to respond and adapt to continuously changing environmental factors. Receptor-like protein kinases (RLKs) comprise one of the largest families of plant transmembrane signaling proteins, which play critical and diverse roles in plant growth, development, and stress response. Here, we identified the necrotic dwarf (ndw) mutant introgression line (IL) 6-2, which demonstrated stunting, leaf curl, and progressive necrosis at low temperatures. Based on map-based cloning and transgenic analysis, we determined that the phenotype of ndw mutant is caused by decreased expression of NDW, which encodes an RLK. NDW is a plasma membrane and cytoplasmic located protein. Overexpression of NDW can restore both of the semi-dwarf and necrotic phenotype in IL6-2 at low temperatures, further we found that NDW could significantly reduce susceptibility to Botrytis cinerea. On the contrary, knockdown NDW in M82 plants could increase the sensitivity to B. cinerea. Furthermore, transcriptional expression analysis showed that NDW affects the expression of genes related to the abscisic acid (ABA) signaling pathway. Taken together, these results indicate that NDW plays an important role in regulating plant growth, cold tolerance and mitigating susceptibility to Botrytis cinerea.

Overexpression of MdCPK1a gene, a calcium dependent protein kinase in apple, increase tobacco cold tolerance via scavenging ROS accumulation

Calcium-dependent protein kinases (CDPKs) are important calcium receptors, which play a crucial part in the process of sensing and decoding intracellular calcium signals during plant development and adaptation to various environmental stresses. In this study, a CDPK gene MdCPK1a, was isolated from apple (Malus×domestica) which contains 1701bp nucleotide and encodes a protein of 566 amino acid residues, and contains the conserved domain of CDPKs. The transient expression and western blot experiment showed that MdCPK1a protein was localized in the nucleus and cell plasma membrane. Ectopic expression of MdCPK1a in Nicotiana benthamiana increased the resistance of the tobacco plants to salt and cold stresses. The mechanism of MdCPK1a regulating cold resistance was further investigated. The overexpressed MdCPK1a tobacco plants had higher survival rates and longer root length than wild type (WT) plants under cold stress, and the electrolyte leakages (EL), the content of malondialdehyde (MDA) and reactive oxygen species (ROS) were lower, and accordingly, antioxidant enzyme activities, such as superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) were higher, suggesting the transgenic plants suffered less chilling injury than WT plants. Moreover, the transcript levels of ROS-scavenging and stress-related genes were higher in the transgenic plants than those in WT plants whether under normal conditions or cold stress. The above results suggest that the improvement of cold tolerance in MdCPK1a-overexpressed plants was due to scavenging ROS accumulation and modulating the expression of stress-related genes.

Long Non-coding RNAs Responsive to Blast Fungus Infection in Rice

BACKGROUND

Long non-coding RNAs (LncRNAs) have emerged as important regulators in many physiological processes in plant. By high-throughput RNA-sequencing, many pathogen-associated LncRNAs were mapped in various plants, and some of them were proved to be involved in plant defense responses. The rice blast disease caused by Magnaporthe oryzae (M. oryzae) is one of the most destructive diseases in rice. However, M. oryzae-induced LncRNAs in rice is yet to be studied.

FINDINGS

We investigated rice LncRNAs that were associated with the rice blast fungus. Totally 83 LncRNAs were up-regulated after blast fungus infection and 78 were down-regulated. Of them, the natural antisense transcripts (NATs) were the most abundant. The expression of some LncRNAs has similar pattern with their host genes or neighboring genes, suggesting a cis function of them in regulating gene transcription level. The deferentially expressed (DE) LncRNAs and genes co-expression analysis revealed some LncRNAs were associated with genes known to be involved in pathogen resistance, and these genes were enriched in terpenoid biosynthesis and defense response by Gene Ontology (GO) enrichment analysis. Interestingly, one of up-regulated DE-intronic RNA was derived from a jasmonate (JA) biosynthetic gene, lipoxygenase RLL (LOX-RLL). Levels of JAs were significantly increased after blast fungus infection. Given that JA is known to regulate blast resistance in rice, we suggested that LncRNA may be involved in JA-mediated rice resistance to blast fungus.

CONCLUSIONS

This study identified blast fungus-responsive LncRNAs in rice, which provides another layer of candidates that regulate rice and blast fungus interactions.

Fungal effectors, the double edge sword of phytopathogens

Phyto-pathogenic fungi can cause huge damage to crop production. During millions of years of coexistence, fungi have evolved diverse life-style to obtain nutrients from the host and to colonize upon them. They deploy various proteinaceous as well as non-proteinaceous secreted molecules commonly referred as effectors to sabotage host machinery during the infection process. The effectors are important virulence determinants of pathogenic fungi and play important role in successful pathogenesis, predominantly by avoiding host-surveillance system. However, besides being important for pathogenesis, the fungal effectors end-up being recognized by the resistant cultivars of the host, which mount a strong immune response to ward-off pathogens. Various recent studies involving different pathosystem have revealed the virulence/avirulence functions of fungal effectors and their involvement in governing the outcome of host-pathogen interactions. However, the effectors and their cognate resistance gene in the host remain elusive for several economically important fungal pathogens. In this review, using examples from some of the biotrophic, hemi-biotrophic and necrotrophic pathogens, we elaborate the double-edged functions of fungal effectors. We emphasize that knowledge of effector functions can be helpful in effective management of fungal diseases in crop plants.

Exogenous Calcium Improved Resistance to Botryosphaeria dothidea by Increasing Autophagy Activity and Salicylic Acid Level in Pear

Pear ring rot, caused by Botryosphaeria dothidea, is one of the most serious diseases in pear. Calcium (Ca²⁺) was reported to play a key role in the plant defense response. Here, we found that exogenous calcium could enhance resistance to B. dothidea in pear leaves. Less H₂O₂ and O₂^- but more activated reactive oxygen species scavenge enzymes accumulated in calcium-treated leaves than in H₂O-treated leaves. Moreover, the increased level of more ascorbic acid-glutathione was maintained by Ca²⁺ treatment under pathogen infection. The expression of core autophagy-related genes and autophagosome formations were enhanced in Ca²⁺-treated leaves. Silencing of PbrATG5 in Pyrus betulaefolia conferred sensitivity to inoculation, which was only slightly recovered by Ca²⁺ treatment. Moreover, the salicylic acid (SA) level and SA-related gene expression were induced more strongly by B. dothidea in Ca²⁺-treated leaves than in H₂O-treated leaves. Taken together, these results demonstrated that exogenous Ca²⁺ enhanced resistance to B. dothidea by increasing autophagic activity and SA accumulation. Our findings reveal a new mechanism of Ca²⁺ in increasing the tolerance of pear to B. dothidea infection.

The Rice DNA-Binding Protein ZBED Controls Stress Regulators and Maintains Disease Resistance After a Mild Drought

BACKGROUND

Identifying new sources of disease resistance and the corresponding underlying resistance mechanisms remains very challenging, particularly in Monocots. Moreover, the modification of most disease resistance pathways made so far is detrimental to tolerance to abiotic stresses such as drought. This is largely due to negative cross-talks between disease resistance and abiotic stress tolerance signaling pathways. We have previously described the role of the rice ZBED protein containing three Zn-finger BED domains in disease resistance against the fungal pathogen Magnaporthe oryzae. The molecular and biological functions of such BED domains in plant proteins remain elusive.

RESULTS

Using Nicotiana benthamiana as a heterologous system, we show that ZBED localizes in the nucleus, binds DNA, and triggers basal immunity. These activities require conserved cysteine residues of the Zn-finger BED domains that are involved in DNA binding. Interestingly, ZBED overexpressor rice lines show increased drought tolerance. More importantly, the disease resistance response conferred by ZBED is not compromised by drought-induced stress.

CONCLUSIONS

Together our data indicate that ZBED might represent a new type of transcriptional regulator playing simultaneously a positive role in both disease resistance and drought tolerance. We demonstrate that it is possible to provide disease resistance and drought resistance simultaneously.

Genome-wide identification, and characterization of the CDPK gene family reveal their involvement in abiotic stress response in Fragaria x ananassa

Calcium-dependent protein kinases (CDPKs) are encoded by a large gene family and play important roles against biotic and abiotic stresses and in plant growth and development. To date, little is known about the CDPK genes in strawberry (Fragaria x ananassa). In this study, analysis of Fragaria x ananassa CDPK gene family was performed, including gene structures, phylogeny, interactome and expression profiles. Nine new CDPK genes in Fragaria x ananassa were identified based on RNA-seq data. These identified strawberry FaCDPK genes were classified into four main groups, based on the phylogenetic analysis and structural features. FaCDPK genes were differentially expressed during fruit development and ripening, as well as in response to abiotic stress (salt and drought), and hormone (abscisic acid) treatment. In addition, the interaction network analysis pointed out proteins involved in the ABA-dependent response to plant stress via Ca2+ signaling, especially RBOHs. To our knowledge, this is the first report on CDPK families in Fragaria x ananassa, and it will provide valuable information for development of biofortified fruits and stress tolerant plants.

Genome-wide lncRNAs identification and association analysis for cold-responsive genes at the booting stage in rice (Oryza sativa L.)

Long non-coding RNAs (lncRNAs) are essential regulators of a broad range of biological processes in plants. The spectacular progress made in next-generation sequencing technologies has enabled a genome-wide identification of lncRNAs in multiple plant species. In this study, a genome-wide lncRNA sequencing technology was used to identify cold-responsive lncRNAs at the booting stage in rice by comparing a tolerant variety, Kongyu131 (KY131) and a sensitive variety, Dongnong422 (DN422). A total of 1485 lncRNAs were identified, and 566 of these lncRNAs were defined as differential lncRNAs by comparing four samples. GO and KEGG enrichment analyses were performed, focusing on the cis- and trans- target genes of the differential lncRNAs. To identify cold-responsive genes, a meta-analysis was used to integrate 35 cold-tolerant QTLs at the booting stage. In summary, 12 candidate genes and their target lncRNAs were identified by qRT-PCR. LncTar was used to identify the interaction between lncRNAs and the candidate genes. In addition, 130 rice cultivars with rich genetic diversity were collected to verify the association of candidate genes with cold-resistance. The results revealed that five SNPs in LOC_Os07g42940, three SNP and one InDel in LOC_Os02g03410 were associated with cold-resistance at a significant level using association analysis. This study provides new gene resources and insights into cold-resistance research for rice.

Role of salicylic acid glucosyltransferase in balancing growth and defence for optimum plant fitness

Salicylic acid (SA), an essential secondary messenger for plant defence responses, plays a role in maintaining a balance (trade-off) between plant growth and resistance induction, but the detailed mechanism has not been explored. Because the SA mimic benzothiadiazole (BTH) is a more stable inducer of plant defence than SA after exogenous application, we analysed expression profiles of defence genes after BTH treatment to better understand SA-mediated immune induction. Transcript levels of the salicylic acid glucosyltransferase (SAGT) gene were significantly lower in BTH-treated Nicotiana tabacum (Nt) plants than in SA-treated Nt control plants, suggesting that SAGT may play an important role in SA-related host defence responses. Treatment with BTH followed by SA suppressed SAGT transcription, indicating that the inhibitory effect of BTH is not reversible. In addition, in BTH-treated Nt and Nicotiana benthamiana (Nb) plants, an early high accumulation of SA and SA 2-O-β-d-glucoside was only transient compared to the control. This observation agreed well with the finding that SAGT-overexpressing (OE) Nb lines contained less SA and jasmonic acid (JA) than in the Nb plants. When inoculated with a virus, the OE Nb plants showed more severe symptoms and accumulated higher levels of virus, while resistance increased in SAGT-silenced (IR) Nb plants. In addition, the IR plants restricted bacterial spread to the inoculated leaves. After the BTH treatment, OE Nb plants were slightly larger than the Nb plants. These results together indicate that SAGT has a pivotal role in the balance between plant growth and SA/JA-mediated defence for optimum plant fitness.

Genotyping for Blast (Pyricularia oryzae) Resistance Genes in F2 Population of Supa Aromatic Rice (Oryza sativa L.)

The ascomycete fungus, Pyricularia oryzae or Magnaporthe oryzae, is known to cause blast disease in more than 80 host plants of the Gramineae family—cereals including rice and grasses. The improvement of the Supa234 rice line (IR97012-27-3-1-1-B, containing badh2 gene for aroma) developed at IRRI-ESA Burundi consisted of introgression of R genes (Pita and Pi9) for blast resistance. The F₂ population obtained via the cross had been screened for blast resistance using inoculation with Pyricularia oryzae spore's suspension. The objectives of this study were to assess the presence of Pita and Pi9 genes for blast resistance and to assess the presence of the badh2 gene for aroma in the screened F₂ plants using molecular markers. Genotyping was carried out in 103 F₂ plants which grew to maturity using the KASP genotyping method with SNP markers (snpOS0007, snpOS0006, and snpOS0022) targeting the Pita and Pi9 genes for blast resistance and the badh2 gene for aromatic fragrance. The genotyping results showed that 38 F₂ plants had the Pita gene present in both alleles, 31 F₂ plants with the Pita gene in one allele, and only one plant (3B1) was found with the Pi9 gene in one allele. The badh2 gene for aroma was detected in 27 F₂ plants on both alleles and in 57 F₂ plants on one allele. There were thirteen plants which had both the Pita gene and the badh2 gene for aroma, and only one plant (3B1) had a combination of the three genes (Pita, Pi9, and badh2). Seven plants resistant to blast disease (2H2, 2H4, 1G2, 1C12, 1E13, 1B12, and 1C5) with the Pita and badh2 genes were found, and only one resistant plant (3B1) had a combination of the three genes Pi9, Pita, and badh2 which is recommended to be bulked for the development of the Supa aromatic rice variety resistant to blast disease. The plants generated by the best line 3B1 should further be evaluated for grain quality (Supa type) after F₅ generation in the field.

Identification of CBL and CIPK gene families and functional characterization of CaCIPK1 under Phytophthora capsici in pepper (Capsicum annuum L.)

Background

Calcineurin B-like proteins (CBLs) are major Ca²⁺ sensors that interact with CBL-interacting protein kinases (CIPKs) to regulate growth and development in plants. The CBL-CIPK network is involved in stress response, yet little is understood on how CBL-CIPK function in pepper (Capsicum annuum L.), a staple vegetable crop that is threatened by biotic and abiotic stressors.

Results

In the present study, nine CaCBL and 26 CaCIPK genes were identified in pepper and the genes were named based on their chromosomal order. Phylogenetic and structural analysis revealed that CaCBL and CaCIPK genes clustered in four and five groups, respectively. Quantitative real-time PCR (qRT-PCR) assays showed that CaCBL and CaCIPK genes were constitutively expressed in different tissues, and their expression patterns were altered when the plant was exposed to Phytophthora capsici, salt and osmotic stress. CaCIPK1 expression changed in response to stress, including exposure to P. capsici, NaCl, mannitol, salicylic acid (SA), methyl jasmonate (MeJA), abscisic acid (ABA), ethylene (ETH), cold and heat stress. Knocking down CaCIPK1 expression increased the susceptibility of pepper to P. capsici, reduced root activity, and altered the expression of defense related genes. Transient overexpression of CaCIPK1 enhanced H₂O₂ accumulation, cell death, and expression of genes involved in defense.

Conclusions

Nine CaCBL and 26 CaCIPK genes were identified in the pepper genome, and the expression of most CaCBL and CaCIPK genes were altered when the plant was exposed to stress. In particular, we found that CaCIPK1 is mediates the pepper plant’s defense against P. capsici. These results provide the groundwork for further functional characterization of CaCBL and CaCIPK genes in pepper.

Regulation of Plant Immune Signaling by Calcium-Dependent Protein Kinases

Activation of Ca²⁺ signaling is a universal response to stress that allows cells to quickly respond to environmental cues. Fluctuations in cytosolic Ca²⁺ are decoded in plants by Ca²⁺-sensing proteins such as Ca²⁺-dependent protein kinases (CDPKs). The perception of microbes results in an influx of Ca²⁺ that activates numerous CDPKs responsible for propagating immune signals required for resistance against disease-causing pathogens. This review describes our current understanding of CDPK activation and regulation, and provides a comprehensive overview of CDPK-mediated immune signaling through interaction with various substrates.

Overexpression of Arabidopsis Nucleotide-Binding and Leucine-Rich Repeat Genes RPS2 and RPM1(D505V) Confers Broad-Spectrum Disease Resistance in Rice

The nucleotide-binding domain leucine-rich repeat (NLR) immune receptors play important roles in innate plant immunity. The activation of NLRs is specifically induced by their cognate effectors released from pathogens. Autoactive NLRs are expected to confer broad-spectrum resistance because they do not need cognate effectors to activate their immune responses. In this study, we demonstrated that the NLR genes RPS2 and RPM1(D505V) from Arabidopsis were autoactive in Oryza sativa and conferred broad-spectrum resistance to fungal pathogen Magnaporthe oryzae, bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo), and pest brown planthopper (BPH, Nilaparvata lugens Stål). These results revealed that interfamily transfer of dicot NLRs to monocot species could be functional. The transgenic plants displayed early and strong induction of reactive oxygen species (ROS), callose deposition, and expression of defense-related genes after challenged with M. oryzae. The transcriptome analysis showed that the expressions of some defense-related genes were primed to adapt the transformed autoactive NLRs in the transgenic plants. This study indicates that autoactive NLRs are a promising resource for breeding crops with broad-spectrum resistance and provides new insights for engineering disease resistance.

Nitrogen Metabolism is Affected in the Nitrogen-Deficient Rice Mutant esl4 with a Calcium-Dependent Protein Kinase Gene Mutation

Calcium-dependent protein kinases are involved in various biological processes, including hormone response, growth and development, abiotic stress response, disease resistance, and nitrogen metabolism. We identified a novel mutant of a calcium-dependent protein-kinase-encoding gene, esl4, by performing map cloning. The esl4 mutant was nitrogen deficient, and expression and enzyme activities of genes related to nitrogen metabolism were down-regulated. ESL4 was mainly expressed in the vascular bundles of roots, stems, leaves, and sheaths. The ESL4 protein was localized in the cell membranes. Enzyme activity and physiological index analyzes and analysis of the expression of nitrogen metabolism and senescence-related genes indicated that ESL4 was involved in nitrogen metabolism. ESL4 overexpression in transgenic homozygous T2 plants increased nitrogen-use efficiency, improving yields when little nitrogen was available. The seed-set rates, yields per plant, numbers of grains per plant, grain nitrogen content ratios, and total nitrogen content per plant were significantly or very significantly higher for two ESL4 overexpression lines than for the control plants. These results suggest that ESL4 may function upstream of nitrogen-metabolism genes. The results will allow ESL4 to be used to breed novel cultivars for growing in low-nitrogen conditions.

Prospects of Understanding the Molecular Biology of Disease Resistance in Rice

Rice is one of the important crops grown worldwide and is considered as an important crop for global food security. Rice is being affected by various fungal, bacterial and viral diseases resulting in huge yield losses every year. Deployment of resistance genes in various crops is one of the important methods of disease management. However, identification, cloning and characterization of disease resistance genes is a very tedious effort. To increase the life span of resistant cultivars, it is important to understand the molecular basis of plant host-pathogen interaction. With the advancement in rice genetics and genomics, several rice varieties resistant to fungal, bacterial and viral pathogens have been developed. However, resistance response of these varieties break down very frequently because of the emergence of more virulent races of the pathogen in nature. To increase the durability of resistance genes under field conditions, understanding the mechanismof resistance response and its molecular basis should be well understood. Some emerging concepts like interspecies transfer of pattern recognition receptors (PRRs) and transgenerational plant immunitycan be employed to develop sustainable broad spectrum resistant varieties of rice.

Calcium Signalling in Plant Biotic Interactions

Calcium (Ca2+) is a universal second messenger involved in various cellular processes, leading to plant development and to biotic and abiotic stress responses. Intracellular variation in free Ca2+ concentration is among the earliest events following the plant perception of environmental change. These Ca2+ variations differ in their spatio-temporal properties according to the nature, strength and duration of the stimulus. However, their conversion into biological responses requires Ca2+ sensors for decoding and relaying. The occurrence in plants of calmodulin (CaM) but also of other sets of plant-specific Ca2+ sensors such as calmodulin-like proteins (CMLs), Ca2+-dependent protein kinases (CDPKs) and calcineurin B-like proteins (CBLs) indicate that plants possess specific tools and machineries to convert Ca2+ signals into appropriate responses. Here, we focus on recent progress made in monitoring the generation of Ca2+ signals at the whole plant or cell level and their long distance propagation during biotic interactions. The contribution of CaM/CMLs and CDPKs in plant immune responses mounted against bacteria, fungi, viruses and insects are also presented.

Overexpression of a constitutively active truncated form of OsCDPK1 confers disease resistance by affecting OsPR10a expression in rice

The rice pathogenesis-related protein OsPR10a was scarcely expressed in OsCDPK1-silenced (Ri-1) rice, which was highly sensitive to pathogen infection. After inoculating the leaves with bacterial blight (Xanthomonas oryzae pv. oryzae; Xoo), we found that the expression of OsPR10a was up- and down-regulated in OEtr-1 (overexpression of the constitutively active truncated form of OsCDPK1) and Ri-1 rice plants, respectively. OsPR10a and OsCDPK1 showed corresponding expression patterns and were up-regulated in response to the jasmonic acid, salicylic acid and Xoo treatments, and OsPR1 and OsPR4 were significantly up-regulated in OEtr-1. These results suggest that OsCDPK1 may be an upstream regulator involved in rice innate immunity and conferred broad-spectrum of disease resistance. Following the Xoo inoculation, the OEtr-1 and Ri-1 seedlings showed enhanced and reduced disease resistance, respectively. The dihybrid rice Ri-1/OsPR10a-Ox not only bypassed the effect of OsCDPK1 silencing on the susceptibility to Xoo but also showed enhanced disease resistance and, consistent with Ri-1 phenotypes, increased plant height and grain size. Our results reveal that OsCDPK1 plays novel key roles in the cross-talk and mediation of the balance between stress response and development and provides a clue for improving grain yield and disease resistance simultaneously in rice.

Calcium-Dependent Protein Kinases in Phytohormone Signaling Pathways

Calcium-dependent protein kinases (CPKs/CDPKs) are Ca²⁺-sensors that decode Ca²⁺ signals into specific physiological responses. Research has reported that CDPKs constitute a large multigene family in various plant species, and play diverse roles in plant growth, development, and stress responses. Although numerous CDPKs have been exhaustively studied, and many of them have been found to be involved in plant hormone biosynthesis and response mechanisms, a comprehensive overview of the manner in which CDPKs participate in phytohormone signaling pathways, regulating nearly all aspects of plant growth, has not yet been undertaken. In this article, we reviewed the structure of CDPKs and the mechanism of their subcellular localization. Some CDPKs were elucidated to influence the intracellular localization of their substrates. Since little work has been done on the interaction between CDPKs and cytokinin signaling pathways, or on newly defined phytohormones such as brassinosteroids, strigolactones and salicylic acid, this paper mainly focused on discussing the integral associations between CDPKs and five plant hormones: auxins, gibberellins, ethylene, jasmonates, and abscisic acid. A perspective on future work is provided at the end.

Improved short-term drought response of transgenic rice over-expressing maize C4 phosphoenolpyruvate carboxylase via calcium signal cascade

To understand the link between long-term drought tolerance and short-term drought responses in plants, transgenic rice (Oryza sativa L.) plants over-expressing the maize C_4-pepc gene encoding phosphoenolpyruvate carboxylase (PC) and wild-type (WT) rice plants were subjected to PEG 6000 treatments to simulate drought stress. Compared with WT, PC had the higher survival rate and net photosynthetic rate after 16days of drought treatment, and had higher relative water content in leaves after 2h of drought treatment as well, conferring drought tolerance. WT accumulated higher amounts of malondialdehyde, superoxide radicals, and H₂O₂ than PC under the 2-h PEG 6000 treatment, indicating greater damages in WT. Results from pretreatments with a Ca²⁺ chelator and/or antagonist showed that the regulation of the early drought response in PC was Ca²⁺-dependent. The NO and H₂O₂ levels in PC lines were also up-regulated via Ca²⁺ signals, indicating that Ca²⁺ in PC lines also reacted upstream of NO and H₂O₂. 2-h drought treatment increased the transcripts of CPK9 and CPK4 in PC via positive up-regulation of Ca²⁺. The transcripts of NAC6 [NACs (NAM, ATAF1, ATAF2, and CUC2)] and bZIP60 (basic leucine zipper, bZIP) were up-regulated, but those of DREB2B (dehydration-responsive element-binding protein, DREB) were down-regulated, both via Ca²⁺ signals in PC. PEPC activity, expressions of C₄-pepc, and the antioxidant enzyme activities in PC lines were up-regulated via Ca²⁺. These results indicated that Ca²⁺ signals in PC lines can up-regulate the NAC6 and bZIP60 and the downstream targets for early drought responses, conferring drought tolerance for the long term.

The calmodulin fused kinase novel gene family is the major system in plants converting Ca2+ signals to protein phosphorylation responses

Eukaryotes utilize Ca²⁺ as a universal second messenger to convert and multiply environmental and developmental signals to downstream protein phosphorylation responses. However, the phylogenetic relationships of the genes that convert Ca²⁺ signal (CS) to protein phosphorylation responses (PPRs) remain highly controversial, and their origin and evolutionary trajectory are unclear, which greatly hinders functional studies. Here we examined the deep phylogeny of eukaryotic CS converter gene families and identified a phylogenetically and structurally distinctive monophyly in Archaeplastida. This monophyly can be divided into four subfamilies, and each can be traced to ancestral members that contain a kinase domain and a calmodulin-like domain. This strongly indicates that the ancestor of this monophyly originated by a de novo fusion of a kinase gene and a calmodulin gene. This gene family, with a proposed new name, Calmodulin Fused Kinase (CFK), had expanded and diverged significantly both in sizes and in structures for efficient and accurate Ca²⁺ signalling, and was shown to play pivotal roles in all the six major plant adaptation events in evolution. Our findings elucidated the common origin of all CS-PPR converter genes except CBL-CIPK converter genes, and revealed that CFKs act as the main CS conversion system in plants.

Calcium-dependent protein kinase OsCPK10 mediates both drought tolerance and blast disease resistance in rice plants

Plant growth and productivity is negatively affected by different stresses. Most stresses trigger calcium signals that initiate acclimation responses in plants. The multigene family of plant calcium-dependent protein kinases (CPKs) functions in multiple stress responses by transducing calcium signals into phosphorylation events. This work reports that the OsCPK10 isoform positively mediates tolerance to different stresses in rice plants by enhancing their antioxidant capacity and protecting them from reactive oxygen species (ROS) damage, with the uncontrolled generation of ROS being a common feature of these stresses. Here, we show that the constitutive accumulation of an HA-tagged OsCPK10 full-length protein enhances the hydrogen peroxide detoxifying capacity of rice plants during desiccation. This is achived by modulating the accumulation of catalase proteins, which reduces the extent of lipid peroxidation and protects the integrity of cell membranes, resulting in drought tolerance. OsCPK10HA accumulation also confers blast disease resistance by interfering with fungal necrotrophic growth via a reduction in the accumulation of hydrogen peroxide. Furthermore, we show by bimolecular complementation assays that OsCPK10 is a plasma membrane protein that physically interacts in vivo with catalase A. OsCPK10 therefore appears to be a good molecular target to improve tolerance to abiotic stresses as well as to blast disease, which limit rice crop productivity.

Enhanced Rice Blast Resistance by CRISPR/Cas9-Targeted Mutagenesis of the ERF Transcription Factor Gene OsERF922

Rice blast is one of the most destructive diseases affecting rice worldwide. The adoption of host resistance has proven to be the most economical and effective approach to control rice blast. In recent years, sequence-specific nucleases (SSNs) have been demonstrated to be powerful tools for the improvement of crops via gene-specific genome editing, and CRISPR/Cas9 is thought to be the most effective SSN. Here, we report the improvement of rice blast resistance by engineering a CRISPR/Cas9 SSN (C-ERF922) targeting the OsERF922 gene in rice. Twenty-one C-ERF922-induced mutant plants (42.0%) were identified from 50 T0 transgenic plants. Sanger sequencing revealed that these plants harbored various insertion or deletion (InDel) mutations at the target site. We showed that all of the C-ERF922-induced allele mutations were transmitted to subsequent generations. Mutant plants harboring the desired gene modification but not containing the transferred DNA were obtained by segregation in the T1 and T2 generations. Six T2 homozygous mutant lines were further examined for a blast resistance phenotype and agronomic traits, such as plant height, flag leaf length and width, number of productive panicles, panicle length, number of grains per panicle, seed setting percentage and thousand seed weight. The results revealed that the number of blast lesions formed following pathogen infection was significantly decreased in all 6 mutant lines compared with wild-type plants at both the seedling and tillering stages. Furthermore, there were no significant differences between any of the 6 T2 mutant lines and the wild-type plants with regard to the agronomic traits tested. We also simultaneously targeted multiple sites within OsERF922 by using Cas9/Multi-target-sgRNAs (C-ERF922S1S2 and C-ERF922S1S2S3) to obtain plants harboring mutations at two or three sites. Our results indicate that gene modification via CRISPR/Cas9 is a useful approach for enhancing blast resistance in rice.

Transcriptome Analysis Highlights Defense and Signaling Pathways Mediated by Rice pi21 Gene with Partial Resistance to Magnaporthe oryzae

Rice blast disease is one of the most destructive rice diseases worldwide. The pi21 gene confers partial and durable resistance to Magnaporthe oryzae. However, little is known regarding the molecular mechanisms of resistance mediated by the loss-of-function of Pi21. In this study, comparative transcriptome profiling of the Pi21-RNAi transgenic rice line and Nipponbare with M. oryzae infection at different time points (0, 12, 24, 48, and 72 hpi) were investigated using RNA sequencing. The results generated 43,222 unique genes mapped to the rice genome. In total, 1109 differentially expressed genes (DEGs) were identified between the Pi21-RNAi line and Nipponbare with M. oryzae infection, with 103, 281, 209, 69, and 678 DEGs at 0, 12, 24, 48, and 72 hpi, respectively. Functional analysis showed that most of the DEGs were involved in metabolism, transport, signaling, and defense. Among the genes assigned to plant-pathogen interaction, we identified 43 receptor kinase genes associated with pathogen-associated molecular pattern recognition and calcium ion influx. The expression levels of brassinolide-insensitive 1, flagellin sensitive 2, and elongation factor Tu receptor, ethylene (ET) biosynthesis and signaling genes, were higher in the Pi21-RNAi line than Nipponbare. This suggested that there was a more robust PTI response in Pi21-RNAi plants and that ET signaling was important to rice blast resistance. We also identified 53 transcription factor genes, including WRKY, NAC, DOF, and ERF families that show differential expression between the two genotypes. This study highlights possible candidate genes that may serve a function in the partial rice blast resistance mediated by the loss-of-function of Pi21 and increase our understanding of the molecular mechanisms involved in partial resistance against M. oryzae.