Genome-Wide Identification of Cyclic Nucleotide-Gated Ion Channel Gene Family in Wheat and Functional Analyses of TaCNGC14 and TaCNGC16

A cyclic nucleotide-gated channel gene HcCNGC21 positively regulates salt and drought stress responses in kenaf (Hibiscus cannabinus L.)

Cyclic Nucleotide-Gated Channels (CNGCs) serve as Ca2+ permeable cation transport pathways, which are involved in the regulation of various biological functions such as plant cell ion selective permeability, growth and development, responses to biotic and abiotic stresses. At the present study, a total of 31 CNGC genes were identified and bioinformatically analyzed in kenaf. Among these genes, HcCNGC21 characterized to localize at the plasma membrane, with the highest expression levels in leaves, followed by roots. In addition, HcCNGC21 could be significantly induced under salt or drought stress. Virus-induced gene silencing (VIGS) of HcCNGC21 in kenaf caused notable growth inhibition under salt or drought stress, characterized by reductions in plant height, stem diameter, leaf area, root length, root surface area, and root tip number. Meanwhile, the activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) were significantly decreased, accompanied by reduced levels of osmoregulatory substances and total chlorophyll content. However, ROS accumulation and Na+ content increased. The expression of stress-responsive genes, such as HcSOD, HcPOD, HcCAT, HcERF3, HcNAC29, HcP5CS, HcLTP, and HcNCED, was significantly downregulated in these silenced lines. However, under salt or drought stress, the physiological performance and expression of stress-related genes in transgenic Arabidopsis thaliana plants overexpressing HcCNGC21 were diametrically opposite to those of TRV2-HcCNGC21 kenaf line. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays revealed that HcCNGC21 interacts with HcAnnexin D1. These findings collectively underscore the positive role of HcCNGC21 in plant resistance to salt and drought stress.

Nano-enabled agrochemicals: mitigating heavy metal toxicity and enhancing crop adaptability for sustainable crop production

The primary factors that restrict agricultural productivity and jeopardize human and food safety are heavy metals (HMs), including arsenic, cadmium, lead, and aluminum, which adversely impact crop yields and quality. Plants, in their adaptability, proactively engage in a multitude of intricate processes to counteract the impacts of HM toxicity. These processes orchestrate profound transformations at biomolecular levels, showing the plant's ability to adapt and thrive in adversity. In the past few decades, HM stress tolerance in crops has been successfully addressed through a combination of traditional breeding techniques, cutting-edge genetic engineering methods, and the strategic implementation of marker-dependent breeding approaches. Given the remarkable progress achieved in this domain, it has become imperative to adopt integrated methods that mitigate potential risks and impacts arising from environmental contamination on yields, which is crucial as we endeavor to forge ahead with the establishment of enduring agricultural systems. In this manner, nanotechnology has emerged as a viable field in agricultural sciences. The potential applications are extensive, encompassing the regulation of environmental stressors like toxic metals, improving the efficiency of nutrient consumption and alleviating climate change effects. Integrating nanotechnology and nanomaterials in agrochemicals has successfully mitigated the drawbacks associated with traditional agrochemicals, including challenges like organic solvent pollution, susceptibility to photolysis, and restricted bioavailability. Numerous studies clearly show the immense potential of nanomaterials and nanofertilizers in tackling the acute crisis of HM toxicity in crop production. This review seeks to delve into using NPs as agrochemicals to effectively mitigate HM toxicity and enhance crop resilience, thereby fostering an environmentally friendly and economically viable approach toward sustainable agricultural advancement in the foreseeable future.

Shoot transcriptome revealed widespread differential expression and potential molecular mechanisms of chickpea (Cicer arietinum L.) against Fusarium wilt

Introduction

The yield of chickpea is severely hampered by infection wilt caused by several races of Fusarium oxysporum f. sp. ciceris (Foc).

Methods

To understand the underlying molecular mechanisms of resistance against Foc4 Fusarium wilt, RNA sequencing-based shoot transcriptome data of two contrasting chickpea genotypes, namely KWR 108 (resistant) and GL 13001 (susceptible), were generated and analyzed.

Results and Discussion

The shoot transcriptome data showed 1,103 and 1,221 significant DEGs in chickpea genotypes KWR 108 and GL 13001, respectively. Among these, 495 and 608 genes were significantly down and up-regulated in genotypes KWR 108, and 427 and 794 genes were significantly down and up-regulated in genotype GL 13001. The gene ontology (GO) analysis of significant DEGs was performed and the GO of the top 50 DEGs in two contrasting chickpea genotypes showed the highest cellular components as membrane and nucleus, and molecular functions including nucleotide binding, metal ion binding, transferase, kinase, and oxidoreductase activity involved in biological processes such as phosphorylation, oxidation-reduction, cell redox homeostasis process, and DNA repair. Compared to the susceptible genotype which showed significant up-regulation of genes involved in processes like DNA repair, the significantly up-regulated DEGs of the resistant genotypes were involved in processes like energy metabolism and environmental adaptation, particularly host-pathogen interaction. This indicates an efficient utilization of environmental adaptation pathways, energy homeostasis, and stable DNA molecules as the strategy to cope with Fusarium wilt infection in chickpea. The findings of the study will be useful in targeting the genes in designing gene-based markers for association mapping with the traits of interest in chickpea under Fusarium wilt which could be efficiently utilized in marker-assisted breeding of chickpea, particularly against Foc4 Fusarium wilt.

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.

Genome-wide identification and expression analysis of the cyclic nucleotide-gated ion channel (CNGC) gene family in Saccharum spontaneum

BACKGROUND

Cyclic nucleotide-gated ion channels (CNGCs) are nonselective cation channels that are ubiquitous in eukaryotic organisms. As Ca²⁺ channels, some CNGCs have also proven to be K⁺-permeable and involved in plant development and responses to environmental stimuli. Sugarcane is an important sugar and energy crop worldwide. However, reports on CNGC genes in sugarcane are limited.

RESULTS

In this study, 16 CNGC genes and their alleles were identified from Saccharum spontaneum and classified into 5 groups based on phylogenetic analysis. Investigation of gene duplication and syntenic relationships between S. spontaneum and both rice and Arabidopsis demonstrated that the CNGC gene family in S. spontaneum expanded primarily by segmental duplication events. Many SsCNGCs showed variable expression during growth and development as well as in tissues, suggesting functional divergence. Light-responsive cis-acting elements were discovered in the promoters of all the identified SsCNGCs, and the expression of most of the SsCNGCs showed a diurnal rhythm. In sugarcane, the expression of some SsCNGCs was regulated by low-K⁺ treatment. Notably, SsCNGC13 may be involved in both sugarcane development and its response to environmental stimuli, including response to low-K⁺ stress.

CONCLUSION

This study identified the CNGC genes in S. spontaneum and provided insights into the transcriptional regulation of these SsCNGCs during development, circadian rhythm and under low-K⁺ stress. These findings lay a theoretical foundation for future investigations of the CNGC gene family in sugarcane.

Identification of CNGCs in Glycine max and Screening of Related Resistance Genes after Fusarium solani Infection

Cyclic nucleotide-gated channels (CNGCs), non-selective cation channels localised on the plasmalemma, are involved in growth, development, and regulatory mechanisms in plants during adverse stress. To date, CNGC gene families in multiple crops have been identified and analysed. However, there have been no systematic studies on the evolution and development of CNGC gene families in legumes. Therefore, in the present study, via transcriptome analysis, we identified 143 CNGC genes in legumes, and thereafter, classified and named them according to the grouping method used for Arabidopsis thaliana. Functional verification for disease stress showed that four GmCNGCs were specifically expressed in the plasmalemma during the stress process. Further, functional enrichment analysis showed that their mode of participation and coordination included inorganic ion concentration regulation inside and outside the membrane via the transmembrane ion channel and participation in stress regulation via signal transduction. The CNGC family genes in G. max involved in disease stress were also identified and physiological stress response and omics analyses were also performed. Our preliminary results revealed the basic laws governing the involvement of CNGCs in disease resistance in G. max, providing important gene resources and a theoretical reference for the breeding of resistant soybean.

Genome-Wide Identification, Characterization and Experimental Expression Analysis of CNGC Gene Family in Gossypium

Cyclic nucleotide-gated ion channels (CNGCs) are channel proteins for calcium ions, and have been reported to play important roles in regulating survival and environmental response of various plants. However, little is known about how the CNGC family works in Gossypium. In this study, 173 CNGC genes, which were identified from two diploid and five tetraploid Gossypium species, were classified into four groups by phylogenetic analysis. The collinearity results demonstrated that CNGC genes are integrally conservative among Gossypium species, but four gene losses and three simple translocations were detected, which is beneficial to analyzing the evolution of CNGCs in Gossypium. The various cis-acting regulatory elements in the CNGCs' upstream sequences revealed their possible functions in responding to multiple stimuli such as hormonal changes and abiotic stresses. In addition, expression levels of 14 CNGC genes changed significantly after being treated with various hormones. The findings in this study will contribute to understanding the function of the CNGC family in cotton, and lay a foundation for unraveling the molecular mechanism of cotton plants' response to hormonal changes.

Wheat Omics: Advancements and Opportunities

Plant omics, which includes genomics, transcriptomics, metabolomics and proteomics, has played a remarkable role in the discovery of new genes and biomolecules that can be deployed for crop improvement. In wheat, great insights have been gleaned from the utilization of diverse omics approaches for both qualitative and quantitative traits. Especially, a combination of omics approaches has led to significant advances in gene discovery and pathway investigations and in deciphering the essential components of stress responses and yields. Recently, a Wheat Omics database has been developed for wheat which could be used by scientists for further accelerating functional genomics studies. In this review, we have discussed various omics technologies and platforms that have been used in wheat to enhance the understanding of the stress biology of the crop and the molecular mechanisms underlying stress tolerance.

Genome-Wide Analysis of Cyclic Nucleotide-Gated Channel Genes Related to Pollen Development in Rice

In the angiosperm, pollen germinates and rapidly expands the pollen tube toward the ovule. This process is important for plant double fertilization and seed setting. It is well known that the tip-focused calcium gradient is essential for pollen germination and pollen tube growth. However, little is known about the Ca²⁺ channels that play a role in rice pollen germination and tube growth. Here, we divided the 16 cyclic nucleotide-gated channel (CNGC) genes from rice into five subgroups and found two subgroups (clades II and III) have pollen-preferential genes. Then, we performed a meta-expression analysis of all OsCNGC genes in anatomical samples and identified three pollen-preferred OsCNGCs (OsCNGC4, OsCNGC5, and OsCNGC8). The subcellular localization of these OsCNGC proteins is matched with their roles as ion channels on the plasma membrane. Unlike other OsCNGCs, these genes have a unique cis-acting element in the promoter. OsCNGC4 can act by forming a homomeric complex or a heteromeric complex with OsCNGC5 or OsCNGC8. In addition, it was suggested that they can form a multi-complex with Mildew Resistance Locus O (MLO) protein or other types of ion transporters, and that their expression can be modulated by Ruptured Pollen tube (RUPO) encoding receptor-like kinase. These results shed light on understanding the regulatory mechanisms of pollen germination and pollen tube growth through calcium channels in rice.

Pangenome-wide analysis of cyclic nucleotide-gated channel (CNGC) gene family in citrus Spp. Revealed their intraspecies diversity and potential roles in abiotic stress tolerance

Cyclic nucleotide-gated channels (CNGC) gene family has been found to be involved in physiological processes including signaling pathways, environmental stresses, plant growth, and development. This gene family of non-selective cation channels is known to regulate the uptake of calcium and is reported in several plant species. The pangenome-wide studies enable researchers to understand the genetic diversity comprehensively; as a comparative analysis of multiple plant species or member of a species at once helps to better understand the evolutionary relationships and diversity present among them. In the current study, pangenome-wide analysis of the CNGC gene family has been performed on five Citrus species. As a result, a total of 32 genes in Citrus sinensis, 27 genes in Citrus recticulata, 30 genes in Citrus grandis, 31 genes in Atalantia buxfolia, and 30 genes in Poncirus trifoliata were identified. In addition, two unique genes CNGC13 and CNGC14 were identified, which may have potential roles. All the identified CNGC genes were unevenly distributed on 9 chromosomes except P. trifoliata had genes distributed on 7 chromosomes and were classified into four major groups and two sub-groups namely I, II, III, IV-A, and IV-B. Cyclic nucleotide binding (CNB) motif, calmodulin-binding motif (CaMB), and motif for IQ-domain were conserved in Citrus Spp. Intron exon structures of citrus species were not exactly as same as the gene structures of Arabidopsis. The majority of cis-regulatory elements (CREs) were light responsive and others include growth, development, and stress-related indicating potential roles of the CNGC gene family in these functions. Both segmental and tandem duplication were involved in the expansion of the CNGC gene family in Citrus Spp. The miRNAs are involved in the response of CsCNGC genes towards drought stress along with having regulatory association in the expression of these genes. Protein- Protein interaction (PPI) analysis also showed the interaction of CNGC proteins with other CNGCs which suggested their potential role in pathways regulating different biological processes. GO enrichment revealed that CNGC genes were involved in the transport of ions across membranes. Furthermore, tissue-specific expression patterns of leaves sample of C. sinensis were studied under drought stress. Out of 32 genes of C. sinensis 3 genes i.e., CsCNGC1.4, CsCNGC2.1, and CsCNGC4.2 were highly up-regulated, and only CsCNGC4.6 was highly down-regulated. The qRT-PCR analysis also showed that CNGC genes were highly expressed after treatment with drought stress, while gene expression was lower under controlled conditions. This work includes findings based on multiple genomes instead of one, therefore, this will provide more genomic information rather than single genome-based studies. These findings will serve as a basis for further functional insights into the CNGC gene family.

Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance

BACKGROUND

Cyclic nucleotide-gated ion channels (CNGCs) are calcium-permeable channels that participate in a variety of biological functions, such as signaling pathways, plant development, and environmental stress and stimulus responses. Nevertheless, there have been few studies on CNGC gene family in cotton.

RESULTS

In this study, a total of 114 CNGC genes were identified from the genomes of 4 cotton species. These genes clustered into 5 main groups: I, II, III, IVa, and IVb. Gene structure and protein motif analysis showed that CNGCs on the same branch were highly conserved. In addition, collinearity analysis showed that the CNGC gene family had expanded mainly by whole-genome duplication (WGD). Promoter analysis of the GhCNGCs showed that there were a large number of cis-acting elements related to abscisic acid (ABA). Combination of transcriptome data and the results of quantitative RT-PCR (qRT-PCR) analysis revealed that some GhCNGC genes were induced in response to salt and drought stress and to exogenous ABA. Virus-induced gene silencing (VIGS) experiments showed that the silencing of the GhCNGC32 and GhCNGC35 genes decreased the salt tolerance of cotton plants (TRV:00). Specifically, physiological indexes showed that the malondialdehyde (MDA) content in gene-silenced plants (TRV:GhCNGC32 and TRV:GhCNGC35) increased significantly under salt stress but that the peroxidase (POD) activity decreased. After salt stress, the expression level of ABA-related genes increased significantly, indicating that salt stress can trigger the ABA signal regulatory mechanism.

CONCLUSIONS

we comprehensively analyzed CNGC genes in four cotton species, and found that GhCNGC32 and GhCNGC35 genes play an important role in cotton salt tolerance. These results laid a foundation for the subsequent study of the involvement of cotton CNGC genes in salt tolerance.

Cadmium in Cereal Crops: Uptake and Transport Mechanisms and Minimizing Strategies

Cadmium (Cd) contamination in soils and accumulation in cereal grains have posed food security risks and serious health concerns worldwide. Understanding the Cd transport process and its management for minimizing Cd accumulation in cereals may help to improve crop growth and grain quality. In this review, we summarize Cd uptake, translocation, and accumulation mechanisms in cereal crops and discuss efficient measures to reduce Cd uptake as well as potential remediation strategies, including the applications of plant growth regulators, microbes, nanoparticles, and cropping systems and developing low-Cd grain cultivars by CRISPR/Cas9. In addition, miRNAs modulate Cd translocation, and accumulation in crops through the regulation of their target genes was revealed. Combined use of multiple remediation methods may successfully decrease Cd concentrations in cereals. The findings in this review provide some insights into innovative and applicable approaches for reducing Cd accumulation in cereal grains and sustainable management of Cd-contaminated paddy fields.

Dynamic Expression, Differential Regulation and Functional Diversity of the CNGC Family Genes in Cotton

Cyclic nucleotide-gated channels (CNGCs) constitute a family of non-selective cation channels that are primarily permeable to Ca2+ and activated by the direct binding of cyclic nucleotides (i.e., cAMP and cGMP) to mediate cellular signaling, both in animals and plants. Until now, our understanding of CNGCs in cotton (Gossypium spp.) remains poorly addressed. In the present study, we have identified 40, 41, 20, 20, and 20 CNGC genes in G. hirsutum, G. barbadense, G. herbaceum, G. arboreum, and G. raimondii, respectively, and demonstrated characteristics of the phylogenetic relationships, gene structures, chromosomal localization, gene duplication, and synteny. Further investigation of CNGC genes in G. hirsutum, named GhCNGC1-40, indicated that they are not only extensively expressed in various tissues and at different developmental stages, but also display diverse expression patterns in response to hormones (abscisic acid, salicylic acid, methyl jasmonate, ethylene), abiotic (salt stress) and biotic (Verticillium dahlia infection) stimuli, which conform with a variety of cis-acting regulatory elements residing in the promoter regions; moreover, a set of GhCNGCs are responsive to cAMP signaling during cotton fiber development. Protein–protein interactions supported the functional aspects of GhCNGCs in plant growth, development, and stress responses. Accordingly, the silencing of the homoeologous gene pair GhCNGC1&18 and GhCNGC12&31 impaired plant growth and development; however, GhCNGC1&18-silenced plants enhanced Verticillium wilt resistance and salt tolerance, whereas GhCNGC12&31-silenced plants had opposite effects. Together, these results unveiled the dynamic expression, differential regulation, and functional diversity of the CNGC family genes in cotton. The present work has laid the foundation for further studies and the utilization of CNGCs in cotton genetic improvement.

Transcription factor BZR2 activates chitinase Cht20.2 transcription to confer resistance to wheat stripe rust

The brassinosteroid pathway promotes a variety of physiological processes in plants and the brassinosteroid insensitive1-ethylmethane sulfonate suppressor (BES)/brassinazole-resistant (BZR) functions as one of its key regulators. We previously showed that the BES/BZR-type transcription factor TaBZR2 mediates the drought stress response in wheat (Triticum aestivum) by directly upregulating the transcriptional activity of glutathione S-transferase 1. However, the function of TaBZR2 in plants under biotic stresses is unknown. In this study, we found that transcript levels of TaBZR2 were upregulated in response to inoculation with wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, Pst) and treatment with flg22 or an elicitor-like protein of Pst, Pst322. Wheat lines overexpressing TaBZR2 conferred increased resistance, whereas TaBZR2-RNAi lines exhibited decreased resistance to multiple races of Pst. TaBZR2 targeted the promoter of the chitinase gene TaCht20.2, activating its transcription. Knockdown of TaCht20.2 in wheat resulted in enhanced susceptibility to Pst, indicating the positive role of TaCht20.2 in wheat resistance. Upon Pst infection in vivo, the overexpression of TaBZR2 increased total chitinase activity, whereas RNAi-mediated silencing of TaBZR2 reduced total chitinase activity. Taken together, our results suggest that TaBZR2 confers broad-spectrum resistance to the stripe rust fungus by increasing total chitinase activity in wheat.

Cyclic nucleotide gated channel genes (CNGCs) in Rosaceae: genome-wide annotation, evolution and the roles on Valsa canker resistance

In Rosaceae, tandem duplication caused the drastic expansion of CNGC gene family Group I. The members MdCN11 and MdCN19 negatively regulate Valsa canker resistance. Apple (Malus domestica) and pear (Pyrus bretschneideri and P. communis) are important fruit crops in Rosaceae family but are suffering from threats of Valsa canker. Cyclic nucleotide-gated ion channels (CNGCs) take crucial roles in plant immune responses. In the present study, a total of 355 CNGCs was identified from 8 Rosaceae plants. Based on phylogenetic analysis, 540 CNGCs from 18 plants (8 in Rosaceae and 10 others) could be divided into four groups. Group I was greatly expanded in Rosaceae resulted from tandem duplications. A large number of cis-acting regulatory elements (cis-elements) responsive to signals from multiple stresses and hormones were identified in the promoter regions of CNGCs in Malus spp. and Pyrus spp. Expressions of most Group I members were obviously up-regulated in Valsa canker susceptible varieties but not in the resistant ones. Furthermore, overexpression of the MdCN11 and MdCN19 in both apple fruits and 'Duli' (P. betulifolia) suspension cells compromised Valsa canker resistance. Overexpression of MdCN11 induced expression of hypersensitive response (HR)-related genes. In conclusion, tandem duplication resulted in a drastic expansion of CNGC Group I members in Rosaceae. Among these, MdCN11 and MdCN19 negatively regulate the Valsa canker resistance via inducting HR.

RNAi-mediated stable silencing of TaCSN5 confers broad-spectrum resistance to Puccinia striiformis f. sp. tritici

The constitutive photomorphogenesis 9 (COP9) signalosome (CSN) is a versatile regulator of plant growth, development, and response to diverse pathogens. However, little research has been done to understand the function of those CSN genes in broad-spectrum resistance to pathogens. In this study, we found that the transcript levels of wheat TaCSN5 were induced in response to inoculation with Puccinia striiformis f. sp. tritici (Pst) and treatment with salicylic acid (SA). Overexpression of TaCSN5 in Arabidopsis resulted in increased susceptibility to Pseudomonas syringae pv. tomato DC3000 infection accompanied by down-regulation of AtPR1 expression. Overexpression of TaCSN5 in wheat lines significantly increased susceptibility to Pst accompanied by decreased SA accumulation, whereas TaCSN5-RNAi wheat lines exhibited opposite trends. Moreover, we found that TaCSN5 negatively regulated TaG3NPR1 genes involved in the SA signalling pathway. In addition, TaCSN5-RNAi lines showed increased resistance to multiple races of Pst. Taken together, we demonstrate that TaCSN5 contributes to negative regulation of wheat resistance to Pst in an SA-dependent manner.

Cadmium toxicity in plants: Impacts and remediation strategies

Cadmium (Cd) is an unessential trace element in plants that is ubiquitous in the environment. Anthropogenic activities such as disposal of urban refuse, smelting, mining, metal manufacturing, and application of synthetic phosphate fertilizers enhance the concentration of Cd in the environment and are carcinogenic to human health. In this manuscript, we reviewed the sources of Cd contamination to the environment, soil factors affecting the Cd uptake, the dynamics of Cd in the soil rhizosphere, uptake mechanisms, translocation, and toxicity of Cd in plants. In crop plants, the toxicity of Cd reduces uptake and translocation of nutrients and water, increases oxidative damage, disrupts plant metabolism, and inhibits plant morphology and physiology. In addition, the defense mechanism in plants against Cd toxicity and potential remediation strategies, including the use of biochar, minerals nutrients, compost, organic manure, growth regulators, and hormones, and application of phytoremediation, bioremediation, and chemical methods are also highlighted in this review. This manuscript may help to determine the ecological importance of Cd stress in interdisciplinary studies and essential remediation strategies to overcome the contamination of Cd in agricultural soils.

The Complex Story of Plant Cyclic Nucleotide-Gated Channels

Plant cyclic nucleotide-gated channels (CNGCs) are tetrameric cation channels which may be activated by the cyclic nucleotides (cNMPs) adenosine 3',5'-cyclic monophosphate (cAMP) and guanosine 3',5'-cyclic monophosphate (cGMP). The genome of Arabidopsis thaliana encodes 20 CNGC subunits associated with aspects of development, stress response and immunity. Recently, it has been demonstrated that CNGC subunits form heterotetrameric complexes which behave differently from the homotetramers produced by their constituent subunits. These findings have widespread implications for future signalling research and may help explain how specificity can be achieved by CNGCs that are known to act in disparate pathways. Regulation of complex formation may involve cyclic nucleotide-gated channel-like proteins.

Genome-Wide Identification and Characterization of Calcium Metabolism Related Gene Families in Arabidopsis thaliana and Their Regulation by Bacillus amyloliquefaciens Under High Calcium Stress

Several gene families involved in calcium signaling have been detected in plants, including calmodulin (CaM), calcium dependent protein kinases (CDPK), calcineurin B-like (CBL) and cyclic nucleotide-gated channels (CNGCs). In our previous study, we demonstrated that Bacillus amyloliquefaciens LZ04 (B. amyloliquefaciens LZ04) regulate genes involved in calcium stress in Arabidopsis thaliana (A. thaliana). Here, we aimed to explore the potential involvement of calcium-related gene families in the response of A. thaliana to calcium stress and the potential regulatory effects of B. amyloliquefaciens LZ04 on these genes. The structure, duplication, synteny, and expression profiles of 102 genes in calcium-related gene families in A. thaliana were investigated. Hidden Markov Models (HMMs) and BLASTP were used to predict candidate genes and conserved domains of the candidate genes were confirmed in SMART and NCBI CDD databases. Gene duplications and synteny were uncovered by BLASTP and phylogenetic analysis. The transcriptome expression profiles of candidate genes were investigated by strand-specific sequencing. Cluster analysis was used to find the expression profiles of calcium-related genes families under different treatment conditions. A total of 102 genes in calcium-related gene families were detected in A. thaliana genome, including 34 CDPK genes, 20 CNGC genes, 18 CIPK genes, 22 IQD genes, and 10 CBP genes. Additionally, of the 102 genes, 33 duplications (32.35%) and 26 gene pairs including 48 genes (47.06%) were detected. Treatment with B. amyloliquefaciens LZ04 enhanced the resistance of A. thaliana under high calcium stress by regulating some of the genes in the calcium-related gene families. Functional enrichment analysis revealed that the genes clustered in the 42nd expression profile which may be B. amyloliquefaciens-responsive genes under calcium stress were enriched in protein phosphorylation and protein modification process. Transcriptome data was validated by RT-PCR and the results generally corroborated the transcriptome sequencing results. These results may be useful for agricultural improvement in high calcium stress regions.

Cadmium Uptake by Wheat (Triticum aestivum L.): An Overview

Cadmium is a toxic heavy metal that may be detected in soils and plants. Wheat, as a food consumed by 60% of the world’s population, may uptake a high quantity of Cd through its roots and translocate Cd to the shoots and grains thus posing risks to human health. Therefore, we tried to explore the journey of Cd in wheat via a review of several papers. Cadmium may reach the root cells by some transporters (such as zinc-regulated transporter/iron-regulated transporter-like protein, low-affinity calcium transporters, and natural resistance-associated macrophages), and some cation channels or Cd chelates via yellow stripe 1-like proteins. In addition, some of the effective factors regarding Cd uptake into wheat, such as pH, organic matter, cation exchange capacity (CEC), Fe and Mn oxide content, and soil texture (clay content), were investigated in this paper. Increasing Fe and Mn oxide content and clay minerals may decrease the Cd uptake by plants, whereas reducing pH and CEC may increase it. In addition, the feasibility of methods to diminish Cd accumulation in wheat was studied. Amongst agronomic approaches for decreasing the uptake of Cd by wheat, using organic amendments is most effective. Using biochar might reduce the Cd accumulation in wheat grains by up to 97.8%.

Transcriptomic analysis identifies novel genes and pathways for salt stress responses in Suaeda salsa leaves

Salinity is a critical abiotic stress, which significantly impacts the agricultural yield worldwide. Identification of the molecular mechanisms underlying the salt tolerance in euhalophyte Suaeda salsa is conducive to the development of salt-resistant crops. In the present study, high-throughput RNA sequencing was performed after S. salsa leaves were exposed to 300 mM NaCl for 7 days, and 7,753 unigenes were identified as differently expressed genes (DEGs) in S. salsa, including 3,638 increased and 4,115 decreased unigenes. Moreover, hundreds of pathways were predicted to participate in salt stress response in S. salsa by Gene Ontology (GO), MapMan and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, including ion transport and sequestration as well as photoprotection of photosystem (PS) II. The GO enrichment analysis indicated that genes related to ion transport, reactive oxygen species (ROS) scavenging and transcriptional factors were highly expressed upon NaCl treatment. The excessive Na+ and Cl- ions were supposed to be absorbed into the vacuole for ion sequestration and balance adjustment by potassium transporters (such as KEA3) with high expressions. Moreover, we predicted that mutiple candidate genes associated with photosynthesis (such as PSB33 and ABA4), ROS (such as TAU9 and PHI8) and transcriptional regulation (HB-7 and MYB78) pathways could mitigate salt stress-caused damage in S. salsa.

Coordinated Transport of Nitrate, Potassium, and Sodium

Potassium (K+) and nitrogen (N) are essential nutrients, and their absorption and distribution within the plant must be coordinated for optimal growth and development. Potassium is involved in charge balance of inorganic and organic anions and macromolecules, control of membrane electrical potential, pH homeostasis and the regulation of cell osmotic pressure, whereas nitrogen is an essential component of amino acids, proteins, and nucleic acids. Nitrate (NO3 -) is often the primary nitrogen source, but it also serves as a signaling molecule to the plant. Nitrate regulates root architecture, stimulates shoot growth, delays flowering, regulates abscisic acid-independent stomata opening, and relieves seed dormancy. Plants can sense K+/NO3 - levels in soils and adjust accordingly the uptake and root-to-shoot transport to balance the distribution of these ions between organs. On the other hand, in small amounts sodium (Na+) is categorized as a "beneficial element" for plants, mainly as a "cheap" osmolyte. However, at high concentrations in the soil, Na+ can inhibit various physiological processes impairing plant growth. Hence, plants have developed specific mechanisms to transport, sense, and respond to a variety of Na+ conditions. Sodium is taken up by many K+ transporters, and a large proportion of Na+ ions accumulated in shoots appear to be loaded into the xylem by systems that show nitrate dependence. Thus, an adequate supply of mineral nutrients is paramount to reduce the noxious effects of salts and to sustain crop productivity under salt stress. In this review, we will focus on recent research unraveling the mechanisms that coordinate the K+-NO3 -; Na+-NO3 -, and K+-Na+ transports, and the regulators controlling their uptake and allocation.

Genome-wide identification of CNGC genes in Chinese jujube (Ziziphus jujuba Mill.) and ZjCNGC2 mediated signalling cascades in response to cold stress

BACKGROUNDS

Cyclic nucleotide gated channels (CNGCs) play multifaceted roles in plant physiological processes, especially with respect to signalling processes, plant development, and responses to environmental stresses. However, little information is known about the CNGC family in the large cosmopolitan family Rhamnaceae, which has strong tolerance to biotic and abiotic stresses.

RESULTS

In the current study, a total of 15 ZjCNGCs which located on 7 chromosomes were firstly identified in Chinese jujube (Ziziphus jujuba Mill.), the most important species of Rhamnaceae in terms of economic and ecological values. Phylogenetic analysis showed that these ZjCNGCs could be classified into four groups, ZjCNGC12 belonged to group IVA, and ZjCNGC13, 14, 15 belonged to group IVB. In addition, the paralogous and orthologous homology duplication of ZjCNGC15 occurred during the evolutionary process. The characteristics of ZjCNGCs regarding to exon-intron numbers and post-translational modifications showed diversified structures and functions. Motif composition and protein sequence analysis revealed that the phosphate-binding cassette and hinge regions were conserved among ZjCNGCs. Prediction of the cis-acting regulatory elements and expression profiles by real-time quantitative PCR analysis showed that some of the ZjCNGCs responded to environmental changes, especially ZjCNGC2, which was significantly downregulated in response to cold stress, and ZjCNGC4 was highly induced in response to cold, salt and alkaline stresses. ZjCNGC13 and 14 were highly induced in the phytoplasma-resistant cultivar and downregulated in the susceptible cultivar. Furthermore, ZjCNGC2 could be regulated by cAMP treatment, microtubule changes and interact with ZjMAPKK4, which suggested that cAMP and microtubule might play important roles in ZjCNGC2 mediated ZjMAPKK4 signalling transduction involved in cold stress.

CONCLUSIONS

The identification and classification analysis of ZjCNGCs were firstly reported, and some key individual ZjCNGCs might play essential roles in the response to biotic and abiotic stresses, especially ZjCNGC2 mediated ZjMAPKK4 signalling transduction involved in cold stress. This systematic analysis could provide important information for further functional characterization of ZjCNGCs with the aim of breeding stress-resistant cultivars.

Cyclic nucleotide gated channels (CNGCs) in plant signalling-Current knowledge and perspectives

Cell signaling is an evolutionarily conserved mechanism that responds and adapts to various internal and external factors. Generally, a signal is mediated by various signaling molecules and is transferred to a cascade of effector proteins. To date, there is significant evidence that cyclic nucleotides (cNMPs), e.g., adenosine 3',5'-cyclic monophosphate (cAMP) and guanosine 3',5'-cyclic monophosphate (cGMP), may represent important elements of many signaling pathways in plants. However, in contrast to the impressive progress made in understanding cyclic nucleotide signaling in mammalian hosts, only few studies have investigated this topic in plants. Existing evidence indicates that cNMPs participate in growth and developmental processes, as well as the response to various stresses. Once synthesized by adenylyl or guanylyl cyclases, these signals are transduced by acting through a number of cellular effectors. The regulatory effects of cNMPs in eukaryotes can be mediated via various downstream effector proteins, such as protein kinases, Exchange Protein directly Activated by cAMP (EPAC), and Cyclic Nucleotide-Gated ion Channels (CNGC). These proteins sense changes in intracellular cNMP levels and regulate numerous cellular responses. Moreover, the amplitude of cNMP levels and the duration of its signal in the cell is also governed by phosphodiesterases (PDEs), enzymes that are responsible for the breakdown of cNMPs. Data collected in recent years strongly suggest that cyclic nucleotide gated channels are the main cNMP effectors in plant cells. These channels are important cellular switches that transduce changes in intracellular concentrations of cyclic nucleotides into changes in membrane potential and ion concentrations. Structurally, these channels belong to the superfamily of pore-loop cation channels. In this review, we provide an overview of the molecular properties of CNGC structure, regulation and ion selectivity, and subcellular localization, as well as describing the signal transduction pathways in which these channels are involved. We will also summarize recent insights into the role of CNGC proteins in plant growth, development and response to stressors.

Genome-Wide Expression Profiling of Genes Associated with the Lr47-Mediated Wheat Resistance to Leaf Rust (Puccinia triticina)

Puccinia triticina (Pt), the causal agent of wheat leaf rust, is one of the most destructive fungal pathogens threatening global wheat cultivations. The rational utilization of leaf rust resistance (Lr) genes is still the most efficient method for the control of such diseases. The Lr47 gene introgressed from chromosome 7S of Aegilops speltoides still showed high resistance to the majority of Pt races collected in China. However, the Lr47 gene has not been cloned yet, and the regulatory network of the Lr47-mediated resistance has not been explored. In the present investigation, transcriptome analysis was applied on RNA samples from three different wheat lines ("Yecora Rojo", "UC1037", and "White Yecora") carrying the Lr47 gene three days post-inoculation with the epidemic Pt race THTT. A comparison between Pt-inoculated and water-inoculated "Lr47-Yecora Rojo" lines revealed a total number of 863 upregulated (q-value < 0.05 and log2foldchange > 1) and 418 downregulated (q-value < 0.05 and log2foldchange < -1) genes. Specifically, differentially expressed genes (DEGs) located on chromosomes 7AS, 7BS, and 7DS were identified, ten of which encoded receptor-like kinases (RLKs). The expression patterns of these RLK genes were further determined by a time-scale qRT-PCR assay. Moreover, heatmaps for the expression profiles of pathogenesis-related (PR) genes and several transcription factor gene families were generated. Using a transcriptomic approach, we initially profiled the transcriptional changes associated with the Lr47-mediated resistance. The identified DEGs, particularly those genes encoding RLKs, might serve as valuable genetic resources for the improvement of wheat resistance to Pt.

Piriformospora indica confers salinity tolerance on tomato (Lycopersicon esculentum Mill.) through amelioration of nutrient accumulation, K+/Na+ homeostasis and water status

Piriformospora indica confers salt tolerance in tomato seedlings by increasing the uptake of nutrients such as N, P and Ca, improving K⁺/Na⁺ homoeostasis by regulating the expression of NHXs, SOS1 and CNGC15 genes, maintaining water status by regulating the expression of aquaporins. Piriformospora indica, an endophytic basidiomycete, has been shown to increase the growth and improve the plants tolerance to stressful conditions, especially salinity, by establishing the arbuscular mycorrhiza-like symbiotic relationship in various plant hosts. In the present research, the effect of NaCl treatment (150 mM) and P. indica inoculation on growth, accumulation of nutrients, the transcription level of genes involved in ionic homeostasis (NHXs, SOS1 and CNGC15) and regulating water status (PIP1;2, PIP2;4, TIP1;1 and TIP2;2) in roots and leaves of tomato seedlings were investigated. The P. indica improved the uptake of N, P, Ca and K, and reduced Na accumulation, and had no significant effect on Cl accumulation in roots and leaves. The endophytic fungus also increased in K⁺/Na⁺ ratio in roots and leaves of tomato by regulating the expression of NHX isoforms and upregulating SOS1 and CNGC15 expression. Salinity stress increased the transcription of PIP2;4 gene and reduced the transcription of PIP1;2, TIP1;1 and TIP2;2 genes compared to the control treatment. However, P. indica inoculation upregulated the expression of PIP1;2 and PIP2;4 genes versus non-inoculated plants but did not have a significant effect on TIP1;1 and TIP2;2 expression. These results conclude that the positive effects of P. indica on nutrients accumulation, ionic homeostasis and water status lead to the increased salinity tolerance and the improved plant growth under NaCl treatment.

Arabidopsis mutant dnd2 exhibits increased auxin and abscisic acid content and reduced stomatal conductance

Arabidopsis thaliana cyclic nucleotide-gated ion channel gene 4 (AtCNGC4) loss-of-function mutant dnd2 exhibits elevated accumulation of salicylic acid (SA), dwarfed morphology, reduced hypersensitive response (HR), altered disease resistance and spontaneous lesions on plant leaves. An orthologous barley mutant, nec1, has been reported to over-accumulate indole-3-acetic acid (IAA) and to exhibit changes in stomatal regulation in response to exogenous auxin. Here we show that the Arabidopsis dnd2 over-accumulates both IAA and abscisic acid (ABA) and displays related phenotypic and physiological changes, such as, reduced stomatal size, higher stomatal density and stomatal index. dnd2 showed increased salt tolerance in root growth assay and significantly reduced stomatal conductance, while maintaining near wt reaction in stomatal conductance upon external application of ABA, and probably consequently increased drought stress tolerance. Introduction of both sid2-1 and fmo1 into dnd2 background resulting in removal of SA did not alter stomatal conductance. Hence, the closed stomata of dnd2 is probably a result of increased ABA levels and not increased SA levels. The triple dnd2sid2abi1-1 mutant exhibited intermediate stomatal conductance compared to dnd2 and abi1-1 (ABA insensitive, open stomata), while the response to external ABA was as in abi1-1 suggesting that reduced stomatal conductance in dnd2 is not due to impaired ABA signaling. In conclusion, Arabidopsis dnd2 mutant exhibited ABA overaccumulation and stomatal phenotypes, which may contribute to the observed improvement in drought stress resistance. Thus, Arabidopsis dnd2 mutant may serve as a model for studying crosstalk between biotic and abiotic stress and hormonal response in plants.

Genome-wide identification and abiotic stress-responsive pattern of heat shock transcription factor family in Triticum aestivum L

Background

Enhancement of crop productivity under various abiotic stresses is a major objective of agronomic research. Wheat (Triticum aestivum L.) as one of the world’s staple crops is highly sensitive to heat stress, which can adversely affect both yield and quality. Plant heat shock factors (Hsfs) play a crucial role in abiotic and biotic stress response and conferring stress tolerance. Thus, multifunctional Hsfs may be potentially targets in generating novel strains that have the ability to survive environments that feature a combination of stresses.

Result

In this study, using the released genome sequence of wheat and the novel Hsf protein HMM (Hidden Markov Model) model constructed with the Hsf protein sequence of model monocot (Oryza sativa) and dicot (Arabidopsis thaliana) plants, genome-wide TaHsfs identification was performed. Eighty-two non-redundant and full-length TaHsfs were randomly located on 21 chromosomes. The structural characteristics and phylogenetic analysis with Arabidopsis thaliana, Oryza sativa and Zea mays were used to classify these genes into three major classes and further into 13 subclasses. A novel subclass, TaHsfC3 was found which had not been documented in wheat or other plants, and did not show any orthologous genes in A. thaliana, O. sativa, or Z. mays Hsf families. The observation of a high proportion of homeologous TaHsf gene groups suggests that the allopolyploid process, which occurred after the fusion of genomes, contributed to the expansion of the TaHsf family. Furthermore, TaHsfs expression profiling by RNA-seq revealed that the TaHsfs could be responsive not only to abiotic stresses but also to phytohormones. Additionally, the TaHsf family genes exhibited class-, subclass- and organ-specific expression patterns in response to various treatments.

Conclusions

A comprehensive analysis of Hsf genes was performed in wheat, which is useful for better understanding one of the most complex Hsf gene families. Variations in the expression patterns under different abiotic stress and phytohormone treatments provide clues for further analysis of the TaHsfs functions and corresponding signal transduction pathways in wheat.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5617-1) contains supplementary material, which is available to authorized users.

Can wheat survive in heat? Assembling tools towards successful development of heat stress tolerance in Triticum aestivum L

Wheat is an important cereal crop that fulfils the calorie demands of the global humanity. Rapidly expanding populations are exposed to a fast approaching acute shortage in the adequate supply of food and fibre from agricultural resources. One of the significant threats to food security lies in the constantly increasing global temperatures which inflict serious injuries to the plants in terms of various physiological, biochemical and molecular processes. Wheat being a cool season crop is majorly impacted by the heat stress which adversely affects crop productivity and yield. These challenges would be potentially defeated with the implementation of genetic engineering strategies coupled with the new genome editing approaches. Development of transgenic plants for various crops has proved very effective for the incorporation of improved varietal traits in context of heat stress. With a similar approach, we need to target for the generation of heat stress tolerant wheat varieties which are capable of survival in such adverse conditions and yet produce well. In this review, we enumerate the current status of research on the heat stress responsive genes/factors and their potential role in mitigating heat stress in plants particularly in wheat with an aim to help the researchers get a holistic view of this topic. Also, we discuss on the prospective signalling pathway that is triggered in plants in general under heat stress.

Calcium as a Modulator of the Adenylyl Cyclase Activity of Potato Cells in Bacterial Pathogenesis

This is the first study to detect the effect of calcium ions on the activity of transmembrane adenylyl cyclase (tmAC), the key enzyme of the adenylyl cyclase signaling system, under normal conditions and after a short-term exposure to exopolysaccharides (EPS) of the bacterial ring rot pathogen Clavibacter michiganensis ssp. sepedonicus (Cms). After the treatment of the roots of plants with the Cms EPS, the response to Ca²⁺ changed: the activity of the tmAC of plants of the resistant cultivar significantly increased, whereas in the cells of the susceptible cultivar it remained unchanged.