Stress signaling in plants: a mitogen-activated protein kinase pathway is activated by cold and drought

A close-up of regulatory networks and signaling pathways of MKK5 in biotic and abiotic stresses

Mitogen-activated protein Kinase Kinase 5 (MKK5) is a central hub in the complex phosphorylation chain reaction of the Mitogen-activated protein kinases (MAPK) cascade, regulating plant responses to biotic and abiotic stresses. This review manuscript aims to provide a comprehensive analysis of the regulatory mechanism of the MKK5 involved in stress adaptation. This review will delve into the intricate post-transcriptional and post-translational modifications of the MKK5, discussing how they affect its expression, activity, and subcellular localization in response to stress signals. We also discuss the integration of the MKK5 into complex signaling pathways, orchestrating plant immunity against pathogens and its modulating role in regulating abiotic stresses, such as: drought, cold, heat, and salinity, through the phytohormonal signaling pathways. Furthermore, we highlight potential applications of the MKK5 for engineering stress-resilient crops and provide future perspectives that may pave the way for future studies. This review manuscript aims to provide valuable insights into the mechanisms underlying MKK5 regulation, bridge the gap from numerous previous findings, and offer a firm base in the knowledge of MKK5, its regulating roles, and its involvement in environmental stress regulation.

Seed Priming with Reactive Oxygen Species-Generating Nanoparticles Enhanced Maize Tolerance to Multiple Abiotic Stresses

Climate change-induced extreme weather events (heat, cold, drought, and flooding) will severely affect crop production. Increasing the resilience of crops to fluctuating environmental conditions is critically important. Here, we report that nanomaterials (NMs) with reactive oxygen species (ROS)-generating properties can be used as seed priming agents to simultaneously enhance the tolerance of maize seeds and seedlings to diverse and even multiple stresses. Maize seeds primed with 40 mg/L silver nanoparticles (AgNPs) exhibited accelerated seed germination and an increased germination rate, greater seedling vigor, and better seedling growth under drought (10% and 20% PEG), saline (50 and 100 mM NaCl), and cold (15 °C) stress conditions, indicating enhanced resilience to diverse stresses. Importantly, maize resistance to simultaneous multiple stresses (drought and cold, drought and salt, and salt and cold) was markedly enhanced. Under drought conditions, seed priming significantly boosted root hair density and length (17.3-82.7%), which enabled greater tolerance to water deficiency. RNA-seq analysis reveals that AgNPs seed priming induced a transcriptomic shift in maize seeds. Plant hormone signal transduction and MAPK signaling pathways were activated upon seed priming. Importantly, low-cost and environmentally friendly ROS-generating Fe-based NMs (Fe2O3 and Fe3O4 NPs) were also demonstrated to enhance the resistance of seeds and seedlings to drought, salt, and cold stresses. These findings demonstrate that a simple seed priming strategy can be used to significantly enhance the climate resilience of crops through modulated ROS homeostasis and that this approach could be a powerful nanoenabled tool for addressing worsening food insecurity.

Transcriptome-based gene regulatory network analyses of differential cold tolerance of two tobacco cultivars

BACKGROUND

Cold is one of the main abiotic stresses that severely affect plant growth and development, and crop productivity as well. Transcriptional changes during cold stress have already been intensively studied in various plant species. However, the gene networks involved in the regulation of differential cold tolerance between tobacco varieties with contrasting cold resistance are quite limited.

RESULTS

Here, we conducted multiple time-point transcriptomic analyses using Tai tobacco (TT, cold susceptibility) and Yan tobacco (YT, cold resistance) with contrasting cold responses. We identified similar DEGs in both cultivars after comparing with the corresponding control (without cold treatment), which were mainly involved in response to abiotic stimuli, metabolic processes, kinase activities. Through comparison of the two cultivars at each time point, in contrast to TT, YT had higher expression levels of the genes responsible for environmental stresses. By applying Weighted Gene Co-Expression Network Analysis (WGCNA), we identified two main modules: the pink module was similar while the brown module was distinct between the two cultivars. Moreover, we obtained 100 hub genes, including 11 important transcription factors (TFs) potentially involved in cold stress, 3 key TFs in the brown module and 8 key TFs in the pink module. More importantly, according to the genetic regulatory networks (GRNs) between TFs and other genes or TFs by using GENIE3, we identified 3 TFs (ABI3/VP1, ARR-B and WRKY) mainly functioning in differential cold responses between two cultivars, and 3 key TFs (GRAS, AP2-EREBP and C2H2) primarily involved in cold responses.

CONCLUSION

Collectively, our study provides valuable resources for transcriptome- based gene network studies of cold responses in tobacco. It helps to reveal how key cold responsive TFs or other genes are regulated through network. It also helps to identify the potential key cold responsive genes for the genetic manipulation of tobacco cultivars with enhanced cold tolerance in the future.

Comparative Transcriptome Analysis Reveals New Insight of Alfalfa (Medicago sativa L.) Cultivars in Response to Abrupt Freezing Stress

Freezing stress is a major limiting environmental factor that affects the productivity and distribution of alfalfa (Medicago sativa L.). There is growing evidence that enhancing freezing tolerance through resistance-related genes is one of the most efficient methods for solving this problem, whereas little is known about the complex regulatory mechanism of freezing stress. Herein, we performed transcriptome profiling of the leaves from two genotypes of alfalfa, freezing tolerance "Gannong NO.3" and freezing-sensitive "WL326GZ" exposure to -10°C to investigate which resistance-related genes could improve the freezing tolerance. Our results showed that a total of 121,366 genes were identified, and there were 7,245 differentially expressed genes (DEGs) between the control and treated leaves. In particular, the DEGs in "Gannong NO.3" were mainly enriched in the metabolic pathways and biosynthesis of secondary metabolites, and most of the DEGs in "WL326GZ" were enriched in the metabolic pathways, the biosynthesis of secondary metabolites, and plant-pathogen interactions. Moreover, the weighted gene co-expression network analysis (WGCNA) showed that ATP-binding cassette (ABC) C subfamily genes were strongly impacted by freezing stress, indicating that ABCC8 and ABCC3 are critical to develop the freezing tolerance. Moreover, our data revealed that numerous Ca2+ signal transduction and CBF/DREB1 pathway-related genes were severely impacted by the freezing resistance, which is believed to alleviate the damage caused by freezing stress. Altogether, these findings contribute the comprehensive information to understand the molecular mechanism of alfalfa adaptation to freezing stress and further provide functional candidate genes that can adapt to abiotic stress.

Comprehensive analysis of MAPK cascade genes in sorghum (Sorghum bicolor L.) reveals SbMPK14 as a potential target for drought sensitivity regulation

The mitogen-activated protein kinase (MAPK) cascade plays a crucial role in regulating many important biological processes in plants. Here, we identified and characterized eight MAPKK and 49 MAPKKK genes in sorghum and analyzed their differential expression under drought treatment; we also characterized 16 sorghum MAPK genes. RNA-seq analysis revealed that 10 MAPK cascade genes were involved in drought stress response at the transcriptome level in sorghum. Overexpression of SbMPK14 in Arabidopsis and maize resulted in hypersensitivity to drought by promoting water loss, indicating that SbMPK14 functions as a negative regulator of the drought response. Subsequent transcriptome analysis and qRT-PCR verification of maize SbMPK14 overexpression lines revealed that SbMPK14 likely increases plant drought sensitivity by suppressing the activity of specific ERF and WRKY transcription factors. This comprehensive study provides valuable insight into the mechanistic basis of MAPK cascade gene function and their responses to drought in sorghum.

Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

Erianthus arundinaceus [Retzius] Jeswiet, a wild relative of sugarcane has a high biomass production potential and a reservoir of many genes for superior agronomic traits and tolerance to biotic and abiotic stresses. A comparative physiological, anatomical and root transcriptome analysis were carried out to identify the salt-responsive genes and metabolic pathways associated with salt-tolerant E. arundinaceus genotype IND99-907 and salinity-sensitive sugarcane genotype Co 97010. IND99-907 recorded growth of young leaves, higher proline content, higher relative water content, intact root anatomical structures and lower Na+/K+, Ca2+/K+ and Mg2+/K+ ratio as compared to the sugarcane genotype Co 97010. We have generated four de novo transcriptome assemblies between stressed and control root samples of IND99-907 and Co 97010. A total of 649 and 501 differentially expressed genes (FDR<0.01) were identified from the stressed and control libraries of IND99-907 and Co 97010 respectively. Genes and pathways related to early stress-responsive signal transduction, hormone signalling, cytoskeleton organization, cellular membrane stabilization, plasma membrane-bound calcium and proton transport, sodium extrusion, secondary metabolite biosynthesis, cellular transporters related to plasma membrane-bound trafficking, nucleobase transporter, clathrin-mediated endocytosis were highly enriched in IND99-907. Whereas in Co 97010, genes related to late stress-responsive signal transduction, electron transport system, senescence, protein degradation and programmed cell death, transport-related genes associated with cellular respiration and mitochondrial respiratory chain, vesicular trafficking, nitrate transporter and fewer secondary metabolite biosynthetic genes were highly enriched. A total of 27 pathways, 24 biological processes, three molecular functions and one cellular component were significantly enriched (FDR≤ 0.05) in IND99-907 as compared to 20 pathways, two biological processes without any significant molecular function and cellular components in Co 97010, indicates the unique and distinct expression pattern of genes and metabolic pathways in both genotypes. The genomic resources developed from this study is useful for sugarcane crop improvement through development of genic SSR markers and genetic engineering approaches.

StCaM2, a calcium binding protein, alleviates negative effects of salinity and drought stress in tobacco

KEY MESSAGE

Overexpression of StCaM2 in tobacco promotes plant growth and confers increased salinity and drought tolerance by enhancing the photosynthetic efficiency, ROS scavenging, and recovery from membrane injury. Calmodulins (CaMs) are important Ca2+ sensors that interact with effector proteins and drive a network of signal transduction pathways involved in regulating the growth and developmental pattern of plants under stress. Herein, using in silico analysis, we identified 17 CaM isoforms (StCaM) in potato. Expression profiling revealed different temporal and spatial expression patterns of these genes, which were modulated under abiotic stress. Among the identified StCaM genes, StCaM2 was found to have the largest number of abiotic stress responsive promoter elements. In addition, StCaM2 was upregulated in response to some of the selected abiotic stress in potato tissues. Overexpression of StCaM2 in transgenic tobacco plants enhanced their tolerance to salinity and drought stress. Accumulation of reactive oxygen species was remarkably decreased in transgenic lines compared to that in wild type plants. Chlorophyll a fluorescence analysis suggested better performance of photosystem II in transgenic plants under stress compared to that in wild type plants. The increase in salinity stress tolerance in StCaM2-overexpressing plants was also associated with a favorable K+/Na+ ratio. The enhanced tolerance to abiotic stresses correlated with the increase in the activities of anti-oxidative enzymes in transgenic tobacco plants. Overall, our results suggest that StCaM2 can be a novel candidate for conferring salt and drought tolerance in plants.

Overexpression of alfalfa SIMK promotes root hair growth, nodule clustering and shoot biomass production

Nitrogen-fixing rhizobia and legumes have developed complex mutualistic mechanism that allows to convert atmospheric nitrogen into ammonia. Signalling by mitogen-activated protein kinases (MAPKs) seems to be involved in this symbiotic interaction. Previously, we reported that stress-induced MAPK (SIMK) shows predominantly nuclear localization in alfalfa root epidermal cells. Nevertheless, SIMK is activated and relocalized to the tips of growing root hairs during their development. SIMK kinase (SIMKK) is a well-known upstream activator of SIMK. Here, we characterized production parameters of transgenic alfalfa plants with genetically manipulated SIMK after infection with Sinorhizobium meliloti. SIMKK RNAi lines, causing strong downregulation of both SIMKK and SIMK, showed reduced root hair growth and lower capacity to form infection threads and nodules. In contrast, constitutive overexpression of GFP-tagged SIMK promoted root hair growth as well as infection thread and nodule clustering. Moreover, SIMKK and SIMK downregulation led to decrease, while overexpression of GFP-tagged SIMK led to increase of biomass in above-ground part of plants. These data suggest that genetic manipulations causing downregulation or overexpression of SIMK affect root hair, nodule and shoot formation patterns in alfalfa, and point to the new biotechnological potential of this MAPK.

Angiosperms at the edge: Extremity, diversity, and phylogeny

A hallmark of flowering plants is their ability to invade some of the most extreme and dynamic habitats, including cold and dry biomes, to a far greater extent than other land plants. Recent work has provided insight to the phylogenetic distribution and evolutionary mechanisms which have enabled this success, yet needed is a synthesis of evolutionary perspectives with plant physiological traits, morphology, and genomic diversity. Linking these disparate components will not only lead to better understand the evolutionary parallelism and diversification of plants with these two strategies, but also to provide the framework needed for directing future research. We summarize the primary physiological and structural traits involved in response to cold- and drought stress, outline the phylogenetic distribution of these adaptations, and describe the recurring association of these changes with rapid diversification events that occurred in multiple lineages over the past 15 million years. Across these threefold facets of dry-cold correlation (traits, phylogeny, and time) we stress the contrast between (a) the amazing diversity of solutions flowering plants have developed in the face of extreme environments and (b) a broad correlation between cold and dry adaptations that in some cases may hint at deep common origins.

Mitogen activated protein kinase (MAPK)-regulated genes with predicted signal peptides function in the Glycine max defense response to the root pathogenic nematode Heterodera glycines

Glycine max has 32 mitogen activated protein kinases (MAPKs), nine of them exhibiting defense functions (defense MAPKs) to the plant parasitic nematode Heterodera glycines. RNA seq analyses of transgenic G. max lines overexpressing (OE) each defense MAPK has led to the identification of 309 genes that are increased in their relative transcript abundance by all 9 defense MAPKs. Here, 71 of those genes are shown to also have measurable amounts of transcript in H. glycines-induced nurse cells (syncytia) produced in the root that are undergoing a defense response. The 71 genes have been grouped into 7 types, based on their expression profile. Among the 71 genes are 8 putatively-secreted proteins that include a galactose mutarotase-like protein, pollen Ole e 1 allergen and extensin protein, endomembrane protein 70 protein, O-glycosyl hydrolase 17 protein, glycosyl hydrolase 32 protein, FASCICLIN-like arabinogalactan protein 17 precursor, secreted peroxidase and a pathogenesis-related thaumatin protein. Functional transgenic analyses of all 8 of these candidate defense genes that employ their overexpression and RNA interference (RNAi) demonstrate they have a role in defense. Overexpression experiments that increase the relative transcript abundance of the candidate defense gene reduces the ability that the plant parasitic nematode Heterodera glycines has in completing its life cycle while, in contrast, RNAi of these genes leads to an increase in parasitism. The results provide a genomic analysis of the importance of MAPK signaling in relation to the secretion apparatus during the defense process defense in the G. max-H. glycines pathosystem and identify additional targets for future studies.

Comparative transcriptomic analysis of contrasting hybrid cultivars reveal key drought-responsive genes and metabolic pathways regulating drought stress tolerance in maize at various stages

Drought stress is the primary environmental factor that negatively influences plant growth and yield in cereal grain crops such as maize (Zea mays L.). Crop breeding efforts for enhanced drought resistance require improved knowledge of plant drought stress responses. In this study, we applied a 12-day water-deficit stress treatment to maize plants of two contrasting (drought tolerant ND476 and drought sensitive ZX978) hybrid cultivars at four (V12, VT, R1, and R4) crop growth stages and we report key cultivar-specific and growth-stage-specific molecular mechanisms regulating drought stress responses in maize. Based on the transcriptome analysis, a total of 3451 and 4088 differentially expressed genes (DEGs) were identified in ND476 and ZX978 from the four experimental comparisons, respectively. These gene expression changes effected corresponding metabolic pathway responses related to drought tolerance in maize. In ND476, the DEGs associated with the ribosome, starch and sucrose metabolism, phenylpropanoid biosynthesis and phenylpropanoid metabolism pathways were predominant at the V12, VT, R2, and R4 stages, respectively, whereas those in ZX978 were related to ribosome, pentose and glucuronate interconversions (PGI), MAPK signaling and sulfur metabolism pathways, respectively. MapMan analysis revealed that DEGs related to secondary metabolism, lipid metabolism, and amino acid metabolism were universal across the four growth stages in ND476. Meanwhile, the DEGs involved in cell wall, photosynthesis and amino acid metabolism were universal across the four growth stages in ZX978. However, K-means analysis clustered those DEGs into clear and distinct expression profiles in ND476 and ZX978 at each stage. Several functional and regulatory genes were identified in the special clusters related to drought defense response. Our results affirmed that maize drought stress adaptation is a cultivar-specific response as well as a stage-specific response process. Additionally, our findings enrich the maize genetic resources and enhance our further understanding of the molecular mechanisms regulating drought stress tolerance in maize. Further, the DEGs screened in this study may provide a foundational basis for our future targeted cloning studies.

Transcriptomic Profiling of Young Cotyledons Response to Chilling Stress in Two Contrasting Cotton (Gossypium hirsutum L.) Genotypes at the Seedling Stage

Young cotyledons of cotton seedlings are most susceptible to chilling stress. To gain insight into the potential mechanism of cold tolerance of young cotton cotyledons, we conducted physiological and comparative transcriptome analysis of two varieties with contrasting phenotypes. The evaluation of chilling injury of young cotyledons among 74 cotton varieties revealed that H559 was the most tolerant and YM21 was the most sensitive. The physiological analysis found that the ROS scavenging ability was lower, and cell membrane damage was more severe in the cotyledons of YM21 than that of H559 under chilling stress. RNA-seq analysis identified a total of 44,998 expressed genes and 19,982 differentially expressed genes (DEGs) in young cotyledons of the two varieties under chilling stress. Weighted gene coexpression network analysis (WGCNA) of all DEGs revealed four significant modules with close correlation with specific samples. The GO-term enrichment analysis found that lots of genes in H559-specific modules were involved in plant resistance to abiotic stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that pathways such as plant hormone signal transduction, MAPK signaling, and plant–pathogen interaction were related to chilling stress response. A total of 574 transcription factors and 936 hub genes in these modules were identified. Twenty hub genes were selected for qRT-PCR verification, revealing the reliability and accuracy of transcriptome data. These findings will lay a foundation for future research on the molecular mechanism of cold tolerance in cotyledons of cotton.

Identification of candidate tolerance genes to low-temperature during maize germination by GWAS and RNA-seqapproaches

BACKGROUND

Maize (Zea mays L.) is one of the main agricultural crops with the largest yield and acreage in the world. However, maize germplasm is very sensitive to low temperatures, mainly during germination, and low temperatures significantly affect plant growth and crop yield. Therefore, the identification of genes capable of increasing tolerance to low temperature has become necessary.

RESULTS

In this study, fourteen phenotypic traits related to seed germination were used to assess the genetic diversity of maize through genome-wide association study (GWAS). A total of 30 single-nucleotide polymorphisms (SNPs) linked to low-temperature tolerance were detected (-log10(P) > 4), fourteen candidate genes were found to be directly related to the SNPs, further additional 68 genes were identified when the screen was extended to include a linkage disequilibrium (LD) decay distance of r2 ≥ 0.2 from the SNPs. RNA-sequencing (RNA-seq) analysis was then used to confirm the linkage between the candidate gene and low-temperature tolerance. A total of ten differentially expressed genes (DEGs) (|log2 fold change (FC)| ≥ 0.585, P < 0.05) were found within the set distance of LD decay (r2 ≥ 0.2). Among these genes, the expression of six DEGs was verified using qRT-PCR. Zm00001d039219 and Zm00001d034319 were putatively involved in 'mitogen activated protein kinase (MAPK) signal transduction' and 'fatty acid metabolic process', respectively, based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Thus, these genes appeared to be related to low-temperature signal transduction and cell membrane fluidity.

CONCLUSION

Overall, by integrating the results of our GWAS and DEG analysis of low-temperature tolerance during germination in maize, we were able to identify a total of 30 SNPs and 82 related candidate genes, including 10 DEGs, two of which were involved in the response to tolerance to low temperature. Functional analysis will provide valuable information for understanding the genetic mechanism of low-temperature tolerance during germination in maize.

Molecular genetic analyses of abiotic stress responses during plant reproductive development

Plant responses to abiotic stresses during vegetative growth have been extensively studied for many years. Daily environmental fluctuations can have dramatic effects on plant vegetative growth at multiple levels, resulting in molecular, cellular, physiological, and morphological changes. Plants are even more sensitive to environmental changes during reproductive stages. However, much less is known about how plants respond to abiotic stresses during reproduction. Fortunately, recent advances in this field have begun to provide clues about these important processes, which promise further understanding and a potential contribution to maximize crop yield under adverse environments. Here we summarize information from several plants, focusing on the possible mechanisms that plants use to cope with different types of abiotic stresses during reproductive development, and present a tentative molecular portrait of plant acclimation during reproductive stages. Additionally, we discuss strategies that plants use to balance between survival and productivity, with some comparison among different plants that have adapted to distinct environments.

Identification of drought resistant miRNA in Macleaya cordata by high-throughput sequencing

Drought is one of the most serious factors affecting crop yields in the world. Macleaya cordata (Willd.) is a draught-tolerant medicinal plant that has been proposed as a pioneer crop to be cultivated in arid areas. However, the exact molecular mechanisms through which M. cordata responds to draught stress remain elusive. In recent years, microRNA (miRNAs) in plants have been associated with stress response. Based on these findings, the current study aimed to shed light on the potential regulatory roles of miRNAs in the draught tolerance of M. cordata by employing high-throughput RNA sequencing and degradation sequencing. Six M. cordata plants were randomly divided into two equal experiment groups, including one draught group and one control group. High-throughput sequencing of the M. cordata samples led to the identification of 895 miRNAs, of which 18 showed significantly different expression levels between the two groups. PsRobot analysis and degradation sequencing predicted the differential miRNAs to target 59 and 36 genes, respectively. Functional analysis showed that 38 of the predicted genes could be implicated in the modulation of stress response. Four miRNAs and eight target genes were selected for quantitative real-time polymerase chain reaction (qRT-PCR) validation. The expression trend of each miRNA analyzed by qRT-PCR was consistent with that determined by sequencing, and was negatively correlated with those of its target genes. The results of our current study supported the involvement of miRNAs in the draught tolerance of M. cordata and could pave the way for further investigation into the related regulatory mechanisms.

Comparative Proteomic and Morpho-Physiological Analyses of Maize Wild-Type Vp16 and Mutant vp16 Germinating Seed Responses to PEG-Induced Drought Stress

Drought stress is a major abiotic factor compromising plant cell physiological and molecular events, consequently limiting crop growth and productivity. Maize (Zea mays L.) is among the most drought-susceptible food crops. Therefore, understanding the mechanisms underlying drought-stress responses remains critical for crop improvement. To decipher the molecular mechanisms underpinning maize drought tolerance, here, we used a comparative morpho-physiological and proteomics analysis approach to monitor the changes in germinating seeds of two incongruent (drought-sensitive wild-type Vp16 and drought-tolerant mutant vp16) lines exposed to polyethylene-glycol-induced drought stress for seven days. Our physiological analysis showed that the tolerant line mutant vp16 exhibited better osmotic stress endurance owing to its improved reactive oxygen species scavenging competency and robust osmotic adjustment as a result of greater cell water retention and enhanced cell membrane stability. Proteomics analysis identified a total of 1200 proteins to be differentially accumulated under drought stress. These identified proteins were mainly involved in carbohydrate and energy metabolism, histone H2A-mediated epigenetic regulation, protein synthesis, signal transduction, redox homeostasis and stress-response processes; with carbon metabolism, pentose phosphate and glutathione metabolism pathways being prominent under stress conditions. Interestingly, significant congruence (R2 = 81.5%) between protein and transcript levels was observed by qRT-PCR validation experiments. Finally, we propose a hypothetical model for maize germinating-seed drought tolerance based on our key findings identified herein. Overall, our study offers insights into the overall mechanisms underpinning drought-stress tolerance and provides essential leads into further functional validation of the identified drought-responsive proteins in maize.

Cold- and menthol-evoked membrane potential changes in the moss Physcomitrella patens: influence of ion channel inhibitors and phytohormones

Microelectrode measurements carried out on leaf cells from Physcomitrella patens revealed that a sudden temperature drop and application of menthol evoked two types of different-shaped membrane potential changes. Cold stimulation evoked spike-type responses. Menthol depolarized the cell membrane with different rates. When it reached above 1 mV s^-1 , the full response was recorded. Characteristic for the full responses was also a few-minute plateau of the membrane potential recorded after depolarization. The influence of inhibitors of calcium channels (5 mM Gd³⁺ ), potassium channels (5 mM Ba²⁺ ), chloride channels (200 μM Zn²⁺ , 50 μM niflumic acid) and proton pumps (10 μM DES), an activator of calcium release from intracellular stores (Sr²⁺ ), calcium chelation (by 400 μM EGTA) and phytohormones (50 μM auxin, 50 μM abscisic acid (ABA), 500 μM salicylic acid) on cold- and menthol-evoked responses was tested. Both responses are different in respect to the ion mechanism: cold-evoked depolarizations were influenced by Ba²⁺ and DES; in turn, menthol-evoked potential changes were most effectively blocked by Zn²⁺ . Moreover, the effectiveness of menthol in generation of full responses was reduced after administration of auxin or ABA, i.e. phytohormones known for their participation in responses to cold and regulation of proton pumps. The effects of DES indicated that one of the main conditions for generation of menthol-evoked responses is inhibition of the proton pump activity. Our results indicate that perception of cold and menthol by plants proceeds in different ways due to the differences in ionic mechanism and hormone dependence of cold- and menthol-evoked responses.

Identification of Genes/Proteins Related to Submergence Tolerance by Transcriptome and Proteome Analyses in Soybean

Flooding can lead to yield reduction of soybean. Therefore, identification of flooding tolerance genes has great significance in production practice. In this study, Qihuang 34, a highly-resistant variety to flooding stress, was selected for submergence treatments. Transcriptome and proteome analyses were conducted, by which twenty-two up-regulated differentially expressed genes (DEGs)/differentially expressed proteins (DEPs) associated with five KEGG pathways were isolated. The number of the DEGs/DEPs enriched in glycolysis/gluconeogenesis was the highest. Four of these genes were confirmed by RT-qPCR, suggesting that glycolysis/gluconeogenesis may be activated to generate energy for plant survival under anaerobic conditions. Thirty-eight down-regulated DEGs/DEPs associated with six KEGG pathways were identified under submergence stress. Eight DEGs/DEPs enriched in phenylpropanoid biosynthesis were assigned to peroxidase, which catalyzes the conversion of coumaryl alcohol to hydroxy-phenyl lignin in the final step of lignin biosynthesis. Three of these genes were confirmed by RT-qPCR. The decreased expression of these genes led to the inhibition of lignin biosynthesis, which may be the cause of plant softening under submergence stress for a long period of time. This study revealed a number of up-/down-regulated pathways and the corresponding DEGs/DEPs, by which, a better understanding of the mechanisms of submergence tolerance in soybean may be achieved.

Key Maize Drought-Responsive Genes and Pathways Revealed by Comparative Transcriptome and Physiological Analyses of Contrasting Inbred Lines

To unravel the molecular mechanisms underpinning maize (Zea mays L.) drought stress tolerance, we conducted comprehensive comparative transcriptome and physiological analyses of drought-tolerant YE8112 and drought-sensitive MO17 inbred line seedlings that had been exposed to drought treatment for seven days. Resultantly, YE8112 seedlings maintained comparatively higher leaf relative water and proline contents, greatly increased peroxidase activity, but decreased malondialdehyde content, than MO17 seedlings. Using an RNA sequencing (RNA-seq)-based approach, we identified a total of 10,612 differentially expressed genes (DEGs). From these, we mined out four critical sets of drought responsive DEGs, including 80 specific to YE8112, 5140 shared between the two lines after drought treatment (SD_TD), five DEGs of YE8112 also regulated in SD_TD, and four overlapping DEGs between the two lines. Drought-stressed YE8112 DEGs were primarily associated with nitrogen metabolism and amino-acid biosynthesis pathways, whereas MO17 DEGs were enriched in the ribosome pathway. Additionally, our physiological analyses results were consistent with the predicted RNA-seq-based findings. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) analysis and the RNA-seq results of twenty representative DEGs were highly correlated (R² = 98.86%). Crucially, tolerant line YE8112 drought-responsive genes were predominantly implicated in stress signal transduction; cellular redox homeostasis maintenance; MYB, NAC, WRKY, and PLATZ transcriptional factor modulated; carbohydrate synthesis and cell-wall remodeling; amino acid biosynthesis; and protein ubiquitination processes. Our findings offer insights into the molecular networks mediating maize drought stress tolerance.

Transcriptomic analysis of grain filling in rice inferior grains under moderate soil drying

Moderate soil drying imposed at the post-anthesis stage significantly increases starch accumulation in inferior grains of rice, but how this process is regulated at the level of gene expression remains unclear. In this study, we applied moderate drying (MD) treatments to the soil at the post-anthesis stage and followed the dynamics of the conversion process of soluble sugars to starch in inferior grains using RNA-seq analysis. An elevated level of ABA induced by MD was consistently associated with down-regulation of ABA8ox2, suggesting that lower expression of this gene may be responsible for the higher ABA content, potentially resulting in better filling in inferior grains. In addition, MD treatments up-regulated genes encoding five key enzymes involved sucrose-to-starch conversion and increased the activities of enzymes responsible for soluble-sugar reduction and starch accumulation in inferior grains. Differentially expressed transcription factors, including NAC, GATA, WRKY, and M-type MADS, were predicted to interact with other proteins in mediating filling of inferior grains as a response to MD. Transient expression analysis showed that NAC activated WAXY expression by binding to its promoter, indicating that NAC played a key role in starch synthesis of inferior grains under MD treatment. Our results provide new insights into the molecular mechanisms that regulate grain filling in inferior grains of rice under moderate soil drying.

Global Phosphoproteomic Analysis Reveals the Defense and Response Mechanisms of Jatropha Curcas Seedling under Chilling Stress

As a promising energy plant for biodiesel, Jatropha curcas is a tropical and subtropical shrub and its growth is affected by one of major abiotic stress, chilling. Therefore, we adopt the phosphoproteomic analysis, physiological measurement and ultrastructure observation to illustrate the responsive mechanism of J. curcas seedling under chilling (4 °C) stress. After chilling for 6 h, 308 significantly changed phosphoproteins were detected. Prolonged the chilling treatment for 24 h, obvious physiological injury can be observed and a total of 332 phosphoproteins were examined to be significantly changed. After recovery (28 °C) for 24 h, 291 phosphoproteins were varied at the phosphorylation level. GO analysis showed that significantly changed phosphoproteins were mainly responsible for cellular protein modification process, transport, cellular component organization and signal transduction at the chilling and recovery periods. On the basis of protein-protein interaction network analysis, phosphorylation of several protein kinases, such as SnRK2, MEKK1, EDR1, CDPK, EIN2, EIN4, PI4K and 14-3-3 were possibly responsible for cross-talk between ABA, Ca²⁺, ethylene and phosphoinositide mediated signaling pathways. We also highlighted the phosphorylation of HOS1, APX and PIP2 might be associated with response to chilling stress in J. curcas seedling. These results will be valuable for further study from the molecular breeding perspective.

Gene expression profiles of Pyropia yezoensis in response to dehydration and rehydration stresses

Pyropia yezoensis is an economically important marine macroalgae, naturally distributed in the upper intertidal zone. Owing to the nature of its habitat, the thallus will periodically be exposed to seawater or atmosphere, and can lose up to 95% of its cellular water content. This makes the alga an ideal research model to investigate the mechanisms of desiccation tolerance. In this study, we investigated the response mechanisms to dehydration and rehydration stresses at the transcription level in Pyropia yezoensis. The differently expressed genes were analyzed based on the different functions of encoding proteins: effector proteins (chloroplast proteins, macromolecular protective substances, and toxicity degradation enzymes) and regulatory proteins (protein kinases and phosphatases). Under osmotic stress, the unigenes related to photosynthesis were down-regulated significantly while those encoding glutathione transferase, superoxide dismutase and heat shock proteins were up-regulated significantly. We inferred that the photosynthetic activity was reduced to prevent damage caused by photosynthetic by-products and that the expression of antioxidant enzyme was increased to prevent the damage associated with reactive oxygen species. Additionally, unigenes encoding serine/threonine kinases and phospholipases were up-regulated in response to osmotic stress, indicating that these kinases play an important role in osmotolerance. Our work will serve as an essential foundation for the understanding of desiccation tolerance mechanisms in Pyropia yezoensis in the upper intertidal zones of rocky coasts.

Sequencing, Characterization, and Comparative Analyses of the Plastome of Caragana rosea var. rosea

To exploit the drought-resistant Caragana species, we performed a comparative study of the plastomes from four species: Caragana rosea, C. microphylla, C. kozlowii, and C. Korshinskii. The complete plastome sequence of the C. rosea was obtained using the next generation DNA sequencing technology. The genome is a circular structure of 133,122 bases and it lacks inverted repeat. It contains 111 unique genes, including 76 protein-coding, 30 tRNA, and four rRNA genes. Repeat analyses obtained 239, 244, 258, and 246 simple sequence repeats in C. rosea, C. microphylla, C. kozlowii, and C. korshinskii, respectively. Analyses of sequence divergence found two intergenic regions: trnI-CAU-ycf2 and trnN-GUU-ycf1, exhibiting a high degree of variations. Phylogenetic analyses showed that the four Caragana species belong to a monophyletic clade. Analyses of Ka/Ks ratios revealed that five genes: rpl16, rpl20, rps11, rps7, and ycf1 and several sites having undergone strong positive selection in the Caragana branch. The results lay the foundation for the development of molecular markers and the understanding of the evolutionary process for drought-resistant characteristics.

Transcriptomic analysis reveals the differentially expressed genes and pathways involved in drought tolerance in pearl millet [Pennisetum glaucum (L.) R. Br]

Pearl millet is a cereal crop known for its high tolerance to drought, heat and salinity stresses as well as for its nutritional quality. The molecular mechanism of drought tolerance in pearl millet is unknown. Here we attempted to unravel the molecular basis of drought tolerance in two pearl millet inbred lines, ICMB 843 and ICMB 863 using RNA sequencing. Under greenhouse condition, ICMB 843 was found to be more tolerant to drought than ICMB 863. We sequenced the root transcriptome from both lines under control and drought conditions using an Illumina Hi-Seq platform, generating 139.1 million reads. Mapping of sequenced reads against the foxtail millet genome, which has been relatively well-annotated, led to the identification of several differentially expressed genes under drought stress. Total of 6799 and 1253 differentially expressed genes were found in ICMB 843 and ICMB 863, respectively. Pathway and gene function analysis by KEGG online tool revealed that the drought response in pearl millet is mainly regulated by pathways related to photosynthesis, plant hormone signal transduction and mitogen-activated protein kinase signaling. The changes in expression of drought-responsive genes determined by RNA sequencing were confirmed by reverse-transcription PCR for 7 genes. These results are a first step to understanding the molecular mechanisms of drought tolerance in pearl millet and lay a foundation for its genetic improvement.

Epigenetic map and genetic map basis of complex traits in cassava population

Cassava (Manihot esculenta Crantz) is an important tropical starchy root crop that is adapted to drought but extremely cold sensitive. A cold-tolerant, high-quality, and robust supply of cassava is urgently needed. Here, we clarify genome-wide distribution and classification of CCGG hemi-methylation and full-methylation, and detected 77 much candidate QTLs^epi for cold stress and 103 much candidate QTLs^epi for storage root quality and yield in 186 cassava population, generated by crossing two non-inbred lines with female parent KU50 and male parent SC124 (KS population). We developed amplified-fragment single nucleotide polymorphism and methylation (AFSM) genetic map in this population. We also constructed the AFSM QTL map, identified 260 much candidate QTL genes for cold stress and 301 much candidate QTL genes for storage root quality and yield, based on the years greenhouse and field trials. This may accounted for a significant amount of the variation in the key traits controlling cold tolerance and the high quality and yield of cassava.

Robust Anti-Icing Performance of a Flexible Superhydrophobic Surface

A material with superhydrophobic and anti-ice/de-icing properties, which has a micro-/nanostructured surface, is produced by a straightforward method. This material comprises a poly(dimethylsiloxane) (PDMS) microstructure with ZnO nanohairs and shows excellent water and ice repellency even at low temperatures (-20 °C) and relatively high humidity (90%) for over three months. These results are expected to be helpful for designing smart, non-wetting materials that can be adapted to low-temperature environments for the development of anti-icing systems.

RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in Maize

The mitogen-activated protein kinase (MAPK) cascade is an evolutionarily conserved signal transduction pathway that is involved in plant development and stress responses. As the first component of this phosphorelay cascade, mitogen-activated protein kinase kinase kinases (MAPKKKs) act as adaptors linking upstream signaling steps to the core MAPK cascade to promote the appropriate cellular responses; however, the functions of MAPKKKs in maize are unclear. Here, we identified 71 MAPKKK genes, of which 14 were novel, based on a computational analysis of the maize (Zea mays L.) genome. Using an RNA-seq analysis in the leaf, stem and root of maize under well-watered and drought-stress conditions, we identified 5,866 differentially expressed genes (DEGs), including 8 MAPKKK genes responsive to drought stress. Many of the DEGs were enriched in processes such as drought stress, abiotic stimulus, oxidation-reduction, and metabolic processes. The other way round, DEGs involved in processes such as oxidation, photosynthesis, and starch, proline, ethylene, and salicylic acid metabolism were clearly co-expressed with the MAPKKK genes. Furthermore, a quantitative real-time PCR (qRT-PCR) analysis was performed to assess the relative expression levels of MAPKKKs. Correlation analysis revealed that there was a significant correlation between expression levels of two MAPKKKs and relative biomass responsive to drought in 8 inbred lines. Our results indicate that MAPKKKs may have important regulatory functions in drought tolerance in maize.

Early transcriptional changes in Beta vulgaris in response to low temperature

Major metabolic pathways and genes affected by low-temperature treatment were identified and a thorough picture of the early transcriptional changes in sugar beet plantlets upon cold stress was given. Sugar beet (Beta vulgaris L.) is an important source of sugar and bioethanol production in temperate areas worldwide. In these areas, plantlet survival and sucrose yield of mature plants can be seriously limited by low temperatures, especially when plantlets are exposed to freezing temperatures (below 0 °C) at the early developmental stages. This frequently occurs when the crop is sown in early spring or even in autumn (autumn sowing) to escape drought at maturity and pathogen outbreaks. The knowledge of molecular responses induced in plantlets early upon exposure to low temperature is necessary to understand mechanisms that allow the plant to survive and to identify reactions that can influence other late-appearing traits. In this work, a wide study of sugar beet transcriptome modulation after a short exposure to a cold stress, mimicking what is experienced in vivo by young plantlets when temperature drops in the early spring nights, was carried out by high-throughput sequencing of leaves and root RNAs (RNA-Seq). A significant picture of the earliest events of temperature sensing was achieved for the first time for sugar beet: the retrieval of a great amount of transcription factors and the intensity of modulation of a large number of genes involved in several metabolic pathways suggest a fast and deep rearrangement of sugar beet plantlets metabolism as early response to cold stress, with both similarities and specificities between the two organs.

Winter cold-tolerance thresholds in field-grown Miscanthus hybrid rhizomes

The cold tolerance of winter-dormant rhizomes was evaluated in diploid, allotriploid, and allotetraploid hybrids of Miscanthus sinensis and Miscanthus sacchariflorus grown in a field setting. Two artificial freezing protocols were tested: one lowered the temperature continuously by 1°C h(-1) to the treatment temperature and another lowered the temperature in stages of 24h each to the treatment temperature. Electrolyte leakage and rhizome sprouting assays after the cold treatment assessed plant and tissue viability. Results from the continuous-cooling trial showed that Miscanthus rhizomes from all genotypes tolerated temperatures as low as -6.5 °C; however, the slower, staged-cooling procedure enabled rhizomes from two diploid lines to survive temperatures as low as -14 °C. Allopolyploid genotypes showed no change in the lethal temperature threshold between the continuous and staged-cooling procedure, indicating that they have little ability to acclimate to subzero temperatures. The results demonstrated that rhizomes from diploid Miscanthus lines have superior cold tolerance that could be exploited to improve performance in more productive polyploid lines. With expected levels of soil insulation, low winter air temperatures should not harm rhizomes of tolerant diploid genotypes of Miscanthus in temperate to sub-boreal climates (up to 60°N); however, the observed winter cold in sub-boreal climates could harm rhizomes of existing polyploid varieties of Miscanthus and thus reduce stand performance.

Mitogen-Activated Protein Kinase 6 and Ethylene and Auxin Signaling Pathways Are Involved in Arabidopsis Root-System Architecture Alterations by Trichoderma atroviride

Trichoderma atroviride is a symbiotic fungus that interacts with roots and stimulates plant growth and defense. Here, we show that Arabidopsis seedlings cocultivated with T. atroviride have an altered root architecture and greater biomass compared with axenically grown seedlings. These effects correlate with increased activity of mitogen-activated protein kinase 6 (MPK6). The primary roots of mpk6 mutants showed an enhanced growth inhibition by T. atroviride when compared with wild-type (WT) plants, while T. atroviride increases MPK6 activity in WT roots. It was also found that T. atroviride produces ethylene (ET), which increases with l-methionine supply to the fungal growth medium. Analysis of growth and development of WT seedlings and etr1, ein2, and ein3 ET-related Arabidopsis mutants indicates a role for ET in root responses to the fungus, since etr1 and ein2 mutants show defective root-hair induction and enhanced primary-root growth inhibition when cocultivated with T. atroviride. Increased MPK6 activity was evidenced in roots of ctr1 mutants, which correlated with repression of primary root growth, thus connecting MPK6 signaling with an ET response pathway. Auxin-inducible gene expression analysis using the DR5:uidA reporter construct further revealed that ET affects auxin signaling through the central regulator CTR1 and that fungal-derived compounds, such as indole-3-acetic acid and indole-3-acetaldehyde, induce MPK6 activity. Our results suggest that T. atroviride likely alters root-system architecture modulating MPK6 activity and ET and auxin action.

Osmotin: a plant sentinel and a possible agonist of mammalian adiponectin

Osmotin is a stress responsive antifungal protein belonging to the pathogenesis-related (PR)-5 family that confers tolerance to both biotic and abiotic stresses in plants. Protective efforts of osmotin in plants range from high temperature to cold and salt to drought. It lyses the plasma membrane of the pathogens. It is widely distributed in fruits and vegetables. It is a differentially expressed and developmentally regulated protein that protects the cells from osmotic stress and invading pathogens as well, by structural or metabolic alterations. During stress conditions, osmotin helps in the accumulation of the osmolyte proline, which quenches reactive oxygen species and free radicals. Osmotin expression results in the accumulation of storage reserves and increases the shelf-life of fruits. It binds to a seven-transmembrane-domain receptor-like protein and induces programmed cell death in Saccharomyces cerevisiae through RAS2/cAMP signaling pathway. Adiponectin, produced in adipose tissues of mammals, is an insulin-sensitizing hormone. Strangely, osmotin acts like the mammalian hormone adiponectin in various in vitro and in vivo models. Adiponectin and osmotin, the two receptor binding proteins do not share sequence similarity at the amino acid level, but interestingly they have a similar structural and functional properties. In experimental mice, adiponectin inhibits endothelial cell proliferation and migration, primary tumor growth, and reduces atherosclerosis. This retrospective work examines the vital role of osmotin in plant defense and as a potential targeted therapeutic drug for humans.

Quantification of stress-induced mitogen-activated protein kinase expressional dynamic using reverse transcription quantitative real-time PCR

Although it is generally accepted that signal transduction in plant mitogen-activated protein kinase signaling cascades is regulated via rapid posttranslational modifications, there are also several compelling examples of swift stress induced transcriptional activation of plant MAP kinase genes. A possible function of these fast and transient events is to compensate for protein losses caused by degradation of phosphorylated MAP kinases within stimulated pathways. Nevertheless, there is still need for additional evidence to precisely describe the regulatory role of plant MAP kinase transcriptional dynamics, especially in the context of whole stress stimulated pathways including also other signaling molecules and transcription factors. During the last two decades a reverse transcription quantitative real-time PCR became a golden choice for the accurate and fast quantification of the gene expression and gene expression dynamic. In here, we provide a robust, cost-effective SYBR Green-based RT-qPCR protocol that is suitable for the quantification of stress induced plant MAP kinase transcriptional dynamics in various plant species.

Transcriptome comparison reveals the patterns of selection in domesticated and wild ramie (Boehmeria nivea L. Gaud)

Ramie is an old fiber crop, cultivated for thousands of years in China. The cultivar ramie evolved from the wild species Qingyezhuma (QYZM, Boehmeria nivea var. tenacissima). However, the mechanism of domestication of this old fiber crop is poorly understood. In order to characterize the selective pattern in ramie domestication, orthologous genes between the transcriptomes of domesticated ramie variety Zhongzhu 1 (ZZ1) and wild QYZM were assessed using bidirectional best-hit method and ratio of non-synonymous (Ka) to synonymous (Ks) nucleotide substitutions was estimated. Sequence comparison of 56,932 and 59,246 unigenes from the wild QYZM and domesticated ZZ1, respectively, helped identify 10,745 orthologous unigene pairs with a total orthologous length of 10.18 Mb. Among these unigenes, 85 and 13 genes were found to undergo significant purifying and positive selection, respectively. Most of the selected genes were homologs of those involved in abiotic stress tolerance or disease resistance in other plants, suggesting that abiotic and biotic stresses were important selective pressures in ramie domestication. Two genes probably related to the fiber yield of ramie were subjected to positive selection, which may be caused by human manipulation. Thus, our results show the pervasive effects of artificial and natural selections on the accelerated domestication of ramie from its wild relative.

Linkage of cold acclimation and disease resistance through plant-pathogen interaction pathway in Vitis amurensis grapevine

Low temperatures cause severe damage to none cold hardy grapevines. A preliminary survey with Solexa sequencing technology was used to analyze gene expression profiles of cold hardy Vitis amurensis 'Zuoshan-1' after cold acclimation at 4 °C for 48 h. A total of 16,750 and 18,068 putative genes were annotated for 4 °C-treated and control library, respectively. Among them, 393 genes were upregulated for at least 20-fold, while 69 genes were downregulated for at least 20-fold under the 4 °C treatment for 48 h. A subset of 101 genes from this survey was investigated further using reverse transcription polymerase chain reaction (RT-PCR). Genes associated with signaling events in pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI), including generation of calcium signals (CNGC, CMLs), jasmonic acid signal (JAZ1), oxidative burst (Rboh), and phosphorylation (FLS2, BAK, MEKK1, MKKs) cascades, were upregulated after cold acclimation. Disease resistance genes (RPM1, RPS5, RIN4, PBS1) in the process of effector-triggered immunity (ETI) were also upregulated in the current condition. Defense-related genes (WRKYs, PR1, MIN7) involved in both PTI and ETI processes were abundantly expressed after cold acclimation. Our results indicated that plant-pathogen interaction pathways were linked to the cold acclimation in V. amurensis grapevine. Other biotic- and abiotic-related genes, such as defense (protein phosphatase 2C, U-box domain proteins, NCED1, stilbene synthase), transcription (DREBs, MYBs, ERFs, ZFPs), signal transduction (kinase, calcium, and auxin signaling), transport (ATP-binding cassette (ABC) transporters, auxin:hydrogen symporter), and various metabolism, were also abundantly expressed in the cold acclimation of V. Amurensis 'Zuoshan-1' grapevine. This study revealed a series of critical genes and pathways to delineate important biological processes affected by low temperature in 'Zuoshan-1'.

MAPK cascades and major abiotic stresses

Plants have evolved with complex signaling circuits that operate under multiple conditions and govern numerous cellular functions. Stress signaling in plant cells is a sophisticated network composed of interacting proteins organized into tiered cascades where the function of a molecule is dependent on the interaction and the activation of another. In a linear scheme, the receptors of cell surface sense the stimuli and convey stress signals through specific pathways and downstream phosphorylation events controlled by mitogen-activated protein (MAP) kinases and second messengers, leading to appropriate adaptive responses. The specificity of the pathway is guided by scaffolding proteins and docking domains inside the interacting partners with distinctive structures and functions. The flexibility and the fine-tuned organization of the signaling molecules drive the activated MAP kinases into the appropriate location and connection to control and integrate the information flow. Here, we overview recent findings of the involvement of MAP kinases in major abiotic stresses (drought, cold and temperature fluctuations) and we shed light on the complexity and the specificity of MAP kinase signaling modules.

Giving drought the cold shoulder: a relationship between drought tolerance and fall dormancy in an agriculturally important crop

The growth of fall dormant/freezing tolerant plants often surpasses the growth of non-fall dormant/non-freezing tolerant types of the same species under water-limited conditions, while under irrigated conditions non-fall dormant types exhibit superior yield performance. To investigate the mechanism behind this phenomenon, we exposed seven diverse alfalfa (Medicago sativa) cultivars to water-limited and fully watered conditions and measured their shoot growth, shoot water potential and gas exchange parameters and the relative abundance of taproot RNA transcripts associated with chilling stress/freezing tolerance. Fall dormant cultivars had greater shoot growth relative to the fully watered controls under a mild water deficit (a cumulative water deficit of 625 mL pot(-1)) and did not close their stomata until lower shoot water potentials compared with the more non-fall dormant cultivars. Several gene transcripts previously associated with freezing tolerance increased in abundance when plants were exposed to a mild water deficit. Two transcripts, corF (encodes galactinol synthase) and cas18 (encodes a dehydrin-like protein), increased in abundance in fall dormant cultivars only. Once water deficit stress became severe (a cumulative water deficit of 2530 mL pot(-1)), the difference between fall dormancy groups disappeared with the exception of the expression of a type 1 sucrose synthase gene, which decreased in fall dormant cultivars. The specific adaptation of fall dormant cultivars to mild water deficit conditions and the increase in abundance of specific genes typically associated with freezing tolerance in these cultivars is further evidence of a link between freezing tolerance/fall dormancy and adaption to drought conditions in this species.

Analysis of differentially expressed genes in abiotic stress response and their role in signal transduction pathways

The study of abiotic stress response of plants is important because they have to cope with environmental changes to survive. The plant genomes have evolved to meet environmental challenges. Salt, temperature, and drought are the main abiotic stresses. The tolerance and response to stress vary differently in plants. The idea was to analyze the genes showing differential expression under abiotic stresses. There are many pathways connecting the perception of external stimuli to cellular responses. In plants, these pathways play an important role in the transduction of abiotic stresses. In the present study, the gene expression data have been analyzed for their involvement in different steps of signaling pathways. The conserved genes were analyzed for their role in each pathway. The functional annotations of these genes and their response under abiotic stresses in other plant species were also studied. The enzymes of signal pathways, showing similarity with conserved genes, were analyzed for their role in different abiotic stresses. Our findings will help to understand the expression of genes in response to various abiotic stresses. These genes may be used to study the response of different abiotic stresses in other plant species and the molecular basis of stress tolerance.

Increased resistance against citrus canker mediated by a citrus mitogen-activated protein kinase

Mitogen-activated protein kinases (MAPK) play crucial roles in plant immunity. We previously identified a citrus MAPK (CsMAPK1) as a differentially expressed protein in response to infection by Xanthomonas aurantifolii, a bacterium that causes citrus canker in Mexican lime but a hypersensitive reaction in sweet oranges. Here, we confirm that, in sweet orange, CsMAPK1 is rapidly and preferentially induced by X. aurantifolii relative to Xanthomonas citri. To investigate the role of CsMAPK1 in citrus canker resistance, we expressed CsMAPK1 in citrus plants under the control of the PR5 gene promoter, which is induced by Xanthomonas infection and wounding. Increased expression of CsMAPK1 correlated with a reduction in canker symptoms and a decrease in bacterial growth. Canker lesions in plants with higher CsMAPK1 levels were smaller and showed fewer signs of epidermal rupture. Transgenic plants also revealed higher transcript levels of defense-related genes and a significant accumulation of hydrogen peroxide in response to wounding or X. citri infection. Accordingly, nontransgenic sweet orange leaves accumulate both CsMAPK1 and hydrogen peroxide in response to X. aurantifolii but not X. citri infection. These data, thus, indicate that CsMAPK1 functions in the citrus canker defense response by inducing defense gene expression and reactive oxygen species accumulation during infection.

Effect of salicylic acid on the attenuation of aluminum toxicity in Coffea arabica L. suspension cells: A possible protein phosphorylation signaling pathway

The protective effect of salicylic acid (SA) on aluminum (Al) toxicity was studied in suspension cells of Coffea arabica L. The results showed that SA does not produce any effect on cell growth and that the growth inhibition produced by aluminum is restored during simultaneous treatment of the cells with Al and SA. In addition, the cells exposed to both compounds, Al and SA, showed evident morphological signals of recovery from the toxic state produced in the presence of Al. The cells treated with SA showed a lower accumulation of Al, which was linked to restoration from Al toxicity because the concentration of Al(3+) outside the cells, measured as the Al(3+)-morin complex, was not modified by the presence of SA. Additionally, the inhibition of phospholipase C by Al treatment was restored during the exposure of the cells to SA and Al. The involvement of protein phosphorylation in the protective effect of SA on Al-toxicity was suggested because staurosporine, a protein kinase inhibitor, reverted the stimulatory effect of the combination of Al and SA on protein kinase activity. These results suggest that SA attenuates aluminum toxicity by affecting a signaling pathway linked to protein phosphorylation.

Cotton GhMKK1 induces the tolerance of salt and drought stress, and mediates defence responses to pathogen infection in transgenic Nicotiana benthamiana

Mitogen-activated protein kinase kinases (MAPKK) mediate a variety of stress responses in plants. So far little is known on the functional role of MAPKKs in cotton. In the present study, Gossypium hirsutum MKK1 (GhMKK1) function was investigated. GhMKK1 protein may activate its specific targets in both the nucleus and cytoplasm. Treatments with salt, drought, and H2O2 induced the expression of GhMKK1 and increased the activity of GhMKK1, while overexpression of GhMKK1 in Nicotiana benthamiana enhanced its tolerance to salt and drought stresses as determined by many physiological data. Additionally, GhMKK1 activity was found to up-regulate pathogen-associated biotic stress, and overexpression of GhMKK1 increased the susceptibility of the transgenic plants to the pathogen Ralstonia solanacearum by reducing the expression of PR genes. Moreover, GhMKK1-overexpressing plants also exhibited an enhanced reactive oxygen species scavenging capability and markedly elevated activities of several antioxidant enzymes. These results indicate that GhMKK1 is involved in plants defence responses and provide new data to further analyze the function of plant MAPK pathways.

Cloning, in silico characterization and induction of TiKpp2 MAP kinase in Tilletia indica under the influence of host factor(s) from wheat spikes

In order to understand the molecular mechanism(s) associated with floret specificity, morphogenetic and disease development of Karnal bunt (KB) pathogen in wheat spikes, host factor(s) was isolated from KB prone susceptible stage of wheat spikes. An orthologue of Kpp2 gene involved in pheromone response and fungal development was isolated from Tilletia indica for analyzing its role in fungal development. The maximum expression of TiKpp2 gene was observed at 14th day and decreased thereafter. To investigate whether the fungus alters the expression levels of same kinase upon interaction with plants, T. indica cultures were treated with 1% of host factor(s). Such treatment induced the expression of TiKpp2 gene in time dependent manner. Host factor(s) treatment tends to increase the myelination in fungal cultures by lowering the sporidial production. Increase in myelination led to impose more pathogenicity levels in the host and prolific multiplication of pathogen inside host causing more damage to developing grains. In silico characterization and protein-protein interaction studies further suggests that isolated gene showed similarity with Ustilago maydis Kpp2 and induction of TiKpp2 might further activate a downstream transcription factor Prf1. The results of present study clearly suggest that host factor(s) derived from wheat spikes provide certain signal(s) which activate TiKpp2 gene during morphogenetic development of T. indica and affect the fungal growth and pathogenicity. In turn it also provides a plausible explanation for floret specificity of KB fungus in wheat.

Identification of Lens culinaris defense genes responsive to the anthracnose pathogen Colletotrichum truncatum

Background

Anthracnose of lentil, caused by the hemibiotrophic fungal pathogen Colletotrichum truncatum is a serious threat to lentil production in western Canada. Colletotrichum truncatum employs a bi-phasic infection strategy characterized by initial symptomless biotrophic and subsequent destructive necrotrophic colonization of its host. The transition from biotrophy to necrotrophy (known as the biotrophy-necrotrophy switch [BNS]) is critical in anthracnose development. Understanding plant responses during the BNS is the key to designing a strategy for incorporating resistance against hemibiotrophic pathogens either via introgression of resistance genes or quantitative trait loci contributing to host defense into elite cultivars, or via incorporation of resistance by biotechnological means.

Results

The in planta BNS of C. truncatum was determined by histochemical analysis of infected lentil leaf tissues in time-course experiments. A total of 2852 lentil expressed sequence tags (ESTs) derived from C. truncatum-infected leaf tissues were analyzed to catalogue defense related genes. These ESTs could be assembled into 1682 unigenes. Of these, 101 unigenes encoded membrane and transport associated proteins, 159 encoded proteins implicated in signal transduction and 387 were predicted to be stress and defense related proteins (GenBank accessions: JG293480 to JG293479). The most abundant class of defense related proteins contained pathogenesis related proteins (encoded by 125 ESTs) followed by heat shock proteins, glutathione S-transferase, protein kinases, protein phosphatase, zinc finger proteins, peroxidase, GTP binding proteins, resistance proteins and syringolide-induced proteins. Quantitative RT-PCR was conducted to compare the expression of two resistance genes of the NBS-LRR class in susceptible and partially resistant genotypes. One (contig186) was induced 6 days post-inoculation (dpi) in a susceptible host genotype (Eston) whereas the mRNA level of another ( LT21-1990) peaked 4 dpi in a partially resistant host genotype (Robin), suggesting roles in conditioning the susceptibility and conferring tolerance to the pathogen, respectively.

Conclusions

Data obtained in this study suggest that lentil cells recognize C. truncatum at the BNS and in response, mount an inducible defense as evident by a high number of transcripts (23% of the total pathogen-responsive lentil transcriptome) encoding defense related proteins. Temporal expression polymorphism of defense related genes could be used to distinguish the response of a lentil genotype as susceptible or resistant.

Physiological and molecular features of Puccinellia tenuiflora tolerating salt and alkaline-salt stress

Saline-alkali soil seriously threatens agriculture productivity; therefore, understanding the mechanism of plant tolerance to alkaline-salt stress has become a major challenge. Halophytic Puccinellia tenuiflora can tolerate salt and alkaline-salt stress, and is thus an ideal plant for studying this tolerance mechanism. In this study, we examined the salt and alkaline-salt stress tolerance of P. tenuiflora, and analyzed gene expression profiles under these stresses. Physiological experiments revealed that P. tenuiflora can grow normally with maximum stress under 600 mmol/L NaCl and 150 mmol/L Na2 CO3 (pH 11.0) for 6 d. We identified 4,982 unigenes closely homologous to rice and barley. Furthermore, 1,105 genes showed differentially expressed profiles under salt and alkaline-salt treatments. Differentially expressed genes were overrepresented in functions of photosynthesis, oxidation reduction, signal transduction, and transcription regulation. Almost all genes downregulated under salt and alkaline-salt stress were related to cell structure, photosynthesis, and protein synthesis. Comparing with salt stress, alkaline-salt stress triggered more differentially expressed genes and significantly upregulated genes related to H(+) transport and citric acid synthesis. These data indicate common and diverse features of salt and alkaline-salt stress tolerance, and give novel insights into the molecular and physiological mechanisms of plant salt and alkaline-salt tolerance.

Cloning and evolutionary analysis of tobacco MAPK gene family

The mitogen-activated protein (MAP) kinase cascade is an important signaling module which is involved in biotic and abiotic stress responses as well as plant growth and development. In this study, we identified 17 tobacco MAPKs including 11 novel tobacco MAPK genes that have not been identified before. Comparative analysis with MAPK gene families from other plants, such as Athaliana thaliana, rice and poplar, suggested that tobacco MAPKs (such as NtMPK1, NtMPK3 and NtMPK8) might play similar functions in response to abiotic and biotic stresses. QRT-PCR analysis revealed that a total of 14 NtMPKs were regulated by SA and/or MeJA, suggesting their potential roles involved in plant defense response. In addition, 6 NtMPKs were induced by drought treatment, implying their roles in response to drought stress. Our results indicated that most of tobacco MAPK might be involved in plant defense response, which provides the basis for further analysis on physiological functions of tobacco MAPKs.

Rapid phosphatidic acid accumulation in response to low temperature stress in Arabidopsis is generated through diacylglycerol kinase

Phosphatidic acid (PtdOH) is emerging as an important signaling lipid in abiotic stress responses in plants. The effect of cold stress was monitored using (32)P-labeled seedlings and leaf discs of Arabidopsis thaliana. Low, non-freezing temperatures were found to trigger a very rapid (32)P-PtdOH increase, peaking within 2 and 5 min, respectively. In principle, PtdOH can be generated through three different pathways, i.e., (1) via de novo phospholipid biosynthesis (through acylation of lyso-PtdOH), (2) via phospholipase D hydrolysis of structural phospholipids, or (3) via phosphorylation of diacylglycerol (DAG) by DAG kinase (DGK). Using a differential (32)P-labeling protocol and a PLD-transphosphatidylation assay, evidence is provided that the rapid (32)P-PtdOH response was primarily generated through DGK. A simultaneous decrease in the levels of (32)P-PtdInsP, correlating in time, temperature dependency, and magnitude with the increase in (32)P-PtdOH, suggested that a PtdInsP-hydrolyzing PLC generated the DAG in this reaction. Testing T-DNA insertion lines available for the seven DGK genes, revealed no clear changes in (32)P-PtdOH responses, suggesting functional redundancy. Similarly, known cold-stress mutants were analyzed to investigate whether the PtdOH response acted downstream of the respective gene products. The hos1, los1, and fry1 mutants were found to exhibit normal PtdOH responses. Slight changes were found for ice1, snow1, and the overexpression line Super-ICE1, however, this was not cold-specific and likely due to pleiotropic effects. A tentative model illustrating direct cold effects on phospholipid metabolism is presented.

OsWRKY30 is activated by MAP kinases to confer drought tolerance in rice

Both the WRKY transcription factor (TF) and MAP kinases have been shown to regulate gene expression in response to biotic and abiotic stresses in plants. Several reports have shown that WRKY TFs may function downstream of MAPK cascades. Here, we have shown that OsWRKY30 interacted with OsMPK3, OsMPK4, OsMPK7, OsMPK14, OsMPK20-4, and OsMPK20-5, and could be phosphorylated by OsMPK3, OsMPK7, and OsMPK14. Overexpression of OsWRKY30 in rice dramatically increased drought tolerance. Overexpression of OsWRKY30AA, in which all SP (serine residue followed by proline residue) sites were replaced by AP (A, alanine), resulted in no improvement in drought tolerance. In addition, the function of transcriptional activation of OsWRKY30 was impaired after SP was replaced by AP. These results proved that the phosphorylation of OsWRKY30 by MAPKs was crucial in order for OsWRKY30 to perform its biological function.