Over-expression of a single Ca2+-dependent protein kinase confers both cold and salt/drought tolerance on rice plants

Comparative transcriptomic analysis reveals the cold acclimation during chilling stress in sensitive and resistant passion fruit (Passiflora edulis) cultivars

Chilling stress (CS) is an important limiting factor for the growth and development of passion fruit (Passiflora edulis) in winter in South China. However, little is known about how the passion fruit responds and adapts to CS. In this study, we performed transcriptome sequencing of cold-susceptible cultivar Huangjinguo (HJG) and cold-tolerant cultivar Tainong 1 (TN1) under normal temperature (NT) and CS conditions, and a total of 47,353 unigenes were obtained by seven databases. Using differentially expressed unigenes (DEGs) analysis, 3,248 and 4,340 DEGs were identified at two stages, respectively. The Gene Ontology (GO) enrichment analysis showed that the DEGs were mainly related to phosphorylation, membrane protein, and catalytic activity. In Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the unigenes of plant-pathogen interaction, plant hormone signal transduction and fatty acid metabolism were enriched. Then, the 12,471 filtered unigenes were clustered into eight co-expression modules, and two modules were correlated with CS. In this two modules, 32 hub unigenes were obtained. Furthermore, the unigenes related to CS were validated using quantitative real-time PCR (RT-qPCR). This work showed that the expression levels of CS-related unigenes were very different in two passion fruit cultivars. The results provide information for the development of passion fruit with increased chilling tolerance.

Advances in Sensing, Response and Regulation Mechanism of Salt Tolerance in Rice

Soil salinity is a serious menace in rice production threatening global food security. Rice responses to salt stress involve a series of biological processes, including antioxidation, osmoregulation or osmoprotection, and ion homeostasis, which are regulated by different genes. Understanding these adaptive mechanisms and the key genes involved are crucial in developing highly salt-tolerant cultivars. In this review, we discuss the molecular mechanisms of salt tolerance in rice—from sensing to transcriptional regulation of key genes—based on the current knowledge. Furthermore, we highlight the functionally validated salt-responsive genes in rice.

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

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

Champions of winter survival: cold acclimation and molecular regulation of cold hardiness in evergreen conifers

Evergreen conifers are champions of winter survival, based on their remarkable ability to acclimate to cold and develop cold hardiness. Counterintuitively, autumn cold acclimation is triggered not only by exposure to low temperature, but also by a combination of decreasing temperature, decreasing photoperiod and changes in light quality. These environmental cues control a network of signaling pathways that coordinate cold acclimation and cold hardiness in overwintering conifers, leading to cessation of growth, bud dormancy, freezing tolerance and changes in energy metabolism. Advances in genomic, transcriptomic and metabolomic tools for conifers have improved our understanding of how trees sense and respond to changes in temperature and light during cold acclimation and the development of cold hardiness, but there remain considerable gaps deserving further research in conifers. In the first section of this review, we focus on the physiological mechanisms used by evergreen conifers to adjust metabolism seasonally and to protect overwintering tissues against winter stresses. In the second section, we review how perception of low temperature and photoperiod regulate the induction of cold acclimation. Finally, we explore the evolutionary context of cold acclimation in conifers and evaluate challenges imposed on them by changing climate and discuss emerging areas of research in the field.

Comparative proteomic analysis reveals novel insights into the interaction between rice and Xanthomonas oryzae pv. oryzae

BACKGROUND

Bacterial blight, which is caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating rice disease worldwide. Rice introgression line H471, derived from the recurrent parent Huang-Hua-Zhan (HHZ) and the donor parent PSBRC28, exhibits broad-spectrum resistance to Xoo, including to the highly virulent Xoo strain PXO99^A, whereas its parents are susceptible to PXO99^A. To characterize the responses to Xoo, we compared the proteome profiles of the host and pathogen in the incompatible interaction (H471 inoculated with PXO99^A) and the compatible interaction (HHZ inoculated with PXO99^A).

RESULTS

In this study, a total of 374 rice differentially abundant proteins (DAPs) and 117 Xoo DAPs were detected in the comparison between H471 + PXO99^A and HHZ + PXO99^A. Most of the Xoo DAPs related to pathogen virulence, including the outer member proteins, type III secretion system proteins, TonB-dependent receptors, and transcription activator-like effectors, were less abundant in the incompatible interaction than in the compatible interaction. The rice DAPs were mainly involved in secondary metabolic processes, including phenylalanine metabolism and the biosynthesis of flavonoids and phenylpropanoids. Additionally, some DAPs involved in the phenolic phytoalexin and salicylic acid (SA) biosynthetic pathways accumulated much more in H471 than in HHZ after the inoculation with PXO99^A, suggesting that phytoalexin and SA productions were induced faster in H471 than in HHZ. Further analyses revealed that the SA content increased much more rapidly in H471 than in HHZ after the inoculation, suggesting that the SA signaling pathway was activated faster in the incompatible interaction than in the compatible interaction.

CONCLUSIONS

Overall, our results indicate that during an incompatible interaction between H471 and PXO99^A, rice plants prevent pathogen invasion and also initiate multi-component defense responses that inhibit disease development.

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

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

Modes of Brassinosteroid Activity in Cold Stress Tolerance

Cold stress is a significant environmental factor that negatively affects plant growth and development in particular when it occurs during the growth phase. Plants have evolved means to protect themselves from damage caused by chilling or freezing temperatures and some plant species, in particular those from temperate geographical zones, can increase their basal level of freezing tolerance in a process termed cold acclimation. Cold acclimation improves plant survival, but also represses growth, since it inhibits activity of the growth-promoting hormones gibberellins (GAs). In addition to GAs, the steroid hormones brassinosteroids (BRs) also take part in growth promotion and cold stress signaling; however, in contrast to Gas, BRs can improve cold stress tolerance with fewer trade-offs in terms of growth and yields. Here we summarize our current understanding of the roles of BRs in cold stress responses with a focus on freezing tolerance and cold acclimation pathways.

Precise Editing of the OsPYL9 Gene by RNA-Guided Cas9 Nuclease Confers Enhanced Drought Tolerance and Grain Yield in Rice (Oryza sativa L.) by Regulating Circadian Rhythm and Abiotic Stress Responsive Proteins

Abscisic acid (ABA) is involved in regulating drought tolerance, and pyrabactin resistance-like (PYL) proteins are known as ABA receptors. To elucidate the role of one of the ABA receptors in rice, OsPYL9 was mutagenized through CRISPR/Cas9 in rice. Homozygous and heterozygous mutant plants lacking any off-targets and T-DNA were screened based on site-specific sequencing and used for morpho-physiological, molecular, and proteomic analysis. Mutant lines appear to accumulate higher ABA, antioxidant activities, chlorophyll content, leaf cuticular wax, and survival rate, whereas a lower malondialdehyde level, stomatal conductance, transpiration rate, and vascular bundles occur under stress conditions. Proteomic analysis found a total of 324 differentially expressed proteins (DEPs), out of which 184 and 140 were up and downregulated, respectively. The OsPYL9 mutants showed an increase in grain yield under both drought and well watered field conditions. Most of the DEPs related to circadian clock rhythm, drought response, and reactive oxygen species were upregulated in the mutant plants. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that DEPs were only involved in circadian rhythm and Gene Ontology (GO) analysis showed that most of the DEPs were involved in response to abiotic stimulus, and abscisic acid-activated signaling pathways. Protein GIGANTEA, Adagio-like, and Pseudo-response regulator proteins showed higher interaction in protein–protein interaction (PPI) network. Thus, the overall results showed that CRISPR/Cas9-generated OsPYL9 mutants have potential to improve both drought tolerance and the yield of rice. Furthermore, global proteome analysis provides new potential biomarkers and understandings of the molecular mechanism of rice drought tolerance.

The moso bamboo drought-induced 19 protein PheDi19-8 functions oppositely to its interacting partner, PheCDPK22, to modulate drought stress tolerance

Drought-induced 19 (Di19) proteins play crucial roles in regulating stress responses, but the exact mechanisms underlying their involvement in moso bamboo are not fully understood. In this study, PheDi19-8 of moso bamboo (Phyllostachys edulis) was isolated and characterized. PheDi19-8 was a nuclear protein and has a high expression under various abiotic stresses, including drought and salt. As revealed by phenotypic and physiological analyses, ectopic overexpression of PheDi19-8 in Arabidopsis and rice enhanced drought tolerance. Under drought stress, the PheDi19-8-overexpressing lines showed smaller stomatal apertures and higher survival rate in comparison to the wild-type plants, as well as the PheDi19-8-overexpressing lines had higher biomass and souble sugar, but lower relative electrolyte leakage and malondialdehyde. Further investigation revealed that PheDi19-8 interacted with PheCDPK22, and their interaction decreased the DNA-binding activity of PheDi19-8. However, overexpression of PheCDPK22 enhanced Arabidopsis sensitivity to drought stress. Moreover, the expression of marker genes, including LEA, RD22, DREB2A and RD29A, was up-regulated in the PheDi19-8-overexpressing lines but down-regulated in the PheCDPK22-overexpressing. Further yeast one-hybrid and EMSA assays indicated that PheDi19-8 directly binds to the promoter of DREB2A. These results provided new insight into the interaction of PheCDPK22 and PheDi19-8 that functions oppositely to regulate drought stress in plants.

Functional characterization and regulatory mechanism of wheat CPK34 kinase in response to drought stress

BACKGROUND

Drought is one of the most adverse environmental factors limiting crop productions and it is important to identify key genetic determinants for food safety. Calcium-dependent protein kinases (CPKs) are known to be involved in plant growth, development, and environmental stresses. However, biological functions and regulatory mechanisms of many plant CPKs have not been explored. In our previous study, abundance of the wheat CPK34 (TaCPK34) protein was remarkably upregulated in wheat plants suffering from drought stress, inferring that it could be involved in this stress. Therefore, here we further detected its function and mechanism in response to drought stress.

RESULTS

Transcripts of the TaCPK34 gene were significantly induced after PEG-stimulated water deficiency (20% PEG6000) or 100 μM abscisic acid (ABA) treatments. The TaCPK34 gene was transiently silenced in wheat genome by using barley stripe mosaic virus-induced silencing (BSMV-VIGS) method. After 14 days of drought stress, the transiently TaCPK34-silenced wheat seedlings showed more sensitivity compared with control, and the plant biomasses and relative water contents significantly decreased, whereas soluble sugar and MDA contents increased. The iTRAQ-based quantitative proteomics was employed to measure the protein expression profiles in leaves of the transiently TaCPK34-silenced wheat plants after drought stress. There were 6103 proteins identified, of these, 51 proteins exhibited significantly altered abundance, they were involved in diverse function. And sequence analysis on the promoters of genes, which encoded the above identified proteins, indicated that some promoters harbored some ABA-responsive elements. We determined the interactions between TaCPK34 and three identified proteins by using bimolecular fluorescent complementation (BiFC) method and our data indicated that TaCPK34directly interacted with the glutathione S-transferase 1 and prx113, respectively.

CONCLUSIONS

Our study suggested that the TaCPK34 gene played positive roles in wheat response to drought stress through directly or indirectly regulating the expression of ABA-dependent manner genes, which were encoding identified proteins from iTRAQ-based quantitative proteomics. And it could be used as one potential gene to develop crop cultivars with improved drought tolerance.

Identification of a Novel Gene, Osbht, in Response to High Temperature Tolerance at Booting Stage in Rice

Rice is one of the world’s leading food crops, and over 90% of the world’s rice production stems from Asia. In particular, an increase of 1 °C in the minimum temperature reduces the quantity of rice by 10%. Therefore, the development of rice varieties that can stably maintain the yield and quality of the rice even under these rapid climate changes is indispensable. In this study, we performed quantitative trait loci (QTL) mapping after treatment with heat stress during the booting stage in rice. We performed a QTL analysis using the Cheongcheong/Nagdong double haploid (CNDH) line and identified 19 QTLs during the 2 year analysis. Of these QTL regions, the 2.2 cM region of RM3709–RM11694 on chromosome 1 was shared among the six traits (heading date; culm length; panicle length; number of tiller; 1000 grain weight; and content of chlorophyll) examined. Rice Microsatellite (RM) 3709–RM11694 contained 27 high-temperature-tolerance candidate genes. Among the candidate genes, OsBHT showed a different gene expression level between CNDH75, which is a high-temperature tolerant line, and CNDH11 which is a susceptible line. Although some existing high-temperature-tolerant genes have been reported, OsBHT can be used more effectively for the development of heat tolerance in rice.

Molecular cloning and expression of AmCDPK from mangrove Avicennia marina under elevated temperature

Considered as an essential calcium sensor, the calcium-dependent protein kinase (CDPK) family plays a critical part in terrestrial plants' responses to both biotic and abiotic stresses. In the study, Avicennia marina was proved to have better heat tolerance than other species. A CDPK gene was cloned from mangrove species A. marina using RACE-PCR and designated as AmCDPK. By predicting and analyzing its properties, structures and expression patterns, we found that the amino acid sequence, containing a kinase domain and four EF-hand Ca²⁺-binding sites, shared high identity with Handroanthus impetiginosus and Sesamum indicum. Quantitative real-time PCR data analysis suggested that AmCDPK demonstrated significant up-regulation under heat stress. It is likely that AmCDPK is a versatile gene involved in various stresses, including dehydration, cold, light, defense and ABA stress responses by analyzing cis-elements. It is the first time that CDPKs from mangroves have been cloned and our results brought evidence to the effect of AmCDPK on heat stress, which is particularly important under the background of global warming.

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.

Integrated RNA-Seq Analysis and Meta-QTLs Mapping Provide Insights into Cold Stress Response in Rice Seedling Roots

Rice (Oryza sativa L.) is a widely cultivated food crop around the world, especially in Asia. However, rice seedlings often suffer from cold stress, which affects their growth and yield. Here, RNA-seq analysis and Meta-QTLs mapping were performed to understand the molecular mechanisms underlying cold tolerance in the roots of 14-day-old seedlings of rice (RPY geng, cold-tolerant genotype). A total of 4779 of the differentially expressed genes (DEGs) were identified, including 2457 up-regulated and 2322 down-regulated DEGs. The GO, COG, KEEG, and Mapman enrichment results of DEGs revealed that DEGs are mainly involved in carbohydrate transport and metabolism, signal transduction mechanisms (plant hormone signal transduction), biosynthesis, transport and catabolism of secondary metabolites (phenylpropanoid biosynthesis), defense mechanisms, and large enzyme families mechanisms. Notably, the AP2/ERF-ERF, NAC, WRKY, MYB, C2H2, and bHLH transcription factors participated in rice’s cold–stress response and tolerance. On the other hand, we mapped the identified DEGs to 44 published cold–stress-related genes and 41 cold-tolerant Meta-QTLs regions. Of them, 12 DEGs were the published cold–stress-related genes and 418 DEGs fell into the cold-tolerant Meta-QTLs regions. In this study, the identified DEGs and the putative molecular regulatory network can provide insights for understanding the mechanism of cold stress tolerance in rice. In addition, DEGs in KEGG term-enriched terms or cold-tolerant Meta-QTLs will help to secure key candidate genes for further functional studies on the molecular mechanism of cold stress response in rice.

The unknown soldier in citrus plants: polyamines-based defensive mechanisms against biotic and abiotic stresses and their relationship with other stress-associated metabolites

Citrus plants are challenged by a broad diversity of abiotic and biotic stresses, which definitely alter their growth, development, and productivity. In order to survive the various stressful conditions, citrus plants relay on multi-layered adaptive strategies, among which is the accumulation of stress-associated metabolites that play vital and complex roles in citrus defensive responses. These metabolites included amino acids, organic acids, fatty acids, phytohormones, polyamines (PAs), and other secondary metabolites. However, the contribution of PAs pathways in citrus defense responses is poorly understood. In this review article, we will discuss the recent metabolic, genetic, and molecular evidence illustrating the potential roles of PAs in citrus defensive responses against biotic and abiotic stressors. We believe that PAs-based defensive role, against biotic and abiotic stress in citrus, is involving the interaction with other stress-associated metabolites, particularly phytohormones. The knowledge gained so far about PAs-based defensive responses in citrus underpins our need for further genetic manipulation of PAs biosynthetic genes to produce transgenic citrus plants with modulated PAs content that may enhance the tolerance of citrus plants against stressful conditions. In addition, it provides valuable information for the potential use of PAs or their synthetic analogs and their emergence as a promising approach to practical applications in citriculture to enhance stress tolerance in citrus plants.

Rare-earth element scandium improves stomatal regulation and enhances salt and drought stress tolerance by up-regulating antioxidant responses of Oryza sativa

Oryza sativa L. cv. Gönen grown in hydroponic culture was treated with scandium (Sc; 25 and 50 μM) alone or in combination with salt (100 mM NaCl) and/or drought (5% PEG-6000). Stress caused a decrease in growth (RGR), water content (RWC), osmotic potential (ΨΠ), chlorophyll fluorescence (Fv/Fm) and potential photochemical efficiency (Fv/Fo). Sc application prevented the decreases of these parameters. Sc also alleviated the changes on gas exchange parameters (carbon assimilation rate (A), stomatal conductance (gs), intercellular CO2 concentrations (Ci), transpiration rate (E) and stomatal limitation (Ls)). Stress caused no increase in superoxide dismutase (SOD) activity. After induvial applied NaCl or PEG, catalase (CAT) and ascorbate peroxidase (APX) showed an enhancement in activation and tried to scavenge of hydrogen peroxide (H2O2). On the other hand, in plants with the combination form of NaCl and PEG, only CAT activity was induced. Sc applications to NaCl-treated rice led to an increase of SOD, APX, glutathione reductase (GR), monodehydroascorbate reductase (MDHAR) and dehydroascorbate reductase (DHAR) as well as peroxidase (POX). Sc under NaCl could be maintained both ascorbate (AsA) and glutathione (GSH) regeneration. Despite of induction of MDHAR and DHAR under Sc plus PEG, Sc did not maintain AsA redox state because of no induction in APX activity. However, GSH pool could be regenerated by induction in DHAR and GR in this group. Sc application (especially for 25 μM) in rice exposed to NaCl + PEG resulted an enhancement in APX and MDHAR and so Sc could be partially provided AsA regeneration. Since no increases in DHAR and GR were observed, GSH pool was reduced. Due to this activation of antioxidant enzymes, stress-induced H2O2 and TBARS content (lipid peroxidation) significantly decreased in rice with Sc applications. Sc in plants with stress also increased the transcript levels of OsCDPK7 and OsBG1 related to stomatal movement and signaling pathway. Consequently, Sc protected the rice plants by minimizing disturbances caused by NaCl or PEG exposure via the AsA-GSH redox-based systems.

PtrCDPK10 of Poncirus trifoliata functions in dehydration and drought tolerance by reducing ROS accumulation via phosphorylating PtrAPX

Calcium-dependent protein kinases (CDPKs) are important calcium signaling components that have been shown to play crucial roles in modulating plant abiotic stress responses. However, the physiological and regulatory roles of most CDPKs are still poorly understood. Here, we report the functional characterization of PtrCDPK10 from trifoliate orange (Poncirus trifoliata (L.) Raf.) in dehydration and drought stress tolerance. PtrCDPK10, categorized in the Type III subgroup of the CDPK family, was localized to the nucleus and plasma membrane. Transcript levels of PtrCDPK10 were up-regulated by dehydration, salt and ABA treatments. Transgenic trifoliate orange plants overexpressing PtrCDPK10 showed enhanced dehydration tolerance compared with the wild type (WT), whereas VIGS (virus-induced gene silencing)-mediated knockdown of PtrCDPK10 resulted in elevated susceptibility to dehydration and drought stresses. Yeast two-hybrid screening identified several proteins that interacted with PtrCDPK10, including an ascorbate peroxidase (PtrAPX). PtrCDPK10 was shown to phosphorylate PtrAPX based on an in vitro kinase assay. PtrCDPK10-overexpressing transgenic lines exhibited higher PtrAPX mRNA abundance and APX activity and accumulated dramatically less ROS in comparison with the WT, while PtrCDPK10-silenced VIGS lines showed decreased PtrAPX expression and increased ROS level. Taken together, these results demonstrate that PtrCDPK10 promotes dehydration and drought tolerance by, at least in part, phosphorylating APX to modulate ROS homeostasis.

Genome-wide investigation of calcium-dependent protein kinase gene family in pineapple: evolution and expression profiles during development and stress

Background

Calcium-dependent protein kinase (CPK) is one of the main Ca²⁺ combined protein kinase that play significant roles in plant growth, development and response to multiple stresses. Despite an important member of the stress responsive gene family, little is known about the evolutionary history and expression patterns of CPK genes in pineapple.

Results

Herein, we identified and characterized 17 AcoCPK genes from pineapple genome, which were unevenly distributed across eight chromosomes. Based on the gene structure and phylogenetic tree analyses, AcoCPKs were divided into four groups with conserved domain. Synteny analysis identified 7 segmental duplication events of AcoCPKs and 5 syntenic blocks of CPK genes between pineapple and Arabidopsis, and 8 between pineapple and rice. Expression pattern of different tissues and development stages suggested that several genes are involved in the functional development of plants. Different expression levels under various abiotic stresses also indicated that the CPK family underwent functional divergence during long-term evolution. AcoCPK1, AcoCPK3 and AcoCPK6, which were repressed by the abiotic stresses, were shown to be function in regulating pathogen resistance.

Conclusions

17 AcoCPK genes from pineapple genome were identified. Our analyses provide an important foundation for understanding the potential roles of AcoCPKs in regulating pineapple response to biotic and abiotic stresses

Genome-wide survey and expression analysis of calcium-dependent protein kinase (CDPK) in grass Brachypodium distachyon

BACKGROUND

Ca2+ played as a ubiquitous secondary messenger involved in plant growth, development, and responses to various environmental stimuli. Calcium-dependent protein kinases (CDPK) were important Ca2+ sensors, which could directly translate Ca2+ signals into downstream phosphorylation signals. Considering the importance of CDPKs as Ca2+ effectors for regulation of plant stress tolerance and few studies on Brachypodium distachyon were available, it was of interest for us to isolate CDPKs from B. distachyon.

RESULTS

A systemic analysis of 30 CDPK family genes in B. distachyon was performed. Results showed that all BdCDPK family members contained conserved catalytic Ser/Thr protein kinase domain, autoinhibitory domain, and EF-hand domain, and a variable N-terminal domain, could be divided into four subgroup (I-IV), based upon sequence homology. Most BdCDPKs had four EF-hands, in which EF2 and EF4 revealed high variability and strong divergence from EF-hand in AtCDPKs. Synteny results indicated that large number of syntenic relationship events existed between rice and B. distachyon, implying their high conservation. Expression profiles indicated that most of BdCDPK genes were involved in phytohormones signal transduction pathways and regulated physiological process in responding to multiple environmental stresses. Moreover, the co-expression network implied that BdCDPKs might be both the activator and the repressor involved in WRKY transcription factors or MAPK cascade genes mediated stress response processes, base on their complex regulatory network.

CONCLUSIONS

BdCDPKs might play multiple function in WRKY or MAPK mediated abiotic stresses response and phytohormone signaling transduction in B. distachyon. Our genomics analysis of BdCDPKs could provide fundamental information for further investigation the functions of CDPKs in integrating Ca2+ signalling pathways in response to environments stresses in B. distachyon.

Expression of maize calcium-dependent protein kinase (ZmCPK11) improves salt tolerance in transgenic Arabidopsis plants by regulating sodium and potassium homeostasis and stabilizing photosystem II

In plants, CALCIUM-DEPENDENT PROTEIN KINASES (CDPKs/CPKs) are involved in calcium signaling in response to endogenous and environmental stimuli. Here, we report that ZmCPK11, one of maize CDPKs, participates in salt stress response and tolerance. Salt stress induced expression and upregulated the activity of ZmCPK11 in maize roots and leaves. Activation of ZmCPK11 upon salt stress was also observed in roots and leaves of transgenic Arabidopsis plants expressing ZmCPK11. The transgenic plants showed a long-root phenotype under control conditions and a short-root phenotype under NaCl, abscisic acid (ABA) or jasmonic acid (JA) treatment. Analysis of ABA and JA content in roots indicated that ZmCPK11 can mediate root growth by regulating the levels of these phytohormones. Moreover, 4-week-old transgenic plants were more tolerant to salinity than the wild-type plants. Their leaves were less chlorotic and showed weaker symptoms of senescence accompanied by higher chlorophyll content and higher quantum efficiency of photosystem II. The expression of Na⁺ /K⁺ transporters (HKT1, SOS1 and NHX1) and transcription factors (CBF1, CBF2, CBF3, ZAT6 and ZAT10) with known links to salinity tolerance was upregulated in roots of the transgenic plants upon salt stress. Furthermore, the transgenic plants accumulated less Na⁺ in roots and leaves under salinity, and showed a higher K⁺ /Na⁺ ratio in leaves. These results show that the improved salt tolerance in ZmCPK11-transgenic plants could be due to an upregulation of genes involved in the maintenance of intracellular Na⁺ and K⁺ homeostasis and a protection of photosystem II against damage.

Genome-Wide Association Mapping for Salt Tolerance of Rice Seedlings Grown in Hydroponic and Soil Systems Using the Bengal and Assam Aus Panel

Salinity is a major abiotic stress which inhibits rice production in coastal, arid and semi-aid areas in many countries, such as India and Bangladesh. Identification of salt tolerant cultivars, quantitative trait loci (QTLs) and genes is essential for breeding salt tolerant rice. The aus subpopulation of rice is considered to have originated predominantly from Bangladesh and India and have rich genetic diversity with wide variation in abiotic stress resistance. The objective of this study was to identify QTLs, and subsequently candidate genes using cultivars from the aus subpopulation and compare the results of two different seedling stage screening methods. Salt tolerance at the rice seedling stage was evaluated on 204 rice accessions from the Bengal and Assam Aus Panel (BAAP) grown in both hydroponics and soil under control and salt stress conditions. Ten salt related traits of stress symptoms, plant growth and the content of sodium and potassium were measured. Three cultivars, BRRI dhan 47, Goria, and T 1 showed more salt tolerance than the tolerant check Pokkali in both systems. Genome-wide association mapping was conducted on salt indices traits with 2 million SNPs using an efficient mixed model (EMMA) controlling population structure and kinship, and a significance threshold of P < 0.0001 was used to determine significant SNPs. A total of 97 and 74 QTLs associated with traits in hydroponic and soil systems were identified, respectively, including 11 QTLs identified in both systems. A total of 65 candidate genes were found including a well-known major gene OsHKT1;5. The most significant QTL was detected at around 40 Mb on chromosome 1 coinciding with two post-translational modifications SUMOylation genes (OsSUMO1 and OsSUMO2), this QTL was investigated. The salt tolerance rice cultivars and QTLs/genes identified here will provide useful information for future studies on genetics and breeding salt tolerant rice.

Multi-Locus Genome Wide Association Mapping for Yield and Its Contributing Traits in Hexaploid Wheat under Different Water Regimes

Multi-locus genome wide association study was undertaken using a set of 320 diverse spring wheat accessions, which were each genotyped for 9,626 SNPs. The association panel was grown in replicated trials in four environments [two each in irrigated (IR) and rainfed (RF) environments], and phenotypic data were recorded for five traits including days to heading, days to maturity, plant height, thousand grain weight and grain yield. Forty-six significant marker-trait associations (MTAs) were identified for five traits. These included 20 MTAs in IR and 19 MTAs in RF environments; seven additional MTAs were common to both the environments. Five of these MTAs were co-localized with previously known QTL/MTAs and the remaining MTAs were novel and add to the existing knowledge. Three desirable haplotypes for agronomic traits, one for improvement in RF environment and two for improvement in IR environment were identified. Eighteen (18) promising candidate genes (CGs) involved in seven different biological activities were also identified. The expression profiles of four (Trehalose-6-Phosphate, APETALA2/Ethylene-responsive factor, DNA-binding One Zinc Finger and Gibberellin-dioxygenases) of the 18 genes showed that they were induced by drought stress in the wheat seedlings. The MTAs, haplotypes and CG-based markers may be used in marker-assisted breeding for drought tolerance in wheat.

Expression, Subcellular Localization, and Interactions of CPK Family Genes in Maize

Calcium-dependent protein kinase (CPKs) is a key player in the calcium signaling pathway to decode calcium signals into various physiological responses. cDNA sequences of 9 ZmCPK genes were successfully cloned from all four phylogenetic groups in maize. qRT-PCR analysis showed the expression variation of these selected genes under abscisic acid (ABA) and calcium chloride (CaCl2) treatment. Due to the presence of N-myristoylation/palmitoylation sites, the selected ZmCPK members were localized in a plasma membrane. To clarify whether ZmCPK, a key player in calcium signaling, interacts with key players of ABA, protein phosphatase 2Cs (PP2Cs) and the SNF1-related protein kinase 2s (SnRK2s) and mitogen-activated protein kinase (MAPK) signaling pathways in maize, we examined the interaction between 9 CPKs, 8 PP2Cs, 5 SnRKs, and 20 members of the MPK family in maize by using yeast two-hybrid assay. Our results showed that three ZmCPKs interact with three different members of ZmSnRKs while four ZmCPK members had a positive interaction with 13 members of ZmMPKs in different combinations. These four ZmCPK proteins are from three different groups in maize. These findings of physical interactions between ZmCPKs, ZmSnRKs, and ZmMPKs suggested that these signaling pathways do not only have indirect influence but also have direct crosstalk that may involve the defense mechanism in maize. The present study may improve the understanding of signal transduction in plants.

Comparative Phosphoproteomic Analysis Reveals a Decay of ABA Signaling in Barley Embryos during After-Ripening

Abscisic acid (ABA) is a phytohormone and a major determinant of seed dormancy in plants. Seed dormancy is gradually lost during dry storage, a process known as 'after-ripening', and this dormancy decay is related to a decline in ABA content and sensitivity in seeds after imbibition. In this study, we aimed at investigating the effect of after-ripening on ABA signaling in barley, our cereal model species. Phosphosignaling networks in barley grains were investigated by a large-scale analysis of phosphopeptides to examine potential changes in response pathways to after-ripening. We used freshly harvested (FH) and after-ripened (AR) barley grains which showed different ABA sensitivity. A total of 1,730 phosphopeptides were identified in barley embryos isolated from half-cut grains. A comparative analysis showed that 329 and 235 phosphopeptides were upregulated or downregulated, respectively after ABA treatment, and phosphopeptides profiles were quite different between FH and AR embryos. These results were supported by peptide motif analysis which suggested that different sets of protein kinases are active in FH and AR grains. Furthermore, in vitro phosphorylation assays confirmed that some phosphopeptides were phosphorylated by SnRK2s, which are major protein kinases involved in ABA signaling. Taken together, our results revealed very distinctive phosphosignaling networks in FH and AR embryos of barley, and suggested that the after-ripening of barley grains is associated with differential regulation of phosphosignaling pathways leading to a decay of ABA signaling.

Effect of aridity and dune type on rhizosphere soil bacterial communities of Caragana microphylla in desert regions of northern China

Understanding the response of soil properties and bacterial communities in rhizosphere soil to aridity and dune types is fundamental to desertification control. This study investigated soil properties and bacterial communities of both rhizosphere and bulk soils of Caragana microphylla from four sites with different aridity indices, and one site with three different types of dunes. All sites were located in the desert regions of northern China. The results indicated that compared with the bulk soil, the soil nutrient content of rhizosphere, especially the content of total phosphorus, was generally significantly improved in different desertification environments. The bacterial richness and diversity were also higher than those of bulk soil, especially in arid regions and fixed dunes. Firmicutes, Actinobacteria, Proteobacteria, and Acidobacteria were the most dominant phyla in all samples. The regression analyses showed that at different sites, soil total organic C, total N, Na⁺, and total P played key roles in determining the bacterial community structure while total organic carbon, electronic conductivity, pH and total phosphorus were the dominant factors at the different dunes. The results further revealed that the dominant phyla strongly affected by environmental factors at different sites were Acidobacteria, Gemmatimonadetes, and Actinobacteria among which, Acidobacteria and Gemmatimonadetes were negatively correlated with Na⁺ content. At different types of dunes, Actinobacteria, Planctomycetes, and Gemmatimonadetes were particularly affected by environmental factors. The increased abundance of Actinobacteria in the rhizosphere soil was mainly caused by the decreased soil pH.

The involvements of calcium-dependent protein kinases and catechins in tea plant [Camellia sinensis (L.) O. Kuntze] cold responses

Temperature is one of the most important environmental factors limiting tea plant growth and tea production. Previously we reported that both Ca²⁺ and ROS signals play important roles in tea plant cold acclimation. Here, we identified 26 CsCPK transcripts, analyzed their phylogenetic and sequence characters, and detected their transcriptions to monitor Ca²⁺ signaling status. Tissue-specific expression profiles indicated that most CsCPK genes were constitutively expressed in tested tissues, suggesting their possible roles in development. Cold along with calcium inhibitor assays suggested that CsCPKs are important cold regulators and CsCPK30/5/4/9 maybe the key members. Moreover, LaCl₃ or EGTA pre-treatment could result in impaired Ca²⁺ signaling and compromised cold-responding network, but higher catechins accumulation revealed their potential positive roles in cold responses. Those findings indicated that catechins and other secondary metabolites in tea plant may form an alternative cold-responding network that closely correlated with Ca²⁺ signaling status.

Identification, Expression, and Interaction Network Analyses of the CDPK Gene Family Reveal Their Involvement in the Development, Ripening, and Abiotic Stress Response in Banana

Calcium-dependent protein kinases (CDPKs) play vital roles in the regulation of plant growth, development, and tolerance to various abiotic stresses. However, little information is available for this gene family in banana. In this study, 44 CDPKs were identified in banana and were classified into four groups based on phylogenetic, gene structure, and conserved motif analyses. The majority of MaCDPKs generally exhibited similar expression patterns in the different tissues. Transcriptome analyses revealed that many CDPKs showed strong transcript accumulation at the early stages of fruit development and postharvest ripening in both varieties. Interaction network and co-expression analysis further identified some CDPKs-mediated network that was potentially active at the early stages of fruit development. Comparative expression analysis suggested that the high levels of CDPK expression in FJ might be related to its fast ripening characteristic. CDPK expression following the abiotic stress treatments indicated a significant transcriptional response to osmotic, cold, and salt treatment, as well as differential expression profiles, between BX and FJ. The findings of this study elucidate the transcriptional control of CDPKs in development, ripening, and the abiotic stress response in banana. Some tissue-specific, development/ripening-dependent, and abiotic stress-responsive candidate MaCDPK genes were identified for further genetic improvement of banana.

CRISPR-Cas9 directed genome engineering for enhancing salt stress tolerance in rice

Crop productivity in rice is harshly limited due to high concentration of salt in the soil. To understand the intricacies of the mechanism it is important to unravel the key pathways operating inside the plant cell. Emerging state-of-the art technologies have provided the tools to discover the key components inside the plant cell for salt tolerance. Among the molecular entities, transcription factors and/or other important components of sensing and signaling cascades have been the attractive targets and the role of NHX and SOS1 transporters amply described. Not only marker assisted programs but also transgenic approaches by using reverse genetic strategies (knockout or knockdown) or overexpression have been extensively used to engineer rice crop. CRISPR/Cas is an attractive paradigm and provides the feasibility for manipulating several genes simultaneously. Here, in this review we highlight some of the molecular entities that could be potentially targeted for generating rice amenable to sustain growth under high salinity conditions by employing CRISPR/Cas. We also try to address key questions for rice salt stress tolerance other than what is already known.

A transcriptomic (RNA-seq) analysis of genes responsive to both cadmium and arsenic stress in rice root

Cadmium (Cd) and arsenic (As) are nonessential and toxic elements in rice that often occur together in contaminated paddy field soils. To understand whether rice has a common molecular response mechanism against Cd and As toxicity, 30-day seedlings (Oryza sativa L. indica) were exposed separately to Cd and As³⁺ in hydroponic cultures for up to 7 days. Root transcriptomic analysis of plants exposed to Cd and As for 3 days revealed that a total of 2224 genes in rice roots responded to Cd stress, while 1503 genes responded to As stress. Of these, 841 genes responded to both stressors. The genes in common to Cd and As stress were associated with redox control, stress response, transcriptional regulation, transmembrane transport, signal transduction, as well as biosynthesis and metabolism of macromolecules and sulfur compounds. In plants exposed to Cd and As separately or in combination for 3 and 7 days, qRT-PCR verification revealed that the glutathione metabolism associated gene Os09g0367700 was significantly up-regulated with respect to unexposed controls and had a positive synergistic effect under combined Cd and As stress. In addition, the redox control related genes Os06g0216000, Os07g0638300 and Os01g0294500, the glutathione metabolism related gene Os01g0530900, the cell wall biogenesis related genes Os05g0247800, Os11g0592000 and Os03g0416200, the expression regulation related genes Os07g0597200 and Os02g0168200, and the transmembrane transport related genes Os04g0524500, also varied significantly with respect to an unexposed control and displayed synergistic effects after 7 days of simultaneous exposure to Cd and As. Our identification of a novel set of genes in rice which responded to both Cd and As³⁺ stress may be of value in mitigating the toxicity of co-contaminated soils. These results also provide a deeper understanding of the molecular mechanisms involved in response to multi-metal/loids stress, and may be used in the genetic improvement of rice varieties.

Calcium-Dependent Protein Kinase Genes in Glycyrrhiza Uralensis Appear to be Involved in Promoting the Biosynthesis of Glycyrrhizic Acid and Flavonoids under Salt Stress

As calcium signal sensors, calcium-dependent protein kinases (CPKs) play vital roles in stimulating the production of secondary metabolites to participate in plant development and response to environmental stress. However, investigations of the Glycyrrhiza uralensis CPK family genes and their multiple functions are rarely reported. In this study, a total of 23 GuCPK genes in G. uralensis were identified, and their phylogenetic relationships, evolutionary characteristics, gene structure, motif distribution, and promoter cis-acting elements were analyzed. Ten GuCPKs showed root-specific preferential expressions, and GuCPKs indicated different expression patterns under treatments of CaCl2 and NaCl. In addition, under 2.5 mM of CaCl2 and 30 mM of NaCl treatments, the diverse, induced expression of GuCPKs and significant accumulations of glycyrrhizic acid and flavonoids suggested the possible important function of GuCPKs in regulating the production of glycyrrhizic acid and flavonoids. Our results provide a genome-wide characterization of CPK family genes in G. uralensis, and serve as a foundation for understanding the potential function and regulatory mechanism of GuCPKs in promoting the biosynthesis of glycyrrhizic acid and flavonoids under salt stress.

Microtubule dynamics modulate sensing during cold acclimation in grapevine suspension cells

Cold acclimation is of practical relevance, since it can avoid cold-induced damage in various crops. To efficiently activate cold acclimation requires that the chilling stress is perceived and processed efficiently. In the current work, we use a transgenic cell line of V. rupestris expressing a GFP-labelled tubulin to follow the effect of cold acclimation and the relation between microtubules and the expression of the transcription factor Cold Box Factor 4 (CBF4) as molecular readout for adaptive responses to cold stress. We find that chilling induced cold tolerance correlated with increased CBF4 expression. We show that cold acclimation can be achieved through stabilisation of microtubules by taxol, as well as through transient elimination of microtubules by pronamide in the absence of cold stress. Furthermore, results from inhibitor studies indicate that transcriptional activation of CBF4 appears to be under control of calcium influx. We screened a population of the ancestor of V. sylvestris and could identify different clades with strong induction of CBF4, indicative of genetic variation in cold adaptability that can be used for breeding. We summarize our findings into a working model where microtubule dynamics controls the sensitivity of cold induced calcium influx mediating the induction of CBF4 culminating in cold hardening.

Genome-Wide Identification of Calcium-Dependent Protein Kinases in Chlamydomonas reinhardtii and Functional Analyses in Nitrogen Deficiency-Induced Oil Accumulation

Calcium-dependent protein kinases (CDPKs) are recognized as important calcium (Ca²⁺) sensors in signal transduction and play multiple roles in plant growth and developmental processes, as well as in response to various environmental stresses. However, little information is available about the CDPK family in the green microalga Chlamydomonas reinhardtii. In this study, 15 CrCDPK genes were identified in C. reinhardtii genome, and their functions in nitrogen (N) deficiency-induced oil accumulation were analyzed. Our results showed that all CrCDPK proteins harbored the typical elongation factor (EF)-hand Ca²⁺-binding and protein kinase domains. Phylogenetic analysis revealed that these CrCDPKs were clustered into one group together with a subclade of several CPKs from Arabidopsis and rice, clearly separating from the remaining AtCPKs and OsCPKs. These genes were located in 10 chromosomes and one scaffold of C. reinhardtii and contained 6-17 exons. RNA sequencing and quantitative reverse transcription (qRT)-PCR assays indicated that most of these CrCDPKs were significantly induced by N deficiency and salt stress. Lanthanum chloride (LaCl₃), a plasma membrane Ca²⁺ channel blocker, limited oil accumulation in C. reinhardtii under N-deficient conditions, suggesting that Ca²⁺ was involved in N deficiency-induced oil accumulation. Furthermore, RNA interference (RNAi) silencing analyses demonstrated that six CrCDPKs played positive roles and three CrCDPKs played negative roles in N deficiency-induced oil accumulation in C. reinhardtii.

Enhancing the abiotic stress tolerance of plants: from chemical treatment to biotechnological approaches

Abiotic stresses affect crop plants and cause decreases in plant quality and productivity. Plants can overcome environmental stresses by activating molecular networks, including signal transduction, stress perception, metabolite production and expressions of specific stress-related genes. Recent research suggests that chemical priming is a promising field in crop stress management because plants can be primed by chemical agents to increase their tolerance to various environmental stresses. We present a concept to meet this objective and protect plants through priming of existing defense mechanisms avoiding manipulation of the genome. In addition, recent developments in plant molecular biology include the discovery of genes related to stress tolerance, including functional genes for protecting cells and regulatory genes for regulating stress responses. Therefore, enhancing abiotic stress tolerance using a transgenic approach to transfer these genes into plant genomes has attracted more investigations. Both chemical priming agents and genetic engineering can enhance regulatory and functional genes in plants and increase stress tolerance of plants. This review summarizes the latest findings of chemical priming agents and major achievements in molecular approaches that can potentially enhance the abiotic stress tolerance of plants.

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

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

Shared and genetically distinct Zea mays transcriptome responses to ongoing and past low temperature exposure

BACKGROUND

Cold temperatures and their alleviation affect many plant traits including the abundance of protein coding gene transcripts. Transcript level changes that occur in response to cold temperatures and their alleviation are shared or vary across genotypes. In this study we identify individual transcripts and groups of functionally related transcripts that consistently respond to cold and its alleviation. Genes that respond differently to temperature changes across genotypes may have limited functional importance. We investigate if these genes share functions, and if their genotype-specific gene expression levels change in magnitude or rank across temperatures.

RESULTS

We estimate transcript abundances from over 22,000 genes in two unrelated Zea mays inbred lines during and after cold temperature exposure. Genotype and temperature contribute to many genes' abundances. Past cold exposure affects many fewer genes. Genes up-regulated in cold encode many cytokinin glucoside biosynthesis enzymes, transcription factors, signalling molecules, and proteins involved in diverse environmental responses. After cold exposure, protease inhibitors and cuticular wax genes are newly up-regulated, and environmentally responsive genes continue to be up-regulated. Genes down-regulated in response to cold include many photosynthesis, translation, and DNA replication associated genes. After cold exposure, DNA replication and translation genes are still preferentially downregulated. Lignin and suberin biosynthesis are newly down-regulated. DNA replication, reactive oxygen species response, and anthocyanin biosynthesis genes have strong, genotype-specific temperature responses. The ranks of genotypes' transcript abundances often change across temperatures.

CONCLUSIONS

We report a large, core transcriptome response to cold and the alleviation of cold. In cold, many of the core suite of genes are up or downregulated to control plant growth and photosynthesis and limit cellular damage. In recovery, core responses are in part to prepare for future stress. Functionally related genes are consistently and greatly up-regulated in a single genotype in response to cold or its alleviation, suggesting positive selection has driven genotype-specific temperature responses in maize.

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.

Cold signaling in plants: Insights into mechanisms and regulation

To survive under cold temperatures plants must be able to perceive a cold signal and transduce it into downstream components that induce appropriate defense mechanisms. In addition to inducing adaptive defenses, such as the production of osmotic factors to prevent freezing and the reprogramming of transcriptional pathways, cold temperatures induce changes in plant growth and development which can affect the plant life cycle. In this review, we summarize recent progress in characterizing cold-related genes and the pathways that allow transduction of the cold signal in plants, focusing primarily on studies in Arabidopsis thaliana and rice (Oryza sativa). We summarize cold perception and signal transduction from the plasma membrane to the nucleus, which involves cold sensors, calcium signals, calcium-binding proteins, mitogen-activated protein kinase cascades, and the C-repeat binding factor/dehydration-responsive element binding pathways, as well as trehalose metabolism. Finally, we describe the balance between plant organogenesis and cold tolerance mechanisms in rice. This review encapsulates the known cold signaling factors in plants and provides perspectives for ongoing cold signaling research.

Improvement of Drought Tolerance in Rice (Oryza sativa L.): Genetics, Genomic Tools, and the WRKY Gene Family

Drought tolerance is an important quantitative trait with multipart phenotypes that are often further complicated by plant phenology. Different types of environmental stresses, such as high irradiance, high temperatures, nutrient deficiencies, and toxicities, may challenge crops simultaneously; therefore, breeding for drought tolerance is very complicated. Interdisciplinary researchers have been attempting to dissect and comprehend the mechanisms of plant tolerance to drought stress using various methods; however, the limited success of molecular breeding and physiological approaches suggests that we rethink our strategies. Recent genetic techniques and genomics tools coupled with advances in breeding methodologies and precise phenotyping will likely reveal candidate genes and metabolic pathways underlying drought tolerance in crops. The WRKY transcription factors are involved in different biological processes in plant development. This zinc (Zn) finger protein family, particularly members that respond to and mediate stress responses, is exclusively found in plants. A total of 89 WRKY genes in japonica and 97 WRKY genes in O. nivara (OnWRKY) have been identified and mapped onto individual chromosomes. To increase the drought tolerance of rice (Oryza sativa L.), research programs should address the problem using a multidisciplinary strategy, including the interaction of plant phenology and multiple stresses, and the combination of drought tolerance traits with different genetic and genomics approaches, such as microarrays, quantitative trait loci (QTLs), WRKY gene family members with roles in drought tolerance, and transgenic crops. This review discusses the newest advances in plant physiology for the exact phenotyping of plant responses to drought to update methods of analysing drought tolerance in rice. Finally, based on the physiological/morphological and molecular mechanisms found in resistant parent lines, a strategy is suggested to select a particular environment and adapt suitable germplasm to that environment.

Ectopic Expression of a Thellungiella salsuginea Aquaporin Gene, TsPIP1;1, Increased the Salt Tolerance of Rice

Aquaporins play important regulatory roles in the transport of water and small molecules in plants. In this study, a Thellungiella salsuginea TsPIP1;1 aquaporin was transformed into Kitaake rice, and three transgenic lines were evaluated by profiling the changes of the physiological metabolism, osmotic potential, and differentially expressed genes under salt stress. The TsPIP1;1 protein contains six transmembrane domains and is localized in the cytoplasm membrane. Overexpression of the TsPIP1;1 gene not only increased the accumulation of prolines, soluble sugars and chlorophyll, but also lowered the osmotic potential and malondialdehyde content in rice under salt stress, and alleviated the amount of salt damage done to rice organs by regulating the distribution of Na/K ions, thereby promoting photosynthetic rates. Transcriptome sequencing confirmed that the differentially expressed genes that are up-regulated in rice positively respond to salt stimulus, the photosynthetic metabolic process, and the accumulation profiles of small molecules and Na/K ions. The co-expressed Rubisco and LHCA4 genes in rice were remarkably up-regulated under salt stress. This data suggests that overexpression of the TsPIP1;1 gene is involved in the regulation of water transport, the accumulation of Na/K ions, and the translocation of photosynthetic metabolites, thus conferring enhanced salt tolerance to rice.

Genome-Wide Analysis of CDPK Family in Foxtail Millet and Determination of SiCDPK24 Functions in Drought Stress

Plant calcium-dependent protein kinases (CDPKs) were reported to play important roles in plant resistance to abiotic stress. Foxtail millet cultivation "H138" was used for RNA-seq analysis. The data from drought-induced de novo transcriptomic sequences of foxtail millet showed that CDPKs were up- or down-regulated by drought to different degrees. In this study, 29 foxtail millet CDPKs were classified into four subgroups. These genes were unevenly distributed on nine foxtail millet chromosomes, and chromosomes 2, 3, and 9 contained the most SiCDPK members. Analysis of putative cis-acting elements showed that most foxtail millet CDPK genes contained the ABRE, LTR, HSE, MYB, MYC, DRE, CGTCA-motif, and TGACG-motif cis-acting elements, which could be activated by abiotic stresses. Real-time PCR analysis indicated that 29 SiCDPK genes experienced different degrees of induction under drought and ABA stresses. SiCDPK24 had the highest expression levels at 6 and 12 h of drought treatment and was chosen for further analysis. SiCDPK24 localized to the cell membrane and the nucleus of Arabidopsis mesophyll protoplasts. Western blot analysis showed that SiCDPK24 protein had autophosphorylation activity. Overexpression of SiCDPK24 in Arabidopsis enhanced drought resistance and improved the survival rate under drought stress. It also activated the expressions of nine stress-related genes, namely RD29A, RD29B, RD22, KIN1, COR15, COR47, LEA14, CBF3/DREB1A, and DREB2A. These genes are involved in resistance to abiotic stresses in Arabidopsis. These results indicate that foxtail millet CDPK genes play important roles in resisting drought stress.

Na+ extrusion from the cytosol and tissue-specific Na+ sequestration in roots confer differential salt stress tolerance between durum and bread wheat

The progress in plant breeding for salinity stress tolerance is handicapped by the lack of understanding of the specificity of salt stress signalling and adaptation at the cellular and tissue levels. In this study, we used electrophysiological, fluorescence imaging, and real-time quantitative PCR tools to elucidate the essentiality of the cytosolic Na+ extrusion in functionally different root zones (elongation, meristem, and mature) in a large number of bread and durum wheat accessions. We show that the difference in the root's ability for vacuolar Na+ sequestration in the mature zone may explain differential salinity stress tolerance between salt-sensitive durum and salt-tolerant bread wheat species. Bread wheat genotypes also had on average 30% higher capacity for net Na+ efflux from the root elongation zone, providing the first direct evidence for the essentiality of the root salt exclusion trait at the cellular level. At the same time, cytosolic Na+ accumulation in the root meristem was significantly higher in bread wheat, leading to the suggestion that this tissue may harbour a putative salt sensor. This hypothesis was then tested by investigating patterns of Na+ distribution and the relative expression level of several key genes related to Na+ transport in leaves in plants with intact roots and in those in which the root meristems were removed. We show that tampering with this sensing mechanism has resulted in a salt-sensitive phenotype, largely due to compromising the plant's ability to sequester Na+ in mesophyll cell vacuoles. The implications of these findings for plant breeding for salinity stress tolerance are discussed.

The role of calcium-dependent protein kinase in hydrogen peroxide, nitric oxide and ABA-dependent cold acclimation

Cold acclimation-induced cold tolerance is associated with the generation of reactive oxygen species (ROS), nitric oxide (NO), and mitogen-activated protein kinases (MPKs) in plants. Here, we hypothesized that calcium-dependent protein kinases (CPKs) induce a crosstalk among ROS, NO, and MPKs, leading to the activation of abscisic acid (ABA) signaling in plant adaptation to cold stress. Results showed that cold acclimation significantly increased the transcript levels of CPK27 along with the biosynthesis of ABA in tomato (Solanum lycopersicum). Silencing of CPK27 compromised acclimation-induced cold tolerance, generation of hydrogen peroxide (H2O2) in the apoplast, NO and ABA accumulation, and the activation of MPK1/2. Crosstalk among H2O2, NO, and MPK1/2 contributes to the homeostasis of H2O2 and NO, activation of MPK1/2, and cold tolerance. ABA is also critical for CPK27-induced cold tolerance, generation of H2O2 and NO, and the activation of MPK1/2. These results strongly suggest that CPK27 may function as a positive regulator of ABA generation by activating the production of ROS and NO as well as MPK1/2 in cold adaptation.

A new Em-like protein from Lactuca sativa, LsEm1, enhances drought and salt stress tolerance in Escherichia coli and rice

Late embryogenesis abundant (LEA) proteins are closely related to abiotic stress tolerance of plants. In the present study, we identified a novel Em-like gene from lettuce, termed LsEm1, which could be classified into group 1 LEA proteins, and shared high homology with Cynara cardunculus Em protein. The LsEm1 protein contained three different 20-mer conserved elements (C-element, N-element, and M-element) in the C-termini, N-termini, and middle-region, respectively. The LsEm1 mRNAs were accumulated in all examined tissues during the flowering and mature stages, with a little accumulation in the roots and leaves during the seedling stage. Furthermore, the LsEm1 gene was also expressed in response to salt, dehydration, abscisic acid (ABA), and cold stresses in young seedlings. The LsEm1 protein could effectively reduce damage to the lactate dehydrogenase (LDH) and protect LDH activity under desiccation and salt treatments. The Escherichia coli cells overexpressing the LsEm1 gene showed a growth advantage over the control under drought and salt stresses. Moreover, LsEm1-overexpressing rice seeds were relatively sensitive to exogenously applied ABA, suggesting that the LsEm1 gene might depend on an ABA signaling pathway in response to environmental stresses. The transgenic rice plants overexpressing the LsEm1 gene showed higher tolerance to drought and salt stresses than did wild-type (WT) plants on the basis of the germination performances, higher survival rates, higher chlorophyll content, more accumulation of soluble sugar, lower relative electrolyte leakage, and higher superoxide dismutase activity under stress conditions. The LsEm1-overexpressing rice lines also showed less yield loss compared with WT rice under stress conditions. Furthermore, the LsEm1 gene had a positive effect on the expression of the OsCDPK9, OsCDPK13, OsCDPK15, OsCDPK25, and rab21 (rab16a) genes in transgenic rice under drought and salt stress conditions, implying that overexpression of these genes may be involved in the enhanced drought and salt tolerance of transgenic rice. Thus, this work paves the way for improvement in tolerance of crops by genetic engineering breeding.

Identification and characterisation of a previously unknown drought tolerance-associated microRNA in barley

Drought is the most serious abiotic stress, and causes crop losses on a worldwide scale. The present study identified a previously unknown microRNA (designated as hvu-miRX) of 21 nucleotides (nt) in length in barley. Its precursor (designated pre-miRX) and primary transcript (designated pri-miRX) were also identified, with lengths of 73 and 559 nt, respectively. The identified upstream sequence of pri-miRX contained both the TATA box and the CAAT box, which are both required for initiation of transcription. Transient promoter activation assays showed that the core promoter region of pri-miRX ranged 500 nt from the transcription start site. In transgenic barley overexpression of the wheat DREB3 transcription factor (TaDREB3) caused hvu-miRX to be highly expressed as compared with the same miRNA in non-transgenic barley. However, the high expression was not directly associated with TaDREB3. Genomic analysis revealed that the hvu-miRX gene was a single copy located on the short arm of chromosome 2 and appeared to be only conserved in Triticeae, but not in other plant species. Notably, transgenic barley that overexpressed hvu-miRX showed drought tolerance. Degradome library analysis and other tests showed that hvu-miRX targeted various genes including transcription factors via the cleavage mode. Our data provides an excellent opportunity to develop drought stress tolerant cereals using hvu-miRX.