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

The CDPK-related protein kinase HvCRK2 and HvCRK4 interact with HvCML32 to negatively regulate drought tolerance in transgenic Arabidopsis thaliana

Calcium-dependent protein kinase (CDPK) as one of calcium sensors were play important roles in stress responses. CDPK-related protein kinase (CRK) was identified as subgroup III of CDPK has been characterized in many plants, but the members and functions of CRK genes in hulless barley (Hordeum vulgare L.) has not been clarified. Here, we identified four HvCRK genes and named HvCRK1-4 according to chromosomes localization. Moreover, the physiological function of highly induced genes of HvCRK2 and HvCRK4 were investigated in drought stress tolerance by examining their overexpression transgenic lines functions generated in Arabidopsis thaliana. Under drought stress, both overexpression HvCRK2 and HvCRK4 displayed reduced drought resistance, and accompanied by higher accumulation levels of ROS. Notably, overexpression of HvCRK2 and HvCRK4 reduced sensitivity to exogenous ABA, meanwhile the expression of ABA-responsive genes in transgenic plants were down-regulated compared to the wild type in response to drought stress. Furthermore, the physically interaction of HvCRK2 and HvCRK4 with calmodulin (CaM) and calmodulin-like (CML) proteins were determined in vivo, the further results showed that HvCML32 binds to HvCRK2/4 S_TKC structural domains and negatively regulates drought tolerance. In summary, this study identified HvCRK members and indicated that HvCRK2 and HvCRK4 genes play negative roles in drought tolerance, and provide insight into potential molecular mechanism of HvCRK2 and HvCRK4 in response to drought stress.

The role of omics in improving the orphan crop tef

Tef or teff [Eragrostis tef (Zucc.) Trotter] is a cereal crop indigenous to the Horn of Africa, where it is a staple food for a large population. The popularity of tef arises from its resilience to environmental stresses and its nutritional value. For many years, tef has been considered an orphan crop, but recent research initiatives from across the globe are helping to unravel its undisclosed potential. Advanced omics tools and techniques have been directed toward the exploration of tef's diversity with the aim of increasing its productivity. In this review, we report on the most recent advances in tef omics that brought the crop into the spotlight of international research.

Overexpression of OsNAR2.1 by OsNAR2.1 promoter increases drought resistance by increasing the expression of OsPLDα1 in rice

BACKGROUND

pOsNAR2.1:OsNAR2.1 expression could significantly increase nitrogen uptake efficiency and grain yield of rice.

RESULT

This study reported the effects of overexpression of OsNAR2.1 by OsNAR2.1 promoter on physiological and agronomic traits associated with drought tolerance. In comparison to the wild-type (WT), the pOsNAR2.1:OsNAR2.1 transgenic lines exhibited a significant improvement in survival rate when subjected to drought stress and then irrigation. Under limited water supply conditions, compared with WT, the photosynthesis and water use efficiency (WUE) of transgenic lines were increased by 39.2% and 28.8%, respectively. Finally, the transgenic lines had 25.5% and 66.4% higher grain yield than the WT under full watering and limited water supply conditions, respectively. Compared with the WT, the agronomic nitrogen use efficiency (NUE) of transgenic lines increased by 25.5% and 66.4% under full watering and limited water supply conditions, and the N recovery efficiency of transgenic lines increased by 29.3% and 50.2%, respectively. The interaction between OsNAR2.1 protein and OsPLDα1 protein was verified by yeast hybrids. After drought treatment, PLDα activity on the plasma membrane of the transgenic line increased 85.0% compared with WT.

CONCLUSION

These results indicated that pOsNAR2.1:OsNAR2.1 expression could improve the drought resistance of rice by increasing nitrogen uptake and regulating the expression of OsPLDα1.

QTLs and Genes for Salt Stress Tolerance: A Journey from Seed to Seed Continued

Rice (Oryza sativa L.) is a crucial crop contributing to global food security; however, its production is susceptible to salinity, a significant abiotic stressor that negatively impacts plant germination, vigour, and yield, degrading crop production. Due to the presence of exchangeable sodium ions (Na+), the affected plants sustain two-way damage resulting in initial osmotic stress and subsequent ion toxicity in the plants, which alters the cell's ionic homeostasis and physiological status. To adapt to salt stress, plants sense and transfer osmotic and ionic signals into their respective cells, which results in alterations of their cellular properties. No specific Na+ sensor or receptor has been identified in plants for salt stress other than the SOS pathway. Increasing productivity under salt-affected soils necessitates conventional breeding supplemented with biotechnological interventions. However, knowledge of the genetic basis of salinity stress tolerance in the breeding pool is somewhat limited because of the complicated architecture of salinity stress tolerance, which needs to be expanded to create salt-tolerant variants with better adaptability. A comprehensive study that emphasizes the QTLs, genes and governing mechanisms for salt stress tolerance is discussed in the present study for future research in crop improvement.

Unraveling wheat's response to salt stress during early growth stages through transcriptomic analysis and co-expression network profiling

BACKGROUND

Soil salinization is one of the vital factors threatening the world's food security. To reveal the biological mechanism of response to salt stress in wheat, this study was conducted to resolve the transcription level difference to salt stress between CM6005 (salt-tolerant) and KN9204 (salt-sensitive) at the germination and seedling stage.

RESULTS

To investigate the molecular mechanism underlying salt tolerance in wheat, we conducted comprehensive transcriptome analyses at the seedling and germination stages. Two wheat cultivars, CM6005 (salt-tolerant) and KN9204 (salt-sensitive) were subjected to salt treatment, resulting in a total of 24 transcriptomes. Through expression-network analysis, we identified 17 modules, 16 and 13 of which highly correlate with salt tolerance-related phenotypes in the germination and seedling stages, respectively. Moreover, we identified candidate Hub genes associated with specific modules and explored their regulatory relationships using co-expression data. Enrichment analysis revealed specific enrichment of gibberellin-related terms and pathways in CM6005, highlighting the potential importance of gibberellin regulation in enhancing salt tolerance. In contrast, KN9204 exhibited specific enrichment in glutathione-related terms and activities, suggesting the involvement of glutathione-mediated antioxidant mechanisms in conferring resistance to salt stress. Additionally, glucose transport was found to be a fundamental mechanism for salt tolerance during wheat seedling and germination stages, indicating its potential universality in wheat. Wheat plants improve their resilience and productivity by utilizing adaptive mechanisms like adjusting osmotic balance, bolstering antioxidant defenses, accumulating compatible solutes, altering root morphology, and regulating hormones, enabling them to better withstand extended periods of salt stress.

CONCLUSION

Through utilizing transcriptome-level analysis employing WGCNA, we have revealed a potential regulatory mechanism that governs the response to salt stress and recovery in wheat cultivars. Furthermore, we have identified key candidate central genes that play a crucial role in this mechanism. These central genes are likely to be vital components within the gene expression network associated with salt tolerance. The findings of this study strongly support the molecular breeding of salt-tolerant wheat, particularly by utilizing the genetic advancements based on CM6005 and KN9204.

Physiological and transcriptomic comparisons shed light on the cold stress response mechanisms of Dendrobium spp

BACKGROUND

Dendrobium spp. comprise a group of tropical orchids with ornamental and medicinal value. Dendrobium spp. are sensitive to low temperature, and the underlying cold response regulatory mechanisms in this group are unclear. To understand how these plants respond to cold stress, we compared the transcriptomic responses of the cold-tolerant cultivar 'Hongxing' (HX) and the cold-sensitive cultivar 'Sonia Hiasakul' (SH) to cold stress.

RESULTS

Chemometric results showed that the physiological response of SH in the later stages of cold stress is similar to that of HX throughout the cold treatment. Orthogonal partial least squares discriminant analysis (OPLS-DA) revealed that soluble protein content and peroxidase activity are key physiological parameters for assessing the cold tolerance of these two Dendrobium spp. cultivars. Additionally, weighted gene co-expression network analysis (WGCNA) results showed that many cold response genes and metabolic pathways significantly associated with the physiological indices were enriched in the 12 detected modules. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) enrichment analyses of the 105 hub genes showed that Dendrobium spp. adapt to cold stress by regulating signal transduction, phytohormones, transcription factors, protein translation and modification, functional proteins, biosynthesis and metabolism, cell structure, light, and the circadian clock. Hub genes of the cold stress response network included the remorin gene pp34, the abscisic acid signaling pathway-related genes PROTEIN PHOSPATASE 2 C (PP2C), SNF1-RELATED PROTEIN KINASE 2 (SnRK2), ABRE-BINDING FACTOR 1 (ABF1) and SKI-INTERACTING PROTEIN 17 (SKIP17), the Ca2+ signaling-related GTP diphosphokinase gene CRSH1, the carbohydrate-related gene STARCH SYNTHASE 2 (SS2), the cell wall biosynthesis gene CINNAMYL ALCOHOL DEHYDROGENASE (CAD7), and the endocytosis-related gene VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 52 A (VPS52A).

CONCLUSIONS

The cold-responsive genes and metabolic pathways of Dendrobium spp. revealed in this study provide important insight to enable the genetic enhancement of cold tolerance in Dendrobium spp., and to facilitate cold tolerance breeding in related plants.

Gene pyramiding for boosted plant growth and broad abiotic stress tolerance

Abiotic stresses such as salinity, heat and drought seriously impair plant growth and development, causing a significant loss in crop yield and ornamental value. Biotechnology approaches manipulating specific genes prove to be effective strategies in crop trait modification. The Arabidopsis vacuolar pyrophosphatase gene AVP1, the rice SUMO E3 ligase gene OsSIZ1 and the cyanobacterium flavodoxin gene Fld have previously been implicated in regulating plant stress responses and conferring enhanced tolerance to different abiotic stresses when individually overexpressed in various plant species. We have explored the feasibility of combining multiple favourable traits brought by individual genes to acquire superior plant performance. To this end, we have simultaneously introduced AVP1, OsSIZ1 and Fld in creeping bentgrass. Transgenic (TG) plants overexpressing these three genes performed significantly better than wild type controls and the TGs expressing individual genes under both normal and various abiotic stress conditions, exhibited significantly enhanced plant growth and tolerance to drought, salinity and heat stresses as well as nitrogen and phosphate starvation, which were associated with altered physiological and biochemical characteristics and delicately fine-tuned expression of genes involved in plant stress responses. Our results suggest that AVP1, OsSIZ1 and Fld function synergistically to regulate plant development and plant stress response, leading to superior overall performance under both normal and adverse environments. The information obtained provides new insights into gene stacking as an effective approach for plant genetic engineering. A similar strategy can be extended for the use of other beneficial genes in various crop species for trait modifications, enhancing agricultural production.

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple stress-related traits obtained by different studies. Making use of a combined set of 46 salinity-related traits from three independent studies that were based on the same chromosome segment substitution line (CSSL) population of rice (Oryza sativa), we demonstrate how our approach can address technical biases and limitations from different QTL studies and calling methods. This allows us to compile a comprehensive list of trait-specific and multi-trait QTLs, as well as salinity-related candidate genes. In doing so, we discover several novel relationships between traits that demonstrate similar trends of phenotype scores across the CSSLs, as well as the similarities between genomic locations that the traits were mapped to. Finally, we experimentally validate our findings by expression analyses and functional validations of several selected candidate genes from multiple pathways in rice and Arabidopsis orthologous genes, including OsKS7 (ENT-KAURENE SYNTHASE 7), OsNUC1 (NUCLEOLIN 1) and OsFRO1 (FERRIC REDUCTASE OXIDASE 1) to name a few. This work not only introduces a novel approach for conducting comparative analyses of multiple QTLs, but also provides a list of candidate genes and testable hypotheses for salinity-related mechanisms across several biological pathways.

Pyramiding D-lactate dehydrogenase with the glyoxalase pathway enhances abiotic stress tolerance in plants

Methylglyoxal is a common cytotoxic metabolite produced in plants during multiple biotic and abiotic stress. To mitigate the toxicity of MG, plants utilize the glyoxalase pathway comprising glyoxalase I (GLYI), glyoxalase II (GLYII), or glyoxalase III (GLYIII). GLYI and GLYII are the key enzymes of glyoxalase pathways that play an important role in abiotic stress tolerance. Earlier research showed that MG level is lower when both GLYI and GLYII are overexpressed together, compared to GLYI or GLYII single gene overexpressed transgenic plants. D-lactate dehydrogenase (D-LDH) is an integral part of MG detoxification which metabolizes the end product (D-lactate) of the glyoxalase pathway. In this study, two Arabidopsis transgenic lines were constructed using gene pyramiding technique: GLYI and GLYII overexpressed (G-I + II), and GLYI, GLYII, and D-LDH overexpressed (G-I + II + D) plants. G-I + II + D exhibits lower MG and D-lactate levels and enhanced abiotic stress tolerance than the G-I + II and wild-type plants. Further study explores the stress tolerance mechanism of G-I + II + D plants through the interplay of different regulators and plant hormones. This, in turn, modulates the expression of ABA-dependent stress-responsive genes like RAB18, RD22, and RD29B to generate adaptive responses during stress. Therefore, there might be a potential correlation between ABA and MG detoxification pathways. Furthermore, higher STY46, GPX3, and CAMTA1 transcripts were observed in G-I + II + D plants during abiotic stress. Thus, our findings suggest that G-I + II + D has significantly improved MG detoxification, reduced oxidative stress-induced damage, and provided a better protective mechanism against abiotic stresses than G-I + II or wild-type plants.

Molecular Mechanisms and Regulatory Pathways Underlying Drought Stress Response in Rice

Rice is a staple food for 350 million people globally. Its yield thus affects global food security. Drought is a serious environmental factor affecting rice growth. Alleviating the inhibition of drought stress is thus an urgent challenge that should be solved to enhance rice growth and yield. This review details the effects of drought on rice morphology, physiology, biochemistry, and the genes associated with drought stress response, their biological functions, and molecular regulatory pathways. The review further highlights the main future research directions to collectively provide theoretical support and reference for improving drought stress adaptation mechanisms and breeding new drought-resistant rice varieties.

Uncovering Novel QTLs and Candidate Genes for Salt Tolerance at the Bud Burst Stage in Rice through Genome-Wide Association Study

Salt stress is one of the most important factors limiting rice growth and yield increase. Salt tolerance of rice at the bud burst (STB) stage determines whether germinated seeds can grow normally under salt stress, which is very important for direct seeding. However, reports on quantitative trait loci (QTLs) and candidate genes for STB in rice are very limited. In this study, a natural population of 130 indica and 81 japonica rice accessions was used to identify STB-related QTLs and candidate genes using a genome-wide association study (GWAS). Nine QTLs, including five for relative shoot length (RSL), two for relative root length (RRL), and two for relative root number (RRN), were identified. Five of these STB-related QTLs are located at the same site as the characterized salt tolerance genes, such as OsMDH1, OsSRFP1, and OsCDPK7. However, an important QTL related to RSL, qRSL1-2, has not been previously identified and was detected on chromosome 1. The candidate region for qRSL1-2 was identified by linkage disequilibrium analysis, 18 genes were found to have altered expression levels under salt stress through the RNA-seq database, and 10 of them were found to be highly expressed in the shoot. It was also found that, eight candidate genes (LOC_Os01g62980, LOC_Os01g63190, LOC_Os01g63230, LOC_Os01g63280, LOC_Os01g63400, LOC_Os01g63460, and LOC_Os01g63580) for qRSL1-2 carry different haplotypes between indica and japonica rice, which exactly corresponds to the significant difference in RSL values between indica and japonica rice in this study. Most of the accessions with elite haplotypes were indica rice, which had higher RSL values. These genes with indica-japonica specific haplotypes were identified as candidate genes. Rice accessions with elite haplotypes could be used as important resources for direct seeding. This study also provides new insights into the genetic mechanism of STB.

Proline interacts with Ca2+-dependent signaling to enhance chromium tolerance in rice by manipulating nitrate reductase and sucrose phosphate synthase

The entrance of chromium (Cr) into the agricultural system would exert a negative influence on the carbon/nitrogen metabolism (CNM) of plants. In this study, we investigated the role of exogenous proline-mediated Ca2+-dependent signaling in the regulation of CNM in rice subjected to Cr(VI) stress, with emphasis on the involvement of nitrate reductase (NR) and sucrose phosphate synthase (SPS). Results demonstrated that proline effectively mitigated the growth inhibition of rice imposed by Cr(VI) stress, which is achieved by a reduction in cytoplasmic Ca and Cr content and the activation of the downstream Ca2+-dependent signaling pathway. Additionally, proline displayed a positive effect in modulating the expression and activities of NR and SPS under Cr(VI) stress, which are attributed to the cross-regulation between calcium-dependent protein kinases (CDPKs) and 14-3-3 proteins (14-3-3s). Consequently, nitrogen use efficiency and sucrose content in rice under Cr(VI) + proline treatments were higher than Cr(VI) treatments. Gene expression variation factors underscored that the regulation of proline on NR is crucial to the Ca2+-dependent signaling pathway, initiated by the interaction between CDPKs and 14-3-3s in rice plants during Cr(VI) stress. These results reveal that proline interacts with Ca2+-dependent signaling pathways to enhance Cr tolerance in rice by regulating NR and SPS.

Genome-Wide Identification and Characterization of CDPK Gene Family in Cultivated Peanut (Arachis hypogaea L.) Reveal Their Potential Roles in Response to Ca Deficiency

This study identified 45 calcium-dependent protein kinase (CDPK) genes in cultivated peanut (Arachis hypogaea L.), which are integral in plant growth, development, and stress responses. These genes, classified into four subgroups based on phylogenetic relationships, are unevenly distributed across all twenty peanut chromosomes. The analysis of the genetic structure of AhCDPKs revealed significant similarity within subgroups, with their expansion primarily driven by whole-genome duplications. The upstream promoter sequences of AhCDPK genes contained 46 cis-acting regulatory elements, associated with various plant responses. Additionally, 13 microRNAs were identified that target 21 AhCDPK genes, suggesting potential post-transcriptional regulation. AhCDPK proteins interacted with respiratory burst oxidase homologs, suggesting their involvement in redox signaling. Gene ontology and KEGG enrichment analyses affirmed AhCDPK genes' roles in calcium ion binding, protein kinase activity, and environmental adaptation. RNA-seq data revealed diverse expression patterns under different stress conditions. Importantly, 26 AhCDPK genes were significantly induced when exposed to Ca deficiency during the pod stage. During the seedling stage, four AhCDPKs (AhCDPK2/-25/-28/-45) in roots peaked after three hours, suggesting early signaling roles in pod Ca nutrition. These findings provide insights into the roles of CDPK genes in plant development and stress responses, offering potential candidates for predicting calcium levels in peanut seeds.

OsWRKY97, an Abiotic Stress-Induced Gene of Rice, Plays a Key Role in Drought Tolerance

Drought stress is one of the major causes of crop losses. The WRKY families play important roles in the regulation of many plant processes, including drought stress response. However, the function of individual WRKY genes in plants is still under investigation. Here, we identified a new member of the WRKY families, OsWRKY97, and analyzed its role in stress resistance by using a series of transgenic plant lines. OsWRKY97 positively regulates drought tolerance in rice. OsWRKY97 was expressed in all examined tissues and could be induced by various abiotic stresses and abscisic acid (ABA). OsWRKY97-GFP was localized to the nucleus. Various abiotic stress-related cis-acting elements were observed in the promoters of OsWRKY97. The results of OsWRKY97-overexpressing plant analyses revealed that OsWRKY97 plays a positive role in drought stress tolerance. In addition, physiological analyses revealed that OsWRKY97 improves drought stress tolerance by improving the osmotic adjustment ability, oxidative stress tolerance, and water retention capacity of the plant. Furthermore, OsWRKY97-overexpressing plants also showed higher sensitivity to exogenous ABA compared with that of wild-type rice (WT). Overexpression of OsWRKY97 also affected the transcript levels of ABA-responsive genes and the accumulation of ABA. These results indicate that OsWRKY97 plays a crucial role in the response to drought stress and may possess high potential value in improving drought tolerance in rice.

Comparative transcriptome analysis of grafting to improve chilling tolerance of cucumber

Grafting with pumpkin as rootstock could improve chilling tolerance of cucumber; however, the underlying mechanism of grafting-induced chilling tolerance remains unclear. Here, we analyzed the difference of physiological and transcriptional level between own-rooted (Cs/Cs) and hetero-grafted (Cs/Cm) cucumber seedlings under chilling stress. The results showed that grafting with pumpkin significantly alleviated the chilling injury as evidenced by slightly symptoms, lower contents of electrolyte leakage (EL), malondialdehyde (MDA), hydrogen peroxide (H2O2), and superoxide anion (O2-) and higher relative water content in Cs/Cm seedlings compared with Cs/Cs seedlings under chilling stress. RNA-seq data showed that grafting induced more DGEs at 8 °C/5 °C compared with 25 °C/18 °C. In accordance with the increase of the activities of antioxidant enzymes (SOD, POD, CAT, APX), grafting upregulated the expression of the regulated redox-related genes such as GST, SOD, and APX. Moreover, grafting increased the expression of genes participated in central carbon metabolism to promote the conversion and decomposition of sugar, which provided more energy for the growth of Cs/Cm seedlings under chilling stress. In addition, grafting regulated the genes involved in the intracellular signal transduction pathways such as calcium signal (CAML, CML, and CDPK) and inositol phospholipid signal (PLC), as well as changed the gene expression of plant hormone signal transduction pathways (ARF, GAI, ABF, and PYR/PYL). These results provide a physiological and transcriptional basis for the molecular mechanism of grafting-induced chilling tolerance of cucumber seedlings.

Genome-wide association analysis provides insights into the genetic basis of photosynthetic responses to low-temperature stress in spring barley

Low-temperature stress (LTS) is among the major abiotic stresses affecting the geographical distribution and productivity of the most important crops. Understanding the genetic basis of photosynthetic variation under cold stress is necessary for developing more climate-resilient barley cultivars. To that end, we investigated the ability of chlorophyll fluorescence parameters (F_VF_M, and F_VF₀) to respond to changes in the maximum quantum yield of Photosystem II photochemistry as an indicator of photosynthetic energy. A panel of 96 barley spring cultivars from different breeding zones of Canada was evaluated for chlorophyll fluorescence-related traits under cold acclimation and freeze shock stresses at different times. Genome-wide association studies (GWAS) were performed using a mixed linear model (MLM). We identified three major and putative genomic regions harboring 52 significant quantitative trait nucleotides (QTNs) on chromosomes 1H, 3H, and 6H for low-temperature tolerance. Functional annotation indicated several QTNs were either within the known or close to genes that play important roles in the photosynthetic metabolites such as abscisic acid (ABA) signaling, hydrolase activity, protein kinase, and transduction of environmental signal transduction at the posttranslational modification levels. These outcomes revealed that barley plants modified their gene expression profile in response to decreasing temperatures resulting in physiological and biochemical modifications. Cold tolerance could influence a long-term adaption of barley in many parts of the world. Since the degree and frequency of LTS vary considerably among production sites. Hence, these results could shed light on potential approaches for improving barley productivity under low-temperature stress.

Recent Molecular Aspects and Integrated Omics Strategies for Understanding the Abiotic Stress Tolerance of Rice

Rice is an important staple food crop for over half of the world's population. However, abiotic stresses seriously threaten rice yield improvement and sustainable production. Breeding and planting rice varieties with high environmental stress tolerance are the most cost-effective, safe, healthy, and environmentally friendly strategies. In-depth research on the molecular mechanism of rice plants in response to different stresses can provide an important theoretical basis for breeding rice varieties with higher stress resistance. This review presents the molecular mechanisms and the effects of various abiotic stresses on rice growth and development and explains the signal perception mode and transduction pathways. Meanwhile, the regulatory mechanisms of critical transcription factors in regulating gene expression and important downstream factors in coordinating stress tolerance are outlined. Finally, the utilization of omics approaches to retrieve hub genes and an outlook on future research are prospected, focusing on the regulatory mechanisms of multi-signaling network modules and sustainable rice production.

Transcriptomic Analysis of Yunwu Tribute Tea Leaves under Cold Stress

Background: Cold stress usually occurs in winter and is one of the most significant environmental factors restricting the growth of the tea plant as well as its geographical distribution. Objective: It is necessary to identify the physiological and molecular mechanisms of plants under cold stress so that cold-tolerant crop varieties can be cultivated to limit production losses. At the same time, this would allow the crop planting area to be expanded, hence improving the economic benefits. Methods: In this study, the transcriptome data of Yunwu Tribute Tea under cold conditions were obtained using the Illumina HiSeq platform. By analyzing changes in transcriptome data associated with the antioxidant enzyme system, plant hormone signal transduction, proline and tyrosine metabolism pathways, and transcription factors, the molecular mechanisms involved in Yunwu Tribute Tea under cold stress were investigated. Results: In this study, Illumina HiSeq technology was applied to investigate the cold-tolerance mechanism. For this purpose, cDNA libraries were obtained from two groups of samples, namely the cold-treated group (DW) and the control group (CK). A total of 185,973 unigenes were produced from 511,987 assembled transcripts; among these, 16,020 differentially expressed genes (DEGs) (corrected p-value < 0.01, |log2(fold change)| >3), including 9606 up-regulated and 6414 down-regulated genes, were obtained. Moreover, the antioxidant enzyme system, plant hormone signal transduction, proline and tyrosine metabolism pathways, and transcription factors were analyzed; based on these results, a series of candidate genes related to cold stress were screened out and discussed. The physiological indexes related to the low-temperature response were tested, along with five DEGs which were validated by quantitative real-time PCR. Conclusions: Differential gene expression analysis has confirmed that substantial cold-responsive genes are related to the antioxidant enzyme system, plant hormone signal transduction, proline metabolism pathway, tyrosine metabolism pathway, and transcription factors.

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

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

Transcriptomic Analysis Provides Novel Insights into the Heat Stress-Induced Response in Codonopsis tangshen

Codonopsis tangshen Oliv (C. tangshen) is a valuable traditional Chinese medicinal herb with tremendous health benefits. However, the growth and development of C. tangshen are seriously affected by high temperatures. Therefore, understanding the molecular responses of C. tangshen to high-temperature stress is imperative to improve its thermotolerance. Here, RNA-Seq analysis was performed to investigate the genome-wide transcriptional changes in C. tangshen in response to short-term heat stress. Heat stress significantly damages membrane stability and chlorophyll biosynthesis in C. tangshen, as evidenced by pronounced malonaldehyde (MDA), electrolyte leakage (EL), and reduced chlorophyll content. Transcriptome analysis showed that 2691 differentially expressed genes (DEGs) were identified, including 1809 upregulated and 882 downregulated. Functional annotations revealed that the DEGs were mainly related to heat shock proteins (HSPs), ROS-scavenging enzymes, calcium-dependent protein kinases (CDPK), HSP-HSP network, hormone signaling transduction pathway, and transcription factors such as bHLHs, bZIPs, MYBs, WRKYs, and NACs. These heat-responsive candidate genes and TFs could significantly regulate heat stress tolerance in C. tangshen. Overall, this study could provide new insights for understanding the underlying molecular mechanisms of thermotolerance in C. tangshen.

A single-nucleotide polymorphism in WRKY33 promoter is associated with the cold sensitivity in cultivated tomato

Natural variations in cis-regulatory regions often affect crop phenotypes by altering gene expression. However, the mechanism of how promoter mutations affect gene expression and crop stress tolerance is still poorly understood. In this study, by analyzing RNA-sequencing (RNA-Seq) data and reverse transcription quantitative real-time PCR validation in the cultivated tomato and its wild relatives, we reveal that the transcripts of WRKY33 are almost unchanged in cold-sensitive cultivated tomato Solanum lycopersicum L. 'Ailsa Craig' but are significantly induced in cold-tolerant wild tomato relatives Solanum habrochaites LA1777 and Solanum pennellii LA0716 under cold stress. Overexpression of SlWRKY33 or ShWRKY33 positively regulates cold tolerance in tomato. Variant of the critical W-box in SlWRKY33 promoter results in the loss of self-transcription function of SlWRKY33 under cold stress. Analysis integrating RNA-Seq and chromatin immunoprecipitation sequencing data reveals that SlWRKY33 directly targets and induces multiple kinases, transcription factors, and molecular chaperone genes, such as CDPK11, MYBS3, and BAG6, thus enhancing cold tolerance. In addition, heat- and Botrytis-induced WRKY33s expression in both wild and cultivated tomatoes are independent of the critical W-box variation. Our findings suggest nucleotide polymorphism in cis-regulatory regions is crucial for different cold sensitivity between cultivated and wild tomato plants.

Heme is involved in the exogenous ALA-promoted growth and antioxidant defense system of cucumber seedlings under salt stress

A biosynthetic precursor of tetrapyrrol, 5-aminolevulinic acid (ALA), is widely used in agricultural production, as an exogenous regulatory substance that effectively regulates plant growth. Previous studies have shown that heme and chlorophyll accumulate in plants under salt stress, when treated with exogenous ALA. In this study, we explored the regulatory role of heme in plants, by spraying 25 mg L^-1 ALA onto the leaves of cucumber seedlings treated with heme synthesis inhibitor (2,2'-dipyridyl, DPD) and heme scavenger (hemopexin, Hx), under 50 mmol L^-1 NaCl stress. The results showed that NaCl alone and DPD + Hx treatments to cucumber seedlings subjected to salt stress adversely affected their growth, by decreasing biomass accumulation, root activity, and root morphology. In addition, these treatments induced an increase in membrane lipid oxidation, as well as enhancement of anti-oxidase activities, proline content, and glutamate betaine. However, exogenous ALA application increased the plant growth and root architecture indices under NaCl stress, owing to a lack of heme in the seedlings. In addition, cucumber seedlings treated with DPD and Hx showed inhibition of growth under salt stress, but exogenous ALA effectively improved cucumber seedling growth as well as the physiological characteristics; moreover, the regulation of ALA in plants was weakened when heme synthesis was inhibited. Heme biosynthesis and metabolism genes, HEMH and HO1, which are involved in the ALA metabolic pathway, were upregulated under salinity conditions, when ferrochelatase activity was inhibited. Application of exogenous ALA increased the heme content in the leaves. Thus, exogenous ALA may supplement the substrates for heme synthesis. These results indicated that heme plays a vital role in the response of plants to salinity stress. In conclusion, heme is involved in ALA-mediated alleviation of damage caused to cucumber seedlings and acts as a positive regulator of plant adaption.

CPK28-NLP7 module integrates cold-induced Ca2+ signal and transcriptional reprogramming in Arabidopsis

Exposure to cold triggers a spike in cytosolic calcium (Ca²⁺) that often leads to transcriptional reprogramming in plants. However, how this Ca²⁺ signal is perceived and relayed to the downstream cold signaling pathway remains unknown. Here, we show that the CALCIUM-DEPENDENT PROTEIN KINASE 28 (CPK28) initiates a phosphorylation cascade to specify transcriptional reprogramming downstream of cold-induced Ca²⁺ signal. Plasma membrane (PM)-localized CPK28 is activated rapidly upon cold shock within 10 seconds in a Ca²⁺-dependent manner. CPK28 then phosphorylates and promotes the nuclear translocation of NIN-LIKE PROTEIN 7 (NLP7), a transcription factor that specifies the transcriptional reprogramming of cold-responsive gene sets in response to Ca²⁺, thereby positively regulating plant response to cold stress. This study elucidates a previously unidentified mechanism by which the CPK28-NLP7 regulatory module integrates cold-evoked Ca²⁺ signal and transcriptome and thus uncovers a key strategy for the rapid perception and transduction of cold signals from the PM to the nucleus.

Cultivar-specific miRNA-mediated RNA silencing in grapes

In-depth comparative degradome analysis of two domesticated grape cultivars with diverse secondary metabolite accumulation reveals differential miRNA-mediated targeting. Small (s)RNAs such as micro(mi)RNAs and secondary small interfering (si) often work as negative switches of gene expression. In plants, it is well known that miRNAs target and cleave mRNAs that have high sequence complementarity. However, it is not known if there are variations in miRNA-mediated targeting between subspecies and cultivars that have been subjected to vast genetic modifications through breeding and other selections. Here, we have used PAREsnip2 tool for analysis of degradome datasets derived from two contrasting domesticated grape cultivars having varied fruit color, habit and leaf shape. We identified several interesting variations in sRNA targeting using degradome and 5'RACE analysis between two contrasting grape cultivars that was further correlated using RNA-seq analysis. Several of the differences we identified are associated with secondary metabolic pathways. We propose possible means by which sRNAs might contribute to diversity in secondary metabolites and other development pathways between two domesticated cultivars of grapes.

AT-HOOK MOTIF NUCLEAR LOCALIZED (AHL) proteins of ancient origin radiate new functions

AHL (AT-HOOK MOTIF NUCLEAR LOCALIZED) protein is an important transcription factor in plants that regulates a wide range of biological process. It is considered to have evolved from an independent PPC domain in prokaryotes to a complete protein in modern plants. AT-hook motif and PPC conserved domains are the main functional domains of AHL. Since the discovery of AHL, their evolution and function have been continuously studied. The AHL gene family has been identified in multiple species and the functions of several members of the gene family have been studied. Here, we summarize the evolution and structural characteristics of AHL genes, and emphasize their biological functions. This review will provide a basis for further functional study and crop breeding.

Overview of the roles of calcium sensors in plants&#x2019; response to osmotic stress signalling

Calcium signals serve an important function as secondary messengers between cells in various biological processes due to their robust homeostatic mechanism, maintaining an intracellular free Ca2+ concentration. Plant growth, development, and biotic and abiotic stress are all regulated by Ca2+ signals. Ca2+ binding proteins decode and convey the messages encoded by Ca2+ ions. In the presence of high quantities of Mg2+ and monovalent cations, such sensors bind to Ca2+ ions and modify their conformation in a Ca2+ -dependent manner. Calcium-dependent protein kinases (CPKs), calmodulins (CaMs), and calcineurin B-like proteins are all calcium sensors (CBLs). To transmit Ca2+ signals, CPKs, CBLs, and CaMs interact with target proteins and regulate the expression of their genes. These target proteins may be protein kinases, metabolic enzymes, or cytoskeletal-associated proteins. Beyond its role in plant nutrition as a macroelement and its involvement in the plant cell wall structure, calcium modulates many aspects of development, growth and adaptation to environmental constraints such as drought, salinity and osmotic stresses. This review summarises current knowledge on calcium sensors in plant responses to osmotic stress signalling.

A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms

Soil salinity is one of the most serious environmental challenges, posing a growing threat to agriculture across the world. Soil salinity has a significant impact on rice growth, development, and production. Hence, improving rice varieties’ resistance to salt stress is a viable solution for meeting global food demand. Adaptation to salt stress is a multifaceted process that involves interacting physiological traits, biochemical or metabolic pathways, and molecular mechanisms. The integration of multi-omics approaches contributes to a better understanding of molecular mechanisms as well as the improvement of salt-resistant and tolerant rice varieties. Firstly, we present a thorough review of current knowledge about salt stress effects on rice and mechanisms behind rice salt tolerance and salt stress signalling. This review focuses on the use of multi-omics approaches to improve next-generation rice breeding for salinity resistance and tolerance, including genomics, transcriptomics, proteomics, metabolomics and phenomics. Integrating multi-omics data effectively is critical to gaining a more comprehensive and in-depth understanding of the molecular pathways, enzyme activity and interacting networks of genes controlling salinity tolerance in rice. The key data mining strategies within the artificial intelligence to analyse big and complex data sets that will allow more accurate prediction of outcomes and modernise traditional breeding programmes and also expedite precision rice breeding such as genetic engineering and genome editing.

Identification and expression assay of calcium-dependent protein kinase family genes in Hevea brasiliensis and determination of HbCDPK5 functions in disease resistance

Calcium (Ca2+) signaling is one of the earliest factors to coordinate plant adaptive responses. As direct sensors and activators of Ca2+ signals, calcium-dependent protein kinases (CDPKs) were reported to be widely involved in regulating different biotic and abiotic stress stimuli. In this study, 32 Hevea brasiliensis CDPK (HbCDPK) genes were predicted and classified into four subgroups. Among them, the full-length coding sequences of 28 HbCDPK genes were confirmed by RT-PCR and verified by sequencing. Putative cis-elements assay in the promoters of HbCDPKs showed that most of the HbCDPK genes contained gibberellic acid-responsive element (GARE), abscisic acid-responsive element (ABRE), salicylic acid-responsive element (SARE), defense and stress responsive element (TC-rich repeats) and low-temperature response element (LTR), which could be activated by different biotic and abiotic stresses. Real-time PCR analysis indicated that 28 HbCDPK genes respond to infection of pathogenic fungi and a variety of phytohormones. Subcellular localization was observed with most HbCDPKs located in cell membrane, cytoplasm or organelles. Some HbCDPKs were confirmed to cause reactive oxygen species (ROS) production and accumulation in rubber tree mesophyll protoplast directly. HbCDPK5 was strongly induced by the inoculation with Colletotrichum gloeosporioides and was chosen for further analysis. HbCDPK5 localized to the cell membrane and cytoplasm, and obviously regulated the accumulation of ROS in rubber tree mesophyll protoplast. Overexpression of HbCDPK5 in Arabidopsis enhanced the resistance to Botrytis cinerea. These results indicate that rubber tree CDPK genes play important roles in plant disease resistance.

Analysis of miRNAs responsive to long-term calcium deficiency in tef (Eragrostis tef (Zucc.) Trotter)

MicroRNAs (miRNAs) play an important role in growth, development, stress resilience, and epigenetic modifications of plants. However, the effect of calcium (Ca²⁺) deficiency on miRNA expression in the orphan crop tef (Eragrostis tef) remains unknown. In this study, we analyzed expression of miRNAs in roots and shoots of tef in response to Ca²⁺ treatment. miRNA-seq followed by bioinformatic analysis allowed us to identify a large number of small RNAs (sRNAs) ranging from 17 to 35 nt in length. A total of 1380 miRNAs were identified in tef experiencing long-term Ca²⁺ deficiency while 1495 miRNAs were detected in control plants. Among the miRNAs identified in this study, 161 miRNAs were similar with those previously characterized in other plant species and 348 miRNAs were novel, while the remaining miRNAs were uncharacterized. Putative target genes and their functions were predicted for all the known and novel miRNAs that we identified. Based on gene ontology (GO) analysis, the predicted target genes are known to have various biological and molecular functions including calcium uptake and transport. Pairwise comparison of differentially expressed miRNAs revealed that some miRNAs were specifically enriched in roots or shoots of low Ca²⁺-treated plants. Further characterization of the miRNAs and their targets identified in this study may help in understanding Ca²⁺ deficiency responses in tef and related orphan crops.

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

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

Gene-coexpression network analysis identifies specific modules and hub genes related to cold stress in rice

Background

When plants are subjected to cold stress, they undergo a series of molecular and physiological changes to protect themselves from injury. Indica cultivars can usually withstand only mild cold stress in a relatively short period. Hormone-mediated defence response plays an important role in cold stress. Weighted gene co-expression network analysis (WGCNA) is a very useful tool for studying the correlation between genes, identifying modules with high phenotype correlation, and identifying Hub genes in different modules. Many studies have elucidated the molecular mechanisms of cold tolerance in different plants, but little information about the recovery process after cold stress is available.

Results

To understand the molecular mechanism of cold tolerance in rice, we performed comprehensive transcriptome analyses during cold treatment and recovery stage in two cultivars of near-isogenic lines (9311 and DC907). Twelve transcriptomes in two rice cultivars were determined. A total of 2509 new genes were predicted by fragment splicing and assembly, and 7506 differentially expressed genes were identified by pairwise comparison. A total of 26 modules were obtained by expression-network analysis, 12 of which were highly correlated with cold stress or recovery treatment. We further identified candidate Hub genes associated with specific modules and analysed their regulatory relationships based on coexpression data. Results showed that various plant-hormone regulatory genes acted together to protect plants from physiological damage under short-term low-temperature stress. We speculated that this may be common in rice. Under long-term cold stress, rice improved the tolerance to low-temperature stress by promoting autophagy, sugar synthesis, and metabolism.

Conclusion

Through WGCNA analysis at the transcriptome level, we provided a potential regulatory mechanism for the cold stress and recovery of rice cultivars and identified candidate central genes. Our findings provided an important reference for the future cultivation of rice strains with good tolerance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08438-3.

Calcium-dependent protein kinase 2 plays a positive role in the salt stress response in potato

StCDPK2 is an early player in the salt stress response in potato plants; its overexpression promoted ROS scavenging, chlorophyll stability, and the induction of stress-responsive genes conferring tolerance to salinity. The salinity of soils affects plant development and is responsible for great losses in crop yields. Calcium-dependent protein kinases (CDPKs) are sensor-transducers that decode Ca²⁺ signatures triggered by abiotic stimuli and translate them into physiological responses. Histochemical analyses of potato plants harboring StCDPK2 promoter fused to the reporter gene β-glucuronidase (Pro_StCDPK2:GUS) revealed that GUS activity was high in the leaf blade and veins, it was restricted to root tips and lateral root primordia, and was observed upon stolon swelling. Comparison with Pro_StCDPK1:GUS and Pro_StCDPK3:GUS plants revealed their differential activities in the plant tissues. Pro_StCDPK2:GUS plants exposed to high salt presented enhanced GUS activity in roots which correlated with the numerous stress-responsive sites predicted in its promoter sequence. Moreover, StCDPK2 expression increased in in vitro potato plants after 2 h of high salt exposure and in greenhouse plants exposed to a dynamic stress condition. As inferred from biometric data and chlorophyll content, plants that overexpress StCDPK2 were more tolerant than wild-type plants when exposed to high salt. Overexpressing plants have a more efficient antioxidant system; they showed reduced accumulation of peroxide and higher catalase activity under salt conditions, and enhanced expression of WRKY6 and ERF5 transcription factors under control conditions. Our results indicate that StCDPK2 is an early player in the salt stress response and support a positive correlation between StCDPK2 overexpression and tolerance towards salt stress.

High-value pleiotropic genes for developing multiple stress-tolerant biofortified crops for 21st-century challenges

The agriculture-based livelihood systems that are already vulnerable due to multiple challenges face immediate risk of increased crop failures due to weather vagaries. As breeders and biotechnologists, our strategy is to advance and innovate breeding for weather-proofing crops. Plant stress tolerance is a genetically complex trait. Additionally, crops rarely face a single type of stress in isolation, and it is difficult for plants to deal with multiple stresses simultaneously. One of the most helpful approaches to creating stress-resilient crops is genome editing and trans- or cis-genesis. Out of hundreds of stress-responsive genes, many have been used to impart tolerance against a particular stress factor, while a few used in combination for gene pyramiding against multiple stresses. However, a better approach would be to use multi-role pleiotropic genes that enable plants to adapt to numerous environmental stresses simultaneously. Herein we attempt to integrate and present the scattered information published in the past three decades about these pleiotropic genes for crop improvement and remodeling future cropping systems. Research articles validating functional roles of genes in transgenic plants were used to create groups of multi-role pleiotropic genes that could be candidate genes for developing weather-proof crop varieties. These biotech crop varieties will help create 'high-value farms' to meet the goal of a sustainable increase in global food productivity and stabilize food prices by ensuring a fluctuation-free assured food supply. It could also help create a gene repository through artificial gene synthesis for 'resilient high-value food production' for the 21st century.

Calcium-dependent Protein Kinase 5 (CPK5) positively modulates drought tolerance through phosphorylating ABA-Responsive Element Binding Factors in oilseed rape (Brassica napus L.)

Drought is an environmental stress that causes severe crop loss. Drought stress can induce abscisic acid (ABA) accumulation and cytoplasmic calcium oscillation. Calcium-dependent protein kinases (CPKs) constitute a group of Ser/Thr protein kinases decoding calcium signals. However, the function and molecular mechanisms of most CPKs in oilseed rape (Brassica napus) remain unknown. Here, we report the functional characterization of BnaCPK5 in drought stress tolerance. BnaCPK5 belongs to Group I of the CPK family and was localized at the plasma membrane and nuclei. Overexpression of BnaCPK5 enhanced drought stress tolerance compared with the control. A screening of interacting proteins identified that BnaCPK5 interacted strongly with two ABA-Responsive Element Binding Factors (ABF/AREBs), BnaABF3 and BnaABF4. BnaCPK5 was shown to phosphorylate both BnaABF3 and BnaABF4 in a kinase assay. Further, it was found that the phosphorylation of BnaABF3 and BnaABF4 by BnaCPK5 increased their transcriptional activities against the famous drought stress marker gene, Responsive to Dehydration (RD) 29B and protein stability. Taken together, these data demonstrate that BnaCPK5 acts as a positive regulator of drought tolerance by, at least in part, phosphorylating two core ABA-signaling components to modulate Late-Embryogenesis Abundant (LEA)-like RD29B expression.

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

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

ERF Transcription Factor OsBIERF3 Positively Contributes to Immunity against Fungal and Bacterial Diseases but Negatively Regulates Cold Tolerance in Rice

We previously showed that overexpression of the rice ERF transcription factor gene OsBIERF3 in tobacco increased resistance against different pathogens. Here, we report the function of OsBIERF3 in rice immunity and abiotic stress tolerance. Expression of OsBIERF3 was induced by Xanthomonas oryzae pv. oryzae, hormones (e.g., salicylic acid, methyl jasmonate, 1-aminocyclopropane-1-carboxylic acid, and abscisic acid), and abiotic stress (e.g., drought, salt and cold stress). OsBIERF3 has transcriptional activation activity that depends on its C-terminal region. The OsBIERF3-overexpressing (OsBIERF3-OE) plants exhibited increased resistance while OsBIERF3-suppressed (OsBIERF3-Ri) plants displayed decreased resistance to Magnaporthe oryzae and X. oryzae pv. oryzae. A set of genes including those for PRs and MAPK kinases were up-regulated in OsBIERF3-OE plants. Cell wall biosynthetic enzyme genes were up-regulated in OsBIERF3-OE plants but down-regulated in OsBIERF3-Ri plants; accordingly, cell walls became thicker in OsBIERF3-OE plants but thinner in OsBIERF3-Ri plants than WT plants. The OsBIERF3-OE plants attenuated while OsBIERF3-Ri plants enhanced cold tolerance, accompanied by altered expression of cold-responsive genes and proline accumulation. Exogenous abscisic acid and 1-aminocyclopropane-1-carboxylic acid, a precursor of ethylene biosynthesis, restored the attenuated cold tolerance in OsBIERF3-OE plants while exogenous AgNO₃, an inhibitor of ethylene action, significantly suppressed the enhanced cold tolerance in OsBIERF3-Ri plants. These data demonstrate that OsBIERF3 positively contributes to immunity against M. oryzae and X. oryzae pv. oryzae but negatively regulates cold stress tolerance in rice.

Chilling tolerance in rice: Past and present

Rice is generally sensitive to chilling stress, which seriously affects growth and yield. Since early in the last century, considerable efforts have been made to understand the physiological and molecular mechanisms underlying the response to chilling stress and improve rice chilling tolerance. Here, we review the research trends and advances in this field. The phenotypic and biochemical changes caused by cold stress and the physiological explanations are briefly summarized. Using published data from the past 20 years, we reviewed the past progress and important techniques in the identification of quantitative trait loci (QTL), novel genes, and cellular pathways involved in rice chilling tolerance. The advent of novel technologies has significantly advanced studies of cold tolerance, and the characterization of QTLs, key genes, and molecular modules have sped up molecular design breeding for cold tolerance in rice varieties. In addition to gene function studies based on overexpression or artificially generated mutants, elucidating natural allelic variation in specific backgrounds is emerging as a novel approach for the study of cold tolerance in rice, and the superior alleles identified using this approach can directly facilitate breeding.

The rice phosphoinositide-specific phospholipase C3 is involved in responses to osmotic stresses via modulating ROS homeostasis

Four members of phosphoinositide-specific phospholipase C (PI-PLC) are predicted in rice genome. Although the involvement of OsPLC1 and OsPLC4 in the responses of rice to salt and drought stresses has been documented, the role of OsPLC3 in which, yet, is elusive. Here, we report that OsPLC3 was ubiquitously expressed in various tissues during the development of rice. The expression of YFP-tagged OsPLC3 was observed at the plasma membrane (PM), cytoplasm and nucleus of rice protoplasts, onion epidermal cells and tobacco leaves. The catalytic activity of OsPLC3 was measured using the thin-layer chromatography (TLC) method. The inhibition of OsPLC3 expression was detected in the treatments of NaCl and mannitol. Overexpression (OE) of OsPLC3 produced plants showing more sensitive to osmotic stresses when they were compared to the wild-type (HJ) and osplc3 mutants, the phenomena such as decreased plant fresh weight and increased water loss rate (WLR) were observed. Under the treatment of NaCl or mannitol, expressions of a subset osmotic stress-related genes were altered, in both OE and osplc3 mutant lines. In addition, the expressions and the enzyme activities of reactive oxygen species (ROS) scavengers were significantly decreased in OE lines, leading to over-accumulation of ROS together with less osmotic adjustment substances including proline, soluble sugars and soluble proteins in OE plants which caused the growth inhibition. Thus, our results suggested that, via modulating ROS homeostasis, OsPLC3 is involved in responses to the osmotic stress in rice.

Data-Independent Acquisition-Based Proteome and Phosphoproteome Profiling Reveals Early Protein Phosphorylation and Dephosphorylation Events in Arabidopsis Seedlings upon Cold Exposure

Protein phosphorylation plays an important role in mediating signal transduction in cold response in plants. To better understand how plants sense and respond to the early temperature drop, we performed data-independent acquisition (DIA) method-based mass spectrometry analysis to profile the proteome and phosphoproteome of Arabidopsis seedlings upon cold stress in a time-course manner (10, 30 and 120 min of cold treatments). Our results showed the rapid and extensive changes at the phosphopeptide levels, but not at the protein abundance levels, indicating cold-mediated protein phosphorylation and dephosphorylation events. Alteration of over 1200 proteins at phosphopeptide levels were observed within 2 h of cold treatment, including over 140 kinases, over 40 transcriptional factors and over 40 E3 ligases, revealing the complexity of regulation of cold adaption. We summarized cold responsive phosphoproteins involved in phospholipid signaling, cytoskeleton reorganization, calcium signaling, and MAPK cascades. Cold-altered levels of 73 phosphopeptides (mostly novel cold-responsive) representing 62 proteins were validated by parallel reaction monitoring (PRM). In summary, this study furthers our understanding of the molecular mechanisms of cold adaption in plants and strongly supports that DIA coupled with PRM are valuable tools in uncovering early signaling events in plants.

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

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

Overexpression of AtDREB1 and BcZAT12 genes confers drought tolerance by reducing oxidative stress in double transgenic tomato (Solanum lycopersicum L.)

Double transgenic tomato developed by AtDREB1A and BcZAT12 genes pyramiding showed significant drought tolerance by reducing oxidative stress with enhanced yield. Although a large number of efforts have been made by different researchers to develop abiotic stress tolerance tomato for improving yield using single gene, however, no reports are available which targets AtDREB1 and BcZAT12 genes together. Hence, in the present study, double transgenic plants were developed using AtDREB1 and BcZAT12 genes to improve yield potential with better drought tolerance. Double transgenic (DZ1-DZ5) tomato lines showed enhanced drought tolerance than their counterpart non-transgenic and single transgenic plants at 0, 07, 14, and 21 days of water deficit, respectively. Double transgenic plants showed increased activity of antioxidant enzymes, like catalase (CAT), superoxide dismutase (SOD), glutathione reductase (GR), ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR), monodehydroascorbate reductase (MDHAR) and guaiacol peroxidase (POD), and accumulation of non-enzymatic antioxidants like ascorbic acid, glutathione as compared to non-transgenic and single transgenic. Additionally, the transcript analysis of antioxidant enzymes revealed the increased level of gene expression in double transgenic tomato lines. Developed double-transgenic tomato plants co-over-expressing both genes exhibited more enzymatic and non-enzymatic anti-oxidative activities as compared to the non-transgenic and single transgenic control, respectively. This is the preliminary report in tomato, which forms the basis for a multigene transgenic approach to cope with drought stress.

Salicylic acid: A key regulator of redox signalling and plant immunity

In plants, the reactive oxygen species (ROS) formed during normal conditions are essential in regulating several processes, like stomatal physiology, pathogen immunity and developmental signaling. However, biotic and abiotic stresses can cause ROS over-accumulation leading to oxidative stress. Therefore, a suitable equilibrium is vital for redox homeostasis in plants, and there have been major advances in this research arena. Salicylic acid (SA) is known as a chief regulator of ROS; however, the underlying mechanisms remain largely unexplored. SA plays an important role in establishing the hypersensitive response (HR) and systemic acquired resistance (SAR). This is underpinned by a robust and complex network of SA with Non-Expressor of Pathogenesis Related protein-1 (NPR1), ROS, calcium ions (Ca²⁺), nitric oxide (NO) and mitogen-activated protein kinase (MAPK) cascades. In this review, we summarize the recent advances in the regulation of ROS and antioxidant defense system signalling by SA at the physiological and molecular levels. Understanding the molecular mechanisms of how SA controls redox homeostasis would provide a fundamental framework to develop approaches that will improve plant growth and fitness, in order to meet the increasing global demand for food and bioenergy.

Overexpression of AtDREB1 and BcZAT12 genes confers drought tolerance by reducing oxidative stress in double transgenic tomato (Solanum lycopersicum L.)

Double transgenic tomato developed by AtDREB1A and BcZAT12 genes pyramiding showed significant drought tolerance by reducing oxidative stress with enhanced yield. Although a large number of efforts have been made by different researchers to develop abiotic stress tolerance tomato for improving yield using single gene, however, no reports are available which targets AtDREB1 and BcZAT12 genes together. Hence, in the present study, double transgenic plants were developed using AtDREB1 and BcZAT12 genes to improve yield potential with better drought tolerance. Double transgenic (DZ1-DZ5) tomato lines showed enhanced drought tolerance than their counterpart non-transgenic and single transgenic plants at 0, 07, 14, and 21 days of water deficit, respectively. Double transgenic plants showed increased activity of antioxidant enzymes, like catalase (CAT), superoxide dismutase (SOD), glutathione reductase (GR), ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR), monodehydroascorbate reductase (MDHAR) and guaiacol peroxidase (POD), and accumulation of non-enzymatic antioxidants like ascorbic acid, glutathione as compared to non-transgenic and single transgenic. Additionally, the transcript analysis of antioxidant enzymes revealed the increased level of gene expression in double transgenic tomato lines. Developed double-transgenic tomato plants co-over-expressing both genes exhibited more enzymatic and non-enzymatic anti-oxidative activities as compared to the non-transgenic and single transgenic control, respectively. This is the preliminary report in tomato, which forms the basis for a multigene transgenic approach to cope with drought stress.

Convergence and Divergence: Signal Perception and Transduction Mechanisms of Cold Stress in Arabidopsis and Rice

Cold stress, including freezing stress and chilling stress, is one of the major environmental factors that limit the growth and productivity of plants. As a temperate dicot model plant species, Arabidopsis develops a capability to freezing tolerance through cold acclimation. The past decades have witnessed a deep understanding of mechanisms underlying cold stress signal perception, transduction, and freezing tolerance in Arabidopsis. In contrast, a monocot cereal model plant species derived from tropical and subtropical origins, rice, is very sensitive to chilling stress and has evolved a different mechanism for chilling stress signaling and response. In this review, the authors summarized the recent progress in our understanding of cold stress response mechanisms, highlighted the convergent and divergent mechanisms between Arabidopsis and rice plasma membrane cold stress perceptions, calcium signaling, phospholipid signaling, MAPK cascade signaling, ROS signaling, and ICE-CBF regulatory network, as well as light-regulated signal transduction system. Genetic engineering approaches of developing freezing tolerant Arabidopsis and chilling tolerant rice were also reviewed. Finally, the future perspective of cold stress signaling and tolerance in rice was proposed.

Genome-Wide Association Study Reveals the Genetic Basis of Chilling Tolerance in Rice at the Reproductive Stage

A genome-wide association study (GWAS) was used to investigate the genetic basis of chilling tolerance in a collection of 117 rice accessions, including 26 Korean landraces and 29 weedy rices, at the reproductive stage. To assess chilling tolerance at the early young microspore stage, plants were treated at 12 °C for 5 days, and tolerance was evaluated using seed set fertility. GWAS, together with principal component analysis and kinship matrix analysis, revealed five quantitative trait loci (QTLs) associated with chilling tolerance on chromosomes 3, 6, and 7. The percentage of phenotypic variation explained by the QTLs was 11-19%. The genomic region underlying the QTL on chromosome 3 overlapped with a previously reported QTL associated with spikelet fertility. Subsequent bioinformatic and haplotype analyses suggested three candidate chilling-tolerance genes within the QTL linkage disequilibrium block: Os03g0305700, encoding a protein similar to peptide chain release factor 2; Os06g0495700, encoding a beta tubulin, autoregulation binding-site-domain-containing protein; and Os07g0137800, encoding a protein kinase, core-domain-containing protein. Further analysis of the detected QTLs and the candidate chilling-tolerance genes will facilitate strategies for developing chilling-tolerant rice cultivars in breeding programs.

Transcriptome profiling of two rice genotypes under mild field drought stress during grain-filling stage

Drought is one of the most critical abiotic stresses that threaten crop production worldwide. This stress affects the rice crop in all stages of rice development; however, the occurrence during reproductive and grain-filling stages has the most impact on grain yield. Although many global transcriptomic studies have been performed during the reproductive stage in rice, very limited information is available for the grain-filling stage. Hence, we intend to investigate how the rice plant responds to drought stress during the grain-filling stage and how the responses change over time under field conditions. Two rice genotypes were selected for RNA-seq analysis: '4610', previously reported as a moderately tolerant breeding line, and Rondo, an elite indica rice cultivar susceptible to drought conditions. Additionally, 10 agronomic traits were evaluated under normal irrigated and drought conditions. Leaf tissues were collected during grain-filling stages at two time points, 14 and 21 days after the drought treatment, from both the drought field and normal irrigated field conditions. Based on agronomic performances, '4610' was less negatively affected than Rondo under mild drought conditions, and expression profiling largely aligned with the phenotypic data. The transcriptomic data indicated that, in general, '4610' had much earlier responses than its counterpart in mitigating the impact of drought stress. Several key genes and gene families related to drought stress or stress-related conditions were found differentially expressed in this study, including transcription factors, drought tolerance genes and reactive oxygen species scavengers. Furthermore, this study identified novel differentially expressed genes (DEGs) without function annotations that may play roles in drought tolerance-related functions. Some of the important DEGs detected in this study can be targeted for future research.

Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize

As one of the major crops, maize (Zea mays L.) is mainly distributed in tropical and temperate regions. However, with the changes of the environments, chilling stress has become a significantly abiotic stress affecting seed germination and thus the reproductive and biomass accumulation of maize. Herein, we investigated five seed germination-related phenotypes among 300 inbred lines under low-temperature condition (10 °C). By combining 43,943 single nucleotide polymorphisms (SNPs), a total of 15 significant (P < 2.03 ×  10^-6) SNPs were identified to correlate with seed germination under cold stress based on the FarmCPU model in GWAS, among which three loci were repeatedly associated with multiple traits. Ten gene models were closely linked to these three variations, among which Zm00001d010454, Zm00001d010458, Zm00001d010459, and Zm00001d050021 were further verified by candidate gene association study and expression pattern analysis. Importantly, these candidate genes were previously reported to involve plant tolerance to chilling stress and other abiotic stress. Our findings contribute to the understanding of the genetic and molecular mechanisms underlying chilling germination in maize.

The protein kinase CPK28 phosphorylates ascorbate peroxidase and enhances thermotolerance in tomato

High temperatures are a major threat to plant growth and development, leading to yield losses in crops. Calcium-dependent protein kinases (CPKs) act as critical components of Ca2+ sensing in plants that transduce rapid stress-induced responses to multiple environmental stimuli. However, the role of CPKs in plant thermotolerance and their mechanisms of action remain poorly understood. To address this issue, tomato (Solanum lycopersicum) cpk28 mutants were generated using a CRISPR-Cas9 gene-editing approach. The responses of mutant and wild-type plants to normal (25°C) and high temperatures (45°C) were documented. Thermotolerance was significantly decreased in the cpk28 mutants, which showed increased heat stress-induced accumulation of reactive oxygen species (ROS) and levels of protein oxidation, together with decreased activities of ascorbate peroxidase (APX) and other antioxidant enzymes. The redox status of ascorbate and glutathione were also modified. Using a yeast two-hybrid library screen and protein interaction assays, we provide evidence that CPK28 directly interacts with cytosolic APX2. Mutations in APX2 rendered plants more sensitive to high temperatures, whereas the addition of exogenous reduced ascorbate (AsA) rescued the thermotolerance phenotype of the cpk28 mutants. Moreover, protein phosphorylation analysis demonstrated that CPK28 phosphorylates the APX2 protein at Thr-59 and Thr-164. This process is suggested to be responsive to Ca2+ stimuli and may be required for CPK28-mediated thermotolerance. Taken together, these results demonstrate that CPK28 targets APX2, thus improving thermotolerance. This study suggests that CPK28 is an attractive target for the development of improved crop cultivars that are better adapted to heat stress in a changing climate.

A Combined Morphological and Molecular Evolutionary Analysis of Karst-Environment Adaptation for the Genus Urophysa (Ranunculaceae)

The karst environment is characterized by low soil water content, periodic water deficiency, and poor nutrient availability, which provides an ideal natural laboratory for studying the adaptive evolution of its inhabitants. However, how species adapt to such a special karst environment remains poorly understood. Here, transcriptome sequences of two Urophysa species (Urophysa rockii and Urophysa henryi), which are Chinese endemics with karst-specific distribution, and allied species in Semiaquilegia and Aquilegia (living in non-karst habitat) were collected. Single-copy genes (SCGs) were extracted to perform the phylogenetic analysis using concatenation and coalescent methods. Positively selected genes (PSGs) and clusters of paralogous genes (Mul_genes) were detected and subsequently used to conduct gene function annotation. We filtered 2,271 SCGs and the coalescent analysis revealed that 1,930 SCGs shared the same tree topology, which was consistent with the topology detected from the concatenated tree. Total of 335 PSGs and 243 Mul_genes were detected, and many were enriched in stress and stimulus resistance, transmembrane transport, cellular ion homeostasis, calcium ion transport, calcium signaling regulation, and water retention. Both molecular and morphological evidences indicated that Urophysa species evolved complex strategies for adapting to hostile karst environments. Our findings will contribute to a new understanding of genetic and phenotypic adaptive mechanisms of karst adaptation in plants.