Physiological Investigation and Transcriptome Analysis of Polyethylene Glycol (PEG)-Induced Dehydration Stress in Cassava

Transcriptomic and physiological analysis of the response of Spirodela polyrrhiza to sodium nitroprusside

BACKGROUND

Spirodela polyrrhiza is a simple floating aquatic plant with great potential in synthetic biology. Sodium nitroprusside (SNP) stimulates plant development and increases the biomass and flavonoid content in some plants. However, the molecular mechanism of SNP action is still unclear.

RESULTS

To determine the effect of SNP on growth and metabolic flux in S. polyrrhiza, the plants were treated with different concentrations of SNP. Our results showed an inhibition of growth, an increase in starch, soluble protein, and flavonoid contents, and enhanced antioxidant enzyme activity in plants after 0.025 mM SNP treatment. Differentially expressed transcripts were analysed in S. polyrrhiza after 0.025 mM SNP treatment. A total of 2776 differentially expressed genes (1425 upregulated and 1351 downregulated) were identified. The expression of some genes related to flavonoid biosynthesis and NO biosynthesis was upregulated, while the expression of some photosynthesis-related genes was downregulated. Moreover, SNP stress also significantly influenced the expression of transcription factors (TFs), such as ERF, BHLH, NAC, and WRKY TFs.

CONCLUSIONS

Taken together, these findings provide novel insights into the mechanisms of underlying the SNP stress response in S. polyrrhiza and show that the metabolic flux of fixed CO2 is redirected into the starch synthesis and flavonoid biosynthesis pathways after SNP treatment.

Extensive post-transcriptional regulation revealed by integrative transcriptome and proteome analyses in salicylic acid-induced flowering in duckweed (Lemna gibba)

Duckweed is an aquatic model plant with tremendous potential in industrial and agricultural applications. Duckweed rarely flowers which significantly hinders the resource collection and heterosis utilization. Salicylic acid (SA) can significantly induce duckweed to flower; however, the underlying regulatory mechanisms remain largely unknown. In this work, transcriptome and proteome were conducted in parallel to examine the expression change of genes and proteins in Lemna gibba under SA treatment. A high-quality reference transcriptome was generated using Iso-Seq strategy, yielding 42,281 full-length transcripts. A total of 422, 423, and 417 differentially expressed genes (DEGs), as well as 213, 51, and 92 differentially expressed proteins (DEPs), were identified at flower induction, flower initiation, and flowering stages by ssRNA-seq and iTRAQ methods. Most DEGs and DEPs were only regulated at either the transcriptomic or proteomic level. Additionally, DEPs exhibited low expression correlations with the corresponding mRNAs, suggesting that post-transcriptional regulation plays a pivotal role in SA-induced flowering in L. gibba. Specifically, the genes related to photosynthesis, stress, and hormone metabolism were mainly regulated at the mRNA level, those associated with mitochondrial electron transport / ATP synthesis, nucleotide synthesis, and secondary metabolism were regulated at the protein level, while those related to redox metabolism were regulated at the mRNA and/or protein levels. The post-transcriptional regulation of genes relevant to hormone synthesis, transcription factors, and flowering was also extensively analyzed and discussed. This is the first study of integrative transcriptomic and proteomic analyses in duckweed, providing novel insights of post-transcriptional regulation in SA-induced flowering of L. gibba.

Transcriptomic responses to cold stress in Dendrobium huoshanense C.Z. Tang et S.J. Cheng

Dendrobium huoshanense C.Z. Tang et S.J. Cheng is a perennial epiphytic herb of the family Orchidaceae. The main metabolites of D. huoshanense include polysaccharides and flavonoids. Low temperature is the main environmental factor that limits the growth and development of plants. However, changes that occur at the molecular level in response to low temperatures in D. huoshanense are poorly understood. We performed a transcriptome analysis at two time points of 0 d (control group) and 7 d (cold stress group) under culture of D. huoshanense at 4 °C. A total of 37.63 Gb transcriptomic data were generated using the MGI 2000 platform. These reads were assembled into 170,754 transcripts and 23,724 differentially expressed genes (DEGs) were obtained. Pathway analysis indicated that "flavonoid biosynthesis," "anthocyanin biosynthesis," "flavone and flavonol biosynthesis," and "plant hormone signal transduction" might play a vital role in the response of D. huoshanense to cold stress. Several important pathway genes were identified to be altered under cold stress, such as genes encoding polysaccharides, flavonoids, and plant hormone-signaling transduction kinase. In addition, the content of mannose and total flavonoids increased under cold stress. Twelve DEGs related to polysaccharides, flavonoid, and hormone pathways were selected from the transcriptome data for validation with real-time quantitative PCR (RT-qPCR). Our results provide a transcriptome database and candidate genes for further study of the response of D. huoshanense to cold stress.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01385-7.

Screening and evaluation of drought resistance traits of winter wheat in the North China Plain

Background

Drought-resistant varieties are an important way to address the conflict between wheat's high water demand and the scarcity of water resources in the North China Plain (NCP). Drought stress impacts many morphological and physiological indicators in winter wheat. To increase the effectiveness of breeding drought-tolerant varieties, choosing indices that can accurately indicate a variety's drought resistance is advantageous.

Results

From 2019 to 2021, 16 representative winter wheat cultivars were cultivated in the field, and 24 traits, including morphological, photosynthetic, physiological, canopy, and yield component traits, were measured to evaluate the drought tolerance of the cultivars. Principal component analysis (PCA) was used to transform 24 conventional traits into 7 independent, comprehensive indices, and 10 drought tolerance indicators were screened out by regression analysis. The 10 drought tolerance indicators were plant height (PH), spike number (SN), spikelet per spike(SP), canopy temperature (CT), leaf water content (LWC), photosynthetic rate (A), intercellular CO2 concentration (Ci), peroxidase activity (POD), malondialdehyde content (MDA), and abscisic acid (ABA). In addition, through membership function and cluster analysis, 16 wheat varieties were divided into 3 categories: drought-resistant, drought weak sensitive, and drought-sensitive.

Conclusion

JM418, HM19,SM22, H4399, HG35, and GY2018 exhibited excellent drought tolerance and,therefore, can be used as ideal references to study the drought tolerance mechanism in wheat and breeding drought-tolerant wheat cultivars.

Grafting enhances drought tolerance by regulating and mobilizing proteome, transcriptome and molecular physiology in okra genotypes

Drought stress poses a serious concern to the growth, development, and quality of the okra crop due to factors including decreased yield, inadequate development of dietary fibre, increased mite infestation, and decreased seed viability. Grafting is one of the strategies that have been developed to increase the drought stress tolerance of crops. We conducted proteomics, transcriptomics and integrated it with molecular physiology to assess the response of sensitive okra genotypes; NS7772 (G1), Green gold (G2) and OH3312 (G3) (scion) grafted to NS7774 (rootstock). In our studies we observed that sensitive okra genotypes grafted to tolerant genotypes mitigated the deleterious effects of drought stress through an increase in physiochemical parameters, and lowered reactive oxygen species. A comparative proteomic analysis showed a stress responsive proteins related to Photosynthesis, energy and metabolism, defence response, protein and nucleic acid biosynthesis. A proteomic investigation demonstrated that scions grafted onto okra rootstocks increased more photosynthesis-related proteins during drought stress, indicating an increase in photosynthetic activity when plants were subjected to drought stress. Furthermore, transcriptome of RD2, PP2C, HAT22, WRKY and DREB increased significantly, specifically for grafted NS7772 genotype. Furthermore, our study also indicated that grafting improved the yield components such as number of pods and seeds per plant, maximum fruit diameter, and maximum plant height in all genotypes which directly contributed towards their high resistance towards drought stress.

Comparative physiological, transcriptomic, and WGCNA analyses reveal the key genes and regulatory pathways associated with drought tolerance in Tartary buckwheat

Drought stress is one of the major abiotic stress factors that affect plant growth and crop productivity. Tartary buckwheat is a nutritionally balanced and flavonoid-rich pseudocereal crop and also has strong adaptability to different adverse environments including drought. However, little is known about its drought tolerance mechanism. In this study, we performed comparative physiological and transcriptomic analyses of two contrasting drought-resistant Tartary buckwheat genotypes under nature drought treatment in the reproductive stage. Under drought stress, the drought-tolerant genotype XZSN had significantly higher contents of relative water, proline, and soluble sugar, as well as lower relative electrolyte leakage in the leaves than the drought-susceptible LK3. A total of 5,058 (2,165 upregulated and 2,893 downregulated) and 5,182 (2,358 upregulated and 2,824 downregulated) potential drought-responsive genes were identified in XZSN and LK3 by transcriptome sequencing analysis, respectively. Among the potential drought-responsive genes of XZSN, 1,206 and 1,274 genes were identified to be potential positive and negative contributors for XZSN having higher drought resistance ability than LK3. Furthermore, 851 out of 1,206 positive drought-resistant genes were further identified to be the core drought-resistant genes of XZSN based on WGCNA analysis, and most of them were induced earlier and quicker by drought stress than those in LK3. Functional annotation of the 851 core drought-resistant genes found that a large number of stress-responsive genes were involved in TFs, abscisic acid (ABA) biosynthesis, signal transduction and response, non-ABA signal molecule biosynthesis, water holding, oxygen species scavenging, osmotic adjustment, cell damage prevention, and so on. Transcriptional regulatory network analyses identified the potential regulators of these drought-resistant functional genes and found that the HD-ZIP and MYB TFs might be the key downstream TFs of drought resistance in Tartary buckwheat. Taken together, these results indicated that the XZSN genotype was more drought-tolerant than the LK3 genotype as evidenced by triggering the rapid and dramatic transcriptional reprogramming of drought-resistant genes to reduce water loss, prevent cell damage, and so on. This research expands our current understanding of the drought tolerance mechanisms of Tartary buckwheat and provides important information for its further drought resistance research and variety breeding.

Ethanol treatment enhances drought stress avoidance in cassava (Manihot esculenta Crantz)

External application of ethanol enhances tolerance to high salinity, drought, and heat stress in various plant species. However, the effects of ethanol application on increased drought tolerance in woody plants, such as the tropical crop "cassava," remain unknown. In the present study, we analyzed the morphological, physiological, and molecular responses of cassava plants subjected to ethanol pretreatment and subsequent drought stress treatment. Ethanol pretreatment induced a slight accumulation of abscisic acid (ABA) and stomatal closure, resulting in a reduced transpiration rate, higher water content in the leaves during drought stress treatment and the starch accumulation in leaves. Transcriptomic analysis revealed that ethanol pretreatment upregulated the expression of ABA signaling-related genes, such as PP2Cs and AITRs, and stress response and protein-folding-related genes, such as heat shock proteins (HSPs). In addition, the upregulation of drought-inducible genes during drought treatment was delayed in ethanol-pretreated plants compared with that in water-pretreated control plants. These results suggest that ethanol pretreatment induces stomatal closure through activation of the ABA signaling pathway, protein folding-related response by activating the HSP/chaperone network and the changes in sugar and starch metabolism, resulting in increased drought avoidance in plants.

Drought-responsive WRKY transcription factor genes IgWRKY50 and IgWRKY32 from Iris germanica enhance drought resistance in transgenic Arabidopsis

Drought greatly affects the growth and development of garden plants and affects their ornamental value. WRKY transcription factors make up one of the largest transcription factor families in plants and they play an important role in the plant response to drought stress. However, the function of the WRKY gene in response to drought stress in Iris germanica, which is commonly used in landscaping, has not been studied. In this study, we isolated two WRKY transcription factor genes from Iris germanica, IgWRKY50 and IgWRKY32, which belong to Group II and Group III of the WRKY family, respectively. IgWRKY50 and IgWRKY32 could be induced by PEG-6000, high temperature and ABA in Iris germanica. IgWRKY50 and IgWRKY32 could quickly respond to drought and they peaked at 3 h after PEG-6000 treatment (19.93- and 23.32-fold). The fusion proteins IgWRKY50-GFP and IgWRKY32-GFP were located in the nucleus of mesophyll protoplasts of Arabidopsis. The overexpression of the IgWRKY50 and IgWRKY32 genes improved the osmotic tolerance of transgenic Arabidopsis, mainly exhibited by the transgenic plants having a higher germination rate and a longer total root length on 1/2 MS medium containing mannitol. Under PEG-6000 stress, the transgenic plants had higher stomatal closure than the wild type (WT). Under natural drought stress, the water loss rate of the isolated leaves of transgenic Arabidopsis was lower than that of WT, the contents of proline (Pro) and soluble protein (SP) and the activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) in the transgenic plants were higher, but the content of malondialdehyde (MDA) was lower. Furthermore, the expression of several stress-related genes (RD29A, DREB2A, PP2CA, and ABA2) was significantly increased in IgWRKY50- and IgWRKY32- overexpressing transgenic Arabidposis plants after drought treatment. These results suggest that IgWRKY50 and IgWRKY32, as two positive regulators, enhance the drought resistance of transgenic Arabidopsis by mediating the ABA signal transduction pathway. IgWRKY50 and IgWRKY32 can be used as candidate genes for molecular breeding of drought resistance in Iris.

Integrated Metabolomic and Transcriptomic Analyses Reveal Novel Insights of Anthocyanin Biosynthesis on Color Formation in Cassava Tuberous Roots

Yellow roots are of higher nutritional quality and better appearance than white roots in cassava, a crucial tropical and subtropical root crop. In this work, two varieties with yellow and white cassava roots were selected to explore the mechanisms of color formation by using comparative metabolome and transcriptome analyses during seven developmental stages. Compared with the white-rooted cassava, anthocyanins, catechin derivatives, coumarin derivatives, and phenolic acids accumulated at higher levels in yellow-rooted cassava. Anthocyanins were particularly enriched and displayed different accumulation patterns during tuberous root development. This was confirmed by metabolic comparisons between five yellow-rooted and five white-rooted cassava accessions. The integrative metabolomic and transcriptomic analysis further revealed a coordinate regulation of 16 metabolites and 11 co-expression genes participating in anthocyanin biosynthesis, suggesting a vital role of anthocyanin biosynthesis in yellow pigmentation in cassava tuberous roots. In addition, two transcriptional factors, i.e., MeMYB5 and MeMYB42, were also identified to co-express with these anthocyanin biosynthesis genes. These findings expand our knowledge on the role of anthocyanin biosynthesis in cassava root color formation, and offer useful information for the genetic breeding of yellow-rooted cassava in the future.

MeSPL9 attenuates drought resistance by regulating JA signaling and protectant metabolite contents in cassava

Analysis of drought-related genes in cassava shows the involvement of MeSPL9 in drought stress tolerance and overexpression of a dominant-negative form of this gene demonstrates its negative roles in drought stress resistance. Drought stress severely impairs crop yield and is considered a primary threat to food security worldwide. Although the SQUAMOSA promoter binding protein-like 9 (SPL9) gene participates extensively in numerous developmental processes and in plant response to abiotic stimuli, its role and regulatory pathway in cassava (Manihot esculenta) response to the drought condition remain elusive. In the current study, we show that cassava SPL9 (MeSPL9) plays negative roles in drought stress resistance. MeSPL9 expression was strongly repressed by drought treatment. Overexpression of a dominant-negative form of miR156-resistant MeSPL9, rMeSPL9-SRDX, in which a 12-amino acid repressor sequence was fused to rMeSPL9 at the C terminus, conferred drought tolerance without penalizing overall growth. rMeSPL9-SRDX-overexpressing lines not only exhibited increased osmoprotectant metabolites including proline and anthocyanin, but also accumulated more endogenous jasmonic acid (JA) and soluble sugars. Transcriptomic and real-time PCR analysis suggested that differentially expressed genes were involved in sugar or JA biosynthesis, signaling, and metabolism in transgenic cassava under drought conditions. Exogenous application of JA further confirmed that JA conferred improved drought resistance and promoted stomatal closure in cassava leaves. Taken together, our findings suggest that MeSPL9 affects drought resistance by modulating protectant metabolite levels and JA signaling, which have substantial implications for engineering drought tolerant crops.

Overexpression of cassava RSZ21b enhances drought tolerance in Arabidopsis

Drought is one of the major environmental constraints affecting crop productivity. Plants have to adjust their developmental and physiological processes to cope with drought. We previously identified 18 cassava serine/arginine-rich (SR) proteins that had a pivotal role in alternative splicing in response to environmental stress. However, functional characterization of SR proteins is rarely explored. Here, we characterized the RSZ subfamily gene MeRSZ21b in cassava. The RSZ21b belongs to the RSZ subfamily, which was widely distributed in major crops and was highly conserved. Quantitative RT-PCR assay showed that the expression of MeRSZ21b was significantly induced by drought. Moreover, overexpression of MeRSZ21b in Arabidopsis was hypersensitive to abscisic acid (ABA) in the phases of seed germination and post-germination seedling growth. Meantime, MeRSZ21b overexpression lines were resistant to sorbitol treatment, and quickly closed the stomata when compared with Col-0 under drought condition. Importantly, overexpression of MeRSZ21b resulted in improved drought tolerance through modulating ABA-dependent signaling. Therefore, our findings refine our knowledge of the SR protein-coding genes and provide novel insights for enhancing plant resistance to environmental stress.

Heterografted chrysanthemums enhance salt stress tolerance by integrating reactive oxygen species, soluble sugar, and proline

Chrysanthemum, one of the most important commercial ornamental crops, is susceptible to salinity, which limits its cultivation and application in coastal and inland saline areas. Grafting is widely used to improve the salt tolerance of horticultural crops, but the mechanisms of grafted chrysanthemum responses to salt stress remain unclear. In this study, we showed that heterografted chrysanthemums with Artemisia annua as rootstock exhibited increased salt tolerance compared with self-grafted and self-rooted chrysanthemums. Under high salt stress, the roots of heterografted chrysanthemums enrich Na⁺, resulting in a reduction of Na⁺ toxicity in the scion, with only a small amount of Na⁺ being transported to the leaves. On the other hand, the roots of heterografted chrysanthemums alleviated high Na⁺ stress via enhanced catalase enzyme activity, downregulation of the expression of reactive oxygen species (ROS) accumulation-related genes, massive accumulation of soluble sugars and proline, and upregulation of the expression of heat shock protein-related genes to enhance salt tolerance. In addition, the leaves of heterografted chrysanthemums respond to low Na⁺ stress by increasing peroxidase enzyme activity and soluble sugar and proline contents, to maintain a healthy state. However, self-grafted and self-rooted plants could not integrate ROS, soluble sugars, and proline in response to salt stress, and thus exhibited a salt-sensitive phenotype. Our research reveals the mechanisms underlying the increased salt tolerance of heterografted chrysanthemums and makes it possible to have large-scale cultivation of chrysanthemums in saline areas.

Evaluation of drought resistance and transcriptome analysis for the identification of drought-responsive genes in Iris germanica

Iris germanica, a species with very high ornamental value, exhibits the strongest drought resistance among the species in the genus Iris, but the molecular mechanism underlying its drought resistance has not been evaluated. To investigate the gene expression profile changes exhibited by high-drought-resistant I. germanica under drought stress, 10 cultivars with excellent characteristics were included in pot experiments under drought stress conditions, and the changes in the chlorophyll (Chl) content, plasma membrane relative permeability (RP), and superoxide dismutase (SOD), malondialdehyde (MDA), free proline (Pro), and soluble protein (SP) levels in leaves were compared among these cultivars. Based on their drought-resistance performance, the 10 cultivars were ordered as follows: 'Little Dream' > 'Music Box' > 'X'Brassie' > 'Blood Stone' > 'Cherry Garden' > 'Memory of Harvest' > 'Immortality' > 'White and Gold' > 'Tantara' > 'Clarence'. Using the high-drought-resistant cultivar 'Little Dream' as the experimental material, cDNA libraries from leaves and rhizomes treated for 0, 6, 12, 24, and 48 h with 20% polyethylene glycol (PEG)-6000 to simulate a drought environment were sequenced using the Illumina sequencing platform. We obtained 1, 976, 033 transcripts and 743, 982 unigenes (mean length of 716 bp) through a hierarchical clustering analysis of the resulting transcriptome data. The unigenes were compared against the Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG, and gene ontology (GO) databases for functional annotation, and the gene expression levels in leaves and rhizomes were compared between the 20% PEG-6000 stress treated (6, 12, 24, and 48 h) and control (0 h) groups using DESeq2. 7849 and 24,127 differentially expressed genes (DEGs) were obtained from leaves and rhizomes, respectively. GO and KEGG enrichment analyses of the DEGs revealed significantly enriched KEGG pathways, including ribosome, photosynthesis, hormone signal transduction, starch and sucrose metabolism, synthesis of secondary metabolites, and related genes, such as heat shock proteins (HSPs), transcription factors (TFs), and active oxygen scavengers. In conclusion, we conducted the first transcriptome sequencing analysis of the I. germanica cultivar 'Little Dream' under drought stress and generated a large amount of genetic information. This study lays the foundation for further exploration of the molecular mechanisms underlying the responses of I. germanica to drought stress and provides valuable genetic resources for the breeding of drought-resistant plants.

Comparative Transcriptome Analysis of Sophora japonica (L.) Roots Reveals Key Pathways and Genes in Response to PEG-Induced Drought Stress under Different Nitrogen Conditions

Sophora japonica is a native leguminous tree species in China. The high stress tolerance contributes to its long lifespan of thousands of years. The lack of genomic resources greatly limits genetic studies on the stress responses of S. japonica. In this study, RNA-seq was conducted for S. japonica roots grown under short-term 20% polyethylene glycol (PEG) 6000-induced drought stress under normal N and N starvation conditions (1 and 0 mM NH4NO3, respectively). In each of the libraries, we generated more than 25 million clean reads, which were then de novo assembled to 46,852 unigenes with an average length of 1310.49 bp. In the differential expression analyses, more differentially expressed genes (DEGs) were found under drought with N starvation than under single stresses. The number of transcripts identified under N starvation and drought in S. japonica was nearly the same, but more upregulated genes were induced by drought, while more downregulated genes were induced by N starvation. Genes involved in “phenylpropanoid biosynthesis” and “biosynthesis of amino acids” pathways were upregulated according to KEGG enrichment analyses, irrespective of the stress treatments. Additionally, upregulated N metabolism genes were enriched upon drought, and downregulated photosynthesis genes were enriched under N starvation. We found 4,372 and 5,430 drought-responsive DEGs under normal N and N starvation conditions, respectively. N starvation may aggravate drought by downregulating transcripts in the “carbon metabolism”, “ribosome”, “arginine biosynthesis pathway”, “oxidative phosphorylation” and “aminoacyl-tRNA biosynthesis” pathways. We identified 78 genes related to N uptake and assimilation, 38 of which exhibited differential expression under stress. A total of 395 DEGs were categorized as transcription factors, of which AR2/ERF-ERF, WRKY, NAC, MYB, bHLH, C3H and C2C2-Dof families played key roles in drought and N starvation stresses. The transcriptome data obtained, and the genes identified facilitate our understanding of the mechanisms of S. japonica responses to drought and N starvation stresses and provide a molecular foundation for understanding the mechanisms of its long lifespan for breeding resistant varieties for greening.

Transcriptome analysis revealed gene regulatory network involved in PEG-induced drought stress in Tartary buckwheat (Fagopyrum Tararicum)

Tartary buckwheat is a nutritious pseudo-cereal crop that is resistant to abiotic stresses, such as drought. However, the buckwheat’s mechanisms for responding to drought stress remains unknown. We investigated the changes in physiology and gene expression under drought stress, which was simulated by treatment with polyethylene glycol (PEG). Five physiological indexes, namely MDA content, H₂O₂ content, CAT activity, SOD activity, and POD activity, were measured over time after 20% PEG treatment. All indexes showed dramatic changes in response to drought stress. A total of 1,190 differentially expressed genes (DEGs) were identified using RNA-seq and the most predominant were related to a number of stress-response genes and late embryogenesis abundant (LEA) proteins. DEGs were gathered into six clusters and were found to be involved in the ABA biosynthesis and signal pathway based on hierarchical clustering and GO and KEGG pathway enrichment. Transcription factors, such as NAC and bZIP, also took part in the response to drought stress. We determined an ABA-dependent and ABA-independent pathway in the regulation of drought stress in Tartary buckwheat. To the best of our knowledge, this is the first transcriptome analysis of drought stress in Tartary buckwheat, and our results provide a comprehensive gene regulatory network of this crop in response to drought stress.

Drought stress-induced physiological mechanisms, signaling pathways and molecular response of chloroplasts in common vegetable crops

Drought stress is one of the most adverse abiotic stresses that hinder plants' growth and productivity, threatening sustainable crop production. It impairs normal growth, disturbs water relations and reduces water-use efficiency in plants. However, plants have evolved many physiological and biochemical responses at the cellular and organism levels, in order to cope with drought stress. Photosynthesis, which is considered one of the most crucial biological processes for survival of plants, is greatly affected by drought stress. A gradual decrease in CO₂ assimilation rates, reduced leaf size, stem extension and root proliferation under drought stress, disturbs plant water relations, reducing water-use efficiency, disrupts photosynthetic pigments and reduces the gas exchange affecting the plants adversely. In such conditions, the chloroplast, organelle responsible for photosynthesis, is found to counteract the ill effects of drought stress by its critical involvement as a sensor of changes occurring in the environment, as the first process that drought stress affects is photosynthesis. Beside photosynthesis, chloroplasts carry out primary metabolic functions such as the biosynthesis of starch, amino acids, lipids, and tetrapyroles, and play a central role in the assimilation of nitrogen and sulfur. Because the chloroplasts are central organelles where the photosynthetic reactions take place, modifications in their physiology and protein pools are expected in response to the drought stress-induced variations in leaf gas exchanges and the accumulation of ROS. Higher expression levels of various transcription factors and other proteins including heat shock-related protein, LEA proteins seem to be regulating the heat tolerance mechanisms. However, several aspects of plastid alterations, following a water deficit environment are still poorly characterized. Since plants adapt to various stress tolerance mechanisms to respond to drought stress, understanding mechanisms of drought stress tolerance in plants will lead toward the development of drought tolerance in crop plants. This review throws light on major droughts stress-induced molecular/physiological mechanisms in response to severe and prolonged drought stress and addresses the molecular response of chloroplasts in common vegetable crops. It further highlights research gaps, identifying unexplored domains and suggesting recommendations for future investigations.

Highly dynamic, coordinated, and stage-specific profiles are revealed by a multi-omics integrative analysis during tuberous root development in cassava

Cassava (Manihot esculenta) is an important starchy root crop that provides food for millions of people worldwide, but little is known about the regulation of the development of its tuberous root at the multi-omics level. In this study, the transcriptome, proteome, and metabolome were examined in parallel at seven time-points during the development of the tuberous root from the early to late stages of its growth. Overall, highly dynamic and stage-specific changes in the expression of genes/proteins were observed during development. Cell wall and auxin genes, which were regulated exclusively at the transcriptomic level, mainly functioned during the early stages. Starch biosynthesis, which was controlled at both the transcriptomic and proteomic levels, was mainly activated in the early stages and was greatly restricted during the late stages. Two main branches of lignin biosynthesis, coniferyl alcohol and sinapyl alcohol, also functioned during the early stages of development at both the transcriptomic and proteomic levels. Metabolomic analysis further supported the stage-specific roles of particular genes/proteins. Metabolites related to lignin and flavonoid biosynthesis showed high abundance during the early stages, those related to lipids exhibited high abundance at both the early and middle stages, while those related to amino acids were highly accumulated during the late stages. Our findings provide a comprehensive resource for broadening our understanding of tuberous root development and will facilitate future genetic improvement of cassava.

Phenological, morpho-physiological and proteomic responses of Triticum boeoticum to drought stress

Drought is the most important abiotic stress limiting wheat production worldwide. Triticum boeoticum, as wild wheat, is a rich gene pool for breeding for drought stress tolerance. In this study, to identify the most drought-tolerant and susceptible genotypes, ten T. boeoticum accessions were evaluated under non-stress and drought-stress conditions for two years. Among the studied traits, water-use efficiency (WUE) was suggested as the most important trait to identify drought-tolerant genotypes. According to the desirable and undesirable areas of the bi-plot, Tb5 and Tb6 genotypes were less and more affected by drought stress, respectively. Therefore, their flag-leaves proteins were used for two-dimensional gel electrophoresis. While, Tb5 contained a high amount of yield, yield components, and WUE, Tb6 had higher levels of water use, phenological related traits, and root related characters. Of the 235 spots found in the studied accessions, 14 spots (11 and 3 spots of Tb5 and Tb6, respectively) were selected for sequencing. Of these 14 spots, 9 and 5 spots were upregulated and downregulated, respectively. The identified proteins were grouped into six functional protein clusters, which were mainly involved in photosynthesis (36%), carbohydrate metabolism (29%), chaperone (7%), oxidation and reduction (7%), lipid metabolism and biological properties of the membrane (7%) and unknown function (14%). We report for the first time that MICP, in the group of lipid metabolism proteins, was significantly changed into wild wheat in response to drought stress. Maybe, the present-identified proteins could play an important role to understand the molecular pathways of wheat drought tolerance. We believe comparing and evaluating the similarity-identified proteins of T. boeoticum with the previously identified proteins of Aegilops tauschii, can provide a new direction to improve wheat tolerance to drought stress.

Transcriptional analysis reveals potential genes and regulatory networks involved in salicylic acid-induced flowering in duckweed (Lemna gibba)

Duckweed is a simple aquatic floating plant having great potential in sewage treatment and bioenergy production. Duckweed rarely flowers in nature, which greatly limits its germplasm collection, conservation, and heterosis usage. Salicylic acid (SA) can efficiently induce flowering of duckweed (e.g., Lemna gibba); however, the related genes and regulatory networks remain unclear. In this work, we demonstrated that L. gibba flowering induced by SA was photoperiod-dependent, stress-involved, and abscisic acid (ABA)-disrupted. Totally 202, 78, and 413 differentially expressed (DE) genes were up-regulated, while 429, 72, and 307 were down-regulated at flower induction, flower initiation, and flowering stages, respectively. At the flower induction stage, the down-regulated genes were mainly involved in cell wall, auxin and ABA, light reaction, and abiotic stress, while the up-regulated genes were involved in development, brassinosteroid, major CHO metabolism, and redox. At the flower initiation stage, the down-regulated genes were enriched in light reaction and lipid metabolism, whereas the up-regulated genes were enriched in starch degradation and Ca²⁺ signaling. At the flowering stage, the down-regulated genes were significantly enriched in photosynthesis, gibberellic acid, starch synthesis, nitrogen metabolism, and redox, while the up-regulated genes were enriched in cell wall, jasmonic acid, secondary metabolism, and Ca²⁺ signaling. Besides, 46 transcription factors and 13 flowering-related DE genes were identified. Finally, a possible floral pathway, where LgTEM1, LgSVP, and LgFT1 might play critical roles in SA-induced flowering in L. gibba, was discussed. These findings provide a useful foundation for further investigation of genes and regulatory networks of SA-induced flowering in duckweed.

Kurup S, Cheruth AJ, Subramaniam S, Hassan Tawfik N, M.A. Amiri K. Transcriptome Profiling of Haloxylon persicum (Bunge ex Boiss and Buhse) an Endangered Plant Species under PEG-Induced Drought Stress

Haloxylon persicum is an endangered western Asiatic desert plant species, which survives under extreme environmental conditions. In this study, we focused on transcriptome analysis of H. persicum to understand the molecular mechanisms associated with drought tolerance. Two different periods of polyethylene glycol (PEG)-induced drought stress (48 h and 72 h) were imposed on H. persicum under in vitro conditions, which resulted in 18 million reads, subsequently assembled by de novo method with more than 8000 transcripts in each treatment. The N50 values were 1437, 1467, and 1524 for the control sample, 48 h samples, and 72 h samples, respectively. The gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis resulted in enrichment of mitogen-activated protein kinase (MAPK) and plant hormone signal transduction pathways under PEG-induced drought conditions. The differential gene expression analysis (DGEs) revealed significant changes in the expression pattern between the control and the treated samples. The KEGG analysis resulted in mapping transcripts with 138 different pathways reported in plants. The differential expression of drought-responsive transcription factors depicts the possible signaling cascades involved in drought tolerance. The present study provides greater insight into the fundamental transcriptome reprogramming of desert plants under drought.

Physiological and Biochemical Responses of four cassava cultivars to drought stress

The antioxidant mechanism is crucial for resisting oxidative damage induced by drought stress in plants. Different antioxidant mechanisms may contribute to the tolerance of cassava to drought stress, but for a specific genotype, the response is still unknown. The objective of this study was to investigate antioxidant response and physiological changes of four cassava genotypes under water stress conditions, by keeping the soil moisture content as 80% (control), 50% (medium), 20% (severe) of field capacity for a week. Genotypes RS01 and SC124 were keeping higher relative water content (RWC) and relative chlorophyll content (SPAD value) and less affected by oxidative stress than SC205 and GR4 under drought stress. RS01 just showed slight membrane damage and oxidative stress even under severe drought conditions. A principal component analysis showed that cassava plant water status was closely related to the antioxidant mechanism. Antioxidant response in genotypes RS01 and SC124 under drought stress might attribute to the increased accumulation of ascorbate (AsA) and glutathione (GSH) content and higher superoxide dismutase (SOD) and catalase (CAT) activities, which explained by the up-regulation of Mn-SOD and CAT genes. However, Genotypes SC205 and GR4 mainly depended on the accumulation of total phenolics (TP) and increased glutathione reductase (GR) activity, which attribute to the up-regulation of the GR gene. Our findings could provide vital knowledge for refining the tactics of cultivation and molecular breeding with drought avoidance in cassava.

The chaperone MeHSP90 recruits MeWRKY20 and MeCatalase1 to regulate drought stress resistance in cassava

The 90 kDa heat shock protein (HSP90) is widely involved in various developmental processes and stress responses in plants. However, the molecular chaperone HSP90-constructed protein complex and its function in cassava remain elusive. In this study, we report that HSP90 is essential for drought stress resistance in cassava by regulating abscisic acid (ABA) and hydrogen peroxide (H₂ O₂ ) using two specific protein inhibitors of HSP90 (geldanamycin (GDA) and radicicol (RAD)). Among 10 MeHSP90s, the transcript of MeHSP90.9 is largely induced during drought stress. Further investigation identifies MeWRKY20 and MeCatalase1 as MeHSP90.9-interacting proteins. MeHSP90.9-, MeWRKY20-, or MeCatalase1-silenced plants through virus-induced gene silencing display drought sensitivity in cassava, indicating that they are important to drought stress response. MeHSP90.9 can promote the direct transcriptional activation of MeWRKY20 on the W-box element of MeNCED5 promoter, encoding a key enzyme in ABA biosynthesis. Moreover, MeHSP90.9 positively regulates the activity of MeCatalase1, and MeHSP90.9-silenced cassava leaves accumulate more H₂ O₂ under drought stress. Taken together, we demonstrate that the MeHSP90.9 chaperone complex is a regulator of drought stress resistance in cassava.

Reactive oxygen species scavenging mechanisms associated with polyethylene glycol mediated osmotic stress tolerance in Chinese potato

Influence of polyethylene glycol (PEG) mediated osmotic stress on reactive oxygen species (ROS) scavenging machinery of Chinese potato (Solenostemon rotundifolius (Poir.) J. K. Morton) was investigated. Five genotypes of Chinese potato were raised in Murashige and Skoog (MS) basal medium containing 6-benzylaminopurine (BAP, 1 mg L-1) along with various concentrations of PEG-6000 mediated stress conditions (0, -0.2 and -0.5 MPa) and evaluated for osmotic stress tolerance in vitro. The medium containing PEG-6000 had a detrimental effect on plantlet growth and development while compared with the control. Accumulation of H2O2 was lower in Sreedhara and Subala and higher in Nidhi under PEG stress, which was evident by in situ detection in leaves. Lipid peroxidation product such as malondialdehyde (MDA) content was increased due to PEG stress which was more in susceptible genotype than that in tolerant ones. An enhanced ROS-scavenging antioxidant enzyme was observed under stress with respect to the control. The enzymes of ascorbate-glutathione cycle showed an important role in scavenging ROS. The imposition of PEG stress also increased the non-enzymatic antioxidants viz., the ascorbate and reduced glutathione content which was prominent in tolerant genotypes in comparison to susceptible. The present study indicated that, Sreedhara and Subala showed more tolerance to osmotic stress with better ROS scavenging machineries which would be the lines of interest for augmenting future breeding strategies in this climate resilient minor tuber crop.

Genome-wide identification and expression of GRAS gene family members in cassava

BACKGROUND

Cassava is highly tolerant to stressful conditions, especially drought stress conditions; however, the mechanisms underlying this tolerance are poorly understood. The GRAS gene family is a large family of transcription factors that are involved in regulating the growth, development, and stress responses of plants. Currently, GRAS transcription factors have not been systematically studied in cassava, which is the sixth most important crop in the world.

RESULTS

Seventy-seven MeGRAS genes were identified from the cassava genome database. Phylogenetic analysis revealed that the MeGRAS proteins could be divided into 14 subfamilies. The gene structure and motif compositions of the proteins were considerably conserved within the same subfamily. Duplication events, particularly segmental duplication, were identified as the main driving force for GRAS gene expansion in cassava. Global expression analysis revealed that MeGRAS genes exhibited similar or distinct expression profiles within different tissues among different varieties. Moreover, qRT-PCR analysis revealed the expression patterns of MeGRAS genes in response to abiotic stress (drought, salt, cold, and H₂O₂), and the results suggest that these genes may have multiple functions.

CONCLUSION

This study is the first to provide comprehensive information on GRAS gene family members in cassava. The data will increase our understanding of both the molecular basis and the effects of GRAS genes. In addition, the results will contribute further to identifying the responses to various environmental conditions and provide insights into the potential functions of GRAS genes.

De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweed Lemna gibba

Lemna gibba is a species of duckweed showing great potential in bioenergy production and wastewater treatment. However, the relevant transcriptomic and genomic resources are very limited for this species, which dramatically hinders its genetic diversity and genome mapping researches. In this work, ~ 233.5 million clean reads were generated from L. gibba by Illumina paired-end sequencing, and subsequently they were de novo assembled into 131,870 unigenes, of which 61,622 were annotated and 43,319 were expressed with Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) > 5. In total, 19,297 simple sequence repeats (SSRs) were identified from 15,261 SSR-containing unigenes. Dinucleotide (78.4%) were the most abundant SSRs, followed by tri- (14.9%), tetra- (4.1%), and penta-nucleotides (1.5%). The top three motifs were AG/CT (69.9%), AC/GT (6.5%), and ATC/ATG (4.9%). Further analysis revealed that the presence of SSR motif was independent of the expression level for a given gene. Based on the sequence of these SSR-containing unigenes, a total of 10,292 SSR markers were developed, of which only 2671 were further retained after removing those derived from unannotated or extra-low expressed (e.g., FPKM ≤ 5) unigenes. Finally, a subset of 70 SSR markers was randomly selected and examined in nine diverse L. gibba genotypes for the PCR amplification and polymorphism, as well as in other duckweed species for the inter-specifically amplifiability. This work is the first report on the transcriptome-based large-scale SSR markers development and analysis in L. gibba. The transcriptome generated and the SSR markers developed in this work will provide a valuable resource for genetic diversity assessment in L. gibba and also for species relationship investigation in Lemnaceae family.

Morpho-physiological and proteomic responses to water stress in two contrasting tobacco varieties

To gain insight into the molecular mechanisms underpinning tobacco (Nicotiana tabacum) tolerance to drought stress, we integrated anatomical, physiological, and proteomic analyses of drought-tolerant (Yuyan6, [Y6]) and -sensitive (Yunyan87 [Y87]) varieties. In comparison to Y87, Y6 exhibited higher water retention capability, improved photosynthetic performance, delayed leaf-senescence, stable leaf ultrastructure, a stronger antioxidant defense, and lesser ROS accumulation when subjected to water stress. Using an iTRAQ-based proteomics approach, 405 and 1,560 differentially accumulated proteins (DAPs) were identified from Y6 and Y87 plants, respectively, of which 114 were found to be present in both cultivars. A subsequent functional characterization analysis revealed that these DAPs were significantly enriched in eight biological processes, six molecular functions, and six cellular components and displayed differential expression patterns in Y6 and Y87 plants, suggesting that the response to water stress between both varieties differed at the proteomic level. Furthermore, we constructed protein coexpression networks and identified hub proteins regulating tobacco defenses to water stress. Additionally, qPCR analysis indicated that the majority of genes encoding selected proteins showed consistency between mRNA levels and their corresponding protein expression levels. Our results provide new insights into the genetic regulatory mechanisms associated with drought response in tobacco plants.

A perspective on crassulacean acid metabolism photosynthesis evolution of orchids on different continents: Dendrobium as a case study

Members of the Orchidaceae, one of the largest families of flowering plants, evolved the crassulacean acid metabolism (CAM) photosynthesis strategy. It is thought that CAM triggers adaptive radiation into new niche spaces, yet very little is known about its origin and diversification on different continents. Here, we assess the prevalence of CAM in Dendrobium, which is one of the largest genera of flowering plants and found in a wide range of environments, from the high altitudes of the Himalayas to relatively arid habitats in Australia. Based on phylogenetic time trees, we estimated that CAM, as determined by δ 13C values less negative than -20.0‰, evolved independently at least eight times in Dendrobium. The oldest lineage appeared in the Asian clade during the middle Miocene, indicating the origin of CAM was associated with a pronounced climatic cooling that followed a period of aridity. Divergence of the four CAM lineages in the Asian clade appeared to be earlier than divergence of those in the Australasian clade. However, CAM species in the Asian clade are much less diverse (25.6%) than those in the Australasian clade (57.9%). These findings shed new light on CAM evolutionary history and the aridity levels of the paleoclimate on different continents.

Physiological and Transcriptomic Analysis Reveals Distorted Ion Homeostasis and Responses in the Freshwater Plant Spirodela polyrhiza L. under Salt Stress

Duckweeds are a family of freshwater angiosperms with morphology reduced to fronds and propagation by vegetative budding. Unlike other angiosperm plants such as Arabidopsis and rice that have physical barriers between their photosynthetic organs and soils, the photosynthetic organs of duckweeds face directly to their nutrient suppliers (waters), therefore, their responses to salinity may be distinct. In this research, we found that the duckweed Spirodela polyrhiza L. accumulated high content of sodium and reduced potassium and calcium contents in large amounts under salt stress. Fresh weight, Rubisco and AGPase activities, and starch content were significantly decreaseded in the first day but recovered gradually in the following days and accumulated more starch than control from Day 3 to Day 5 when treated with 100 mM and 150 mM NaCl. A total of 2156 differentially expressed genes were identified. Overall, the genes related to ethylene metabolism, major CHO degradation, lipid degradation, N-metabolism, secondary metabolism of flavonoids, and abiotic stress were significantly increased, while those involved in cell cycle and organization, cell wall, mitochondrial electron transport of ATP synthesis, light reaction of photosynthesis, auxin metabolism, and tetrapyrrole synthesis were greatly inhibited. Moreover, salt stress also significantly influenced the expression of transcription factors that are mainly involved in abiotic stress and cell differentiation. However, most of the osmosensing calcium antiporters (OSCA) and the potassium inward channels were downregulated, Na⁺/H⁺ antiporters (SOS1 and NHX) and a Na⁺/Ca²⁺ exchanger were slightly upregulated, but most of them did not respond significantly to salt stress. These results indicated that the ion homeostasis was strongly disturbed. Finally, the shared and distinct regulatory networks of salt stress responses between duckweeds and other plants were intensively discussed. Taken together, these findings provide novel insights into the underlying mechanisms of salt stress response in duckweeds, and can be served as a useful foundation for salt tolerance improvement of duckweeds for the application in salinity conditions.

The chloroplast proteome response to drought stress in cassava leaves

Cassava is an important tropical crop with strong resistance to drought stress. The chloroplast, the site of photosynthesis, is sensitive to stress, and the drought-response proteins in cassava chloroplasts are worthy of investigation. In this study, cassava leaves were collected for ultra-structure observation from plants subjected to different drought stress conditions. Our results showed that drought stress can promote starch accumulation in cassava chloroplasts. To evaluate changes in chloroplast proteins under different drought conditions, two-dimensional electrophoresis was performed using purified chloroplasts, which resulted in the identification of 26 unique chloroplast proteins responsive to drought stress. These drought-responsive proteins are predominantly related to photosynthesis, carbon and nitrogen metabolism, and amino acid metabolism. Among them, most photosynthesis-related proteins are downregulated, with decreases in photosynthetic parameters upon drought stress. Several proteins associated with carbon and nitrogen metabolism, including rubisco and carbonic anhydrase, were upregulated, which might promote drought tolerance in cassava by enhancing the carbohydrate conversion efficiency and protecting the plant from oxidative stress. Our proteomic data not only provide insight into the complement of proteins in cassava chloroplasts but also further our overall understanding of drought-responsive proteins in cassava chloroplasts.

Transcriptome profiling reveals candidate flavonol-related genes of Tetrastigma hemsleyanum under cold stress

Background

Tetrastigma hemsleyanum Diels et Gilg is a valuable medicinal herb, whose main bioactive constituents are flavonoids. Chilling sensitivity is the dominant environmental factor limiting growth and development of the plants. But the mechanisms of cold sensitivity in this plant are still unclear. Also, not enough information on genes involved in flavonoid biosynthesis in T. hemsleyanum is available to understand the mechanisms of its physiological and pharmaceutical effects.

Results

The electrolyte leakage, POD activity, soluble protein, and MDA content showed a linear sustained increase under cold stress. The critical period of cold damage in T. hemsleyanum was from 12 h to 48 h. Expression profiles revealed 18,104 differentially expressed genes (DEGs) among these critical time points. Most of the cold regulated DEGs were early-response genes. A total of 114 unigenes were assigned to the flavonoid biosynthetic pathway. Fourteen genes most likely to encode flavonoid biosynthetic enzymes were identified. Flavonols of T. hemsleyanum might play a crucial role in combating cold stress. Genes encoding PAL, 4CL, CHS, ANR, FLS, and LAR were significantly up-regulated by cold stress, which could result in a significant increase in crucial flavonols (catechin, epicatechin, rutin, and quercetin) in T. hemsleyanum.

Conclusions

Overall, our results show that the expression of genes related to flavonol biosynthesis as well as flavonol content increased in T. hemsleyanum under cold stress. These findings provide valuable information regarding the transcriptome changes in response to cold stress and give a clue for identifying candidate genes as promising targets that could be used for improving cold tolerance via molecular breeding. The study also provides candidate genes involved in flavonoid biosynthesis and may be useful for clarifying the biosynthetic pathway of flavonoids in T. hemsleyanum.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6045-y) contains supplementary material, which is available to authorized users.

Strand-specific RNA-seq based identification and functional prediction of lncRNAs in response to melatonin and simulated drought stresses in cassava

Melatonin (MT) plays important roles in mediating plant responses to abiotic stresses such as drought. lncRNAs also play crucial roles in regulating responses to drought stress, however, their roles in MT-mediated drought stress responses in plants remain largely unknown. In this study, a total of 1405 high-confidence lncRNAs were identified in leaves of cassava, an important food crop in tropical and sub-tropical regions, using strand-specific RNA-seq technology. Of which, 185 were differentially expressed between polyethylene glycol (PEG) or MT treatment and the control condition. Trans-regulatory co-expression network revealed that MT-uniquely-responsive lncRNAs were mainly involved in tetrapyrrole synthesis, cytochrome P450, and cell wall modification; PEG-uniquely-responsive lncRNAs mainly participated in RNA regulation of transcription, calcium signaling, mitochondrial electron transport/ATP synthesis, hormone metabolism, and transport; and MT and PEG both-responsive lncRNAs were mainly involved in light reaction, light signaling, FA synthesis and FA elongation, secondary metabolism, and tetrapyrrole synthesis. In addition, 28 lncRNA-mRNA pairs referred to cis-acting regulation were identified, and these lncRNAs regulated the expression of their neighboring genes mainly through calcium signaling, RNA regulation of transcription, ABA and ethylene metabolism, and redox homeostasis. Besides, 78 lncRNAs (especially TCONS_00003360, TCONS_00015102, and TCONS_00149293) responsive to MT and/or PEG treatment were identified as putative targets of cassava known miRNAs. These findings provide a comprehensive view of the lncRNAs and their roles in response to MT and drought stress in cassava, which will enable in-depth functional analyses in the near future.

The Class III Peroxidase (POD) Gene Family in Cassava: Identification, Phylogeny, Duplication, and Expression

The class III peroxidase (POD) enzymes participate in plant development, hormone signaling, and stress responses. However, little is known about the POD family in cassava. Here, we identified 91 cassava POD genes (MePODs) and classified them into six subgroups using phylogenetic analysis. Conserved motif analysis demonstrated that all MePOD proteins have typical peroxidase domains, and gene structure analysis showed that MePOD genes have between one and nine exons. Duplication pattern analysis suggests that tandem duplication has played a role in MePOD gene expansion. Comprehensive transcriptomic analysis revealed that MePOD genes in cassava are involved in the drought response and postharvest physiological deterioration. Several MePODs underwent transcriptional changes after various stresses and related signaling treatments were applied. In sum, we characterized the POD family in cassava and uncovered the transcriptional control of POD genes in response to various stresses and postharvest physiological deterioration conditions. These results can be used to identify potential target genes for improving the stress tolerance of cassava crops.

The regulatory effects of MeTCP4 on cold stress tolerance in Arabidopsis thaliana: A transcriptome analysis

Cassava (Manihot esculenta), an important food crop in tropical areas, is well-adapted to drought conditions, but is sensitive to cold. The expression of MeTCP4, a transcription factor involved in the regulation of plant development and abiotic stresses responses, was altered under cold stress. However, its biological function under abiotic stress responses is still unclear. Here, we show that increased MeTCP4 expression enhances cold stress tolerance in Arabidopsis (Arabidopsis thaliana). To better understand the biological role of MeTCP4, the mRNA from overexpression and wild-type (WT) plants was isolated for whole genome sequencing to identify MeTCP4-mediated cold-responsive genes. Our results identify 1341 and 797 differentially expressed genes (DEGs) affected by MeTCP4 overexpression under normal and cold conditions, respectively. Gene ontology analysis revealed that a portion of the DEGs were involved in reactive oxygen species (ROS) metabolism process after cold treatment. qRT-PCR analysis revealed that the expression of cold-responsive genes and ROS-scavenging-related genes were increased in MeTCP4 overexpression plant, which could be responsible for the reduced ROS levels and enhanced cold resistance observed in transgenic plant. The findings provide insight into mechanisms of MeTCP4-mediated cold stress response, and provide clues for development of low temperature-tolerant cassava cultivars.

Acetic Acid Treatment Enhances Drought Avoidance in Cassava (Manihot esculenta Crantz)

The external application of acetic acid has recently been reported to enhance survival of drought in plants such as Arabidopsis, rapeseed, maize, rice, and wheat, but the effects of acetic acid application on increased drought tolerance in woody plants such as a tropical crop "cassava" remain elusive. A molecular understanding of acetic acid-induced drought avoidance in cassava will contribute to the development of technology that can be used to enhance drought tolerance, without resorting to transgenic technology or advancements in cassava cultivation. In the present study, morphological, physiological, and molecular responses to drought were analyzed in cassava after treatment with acetic acid. Results indicated that the acetic acid-treated cassava plants had a higher level of drought avoidance than water-treated, control plants. Specifically, higher leaf relative water content, and chlorophyll and carotenoid levels were observed as soils dried out during the drought treatment. Leaf temperatures in acetic acid-treated cassava plants were higher relative to leaves on plants pretreated with water and an increase of ABA content was observed in leaves of acetic acid-treated plants, suggesting that stomatal conductance and the transpiration rate in leaves of acetic acid-treated plants decreased to maintain relative water contents and to avoid drought. Transcriptome analysis revealed that acetic acid treatment increased the expression of ABA signaling-related genes, such as OPEN STOMATA 1 (OST1) and protein phosphatase 2C; as well as the drought response and tolerance-related genes, such as the outer membrane tryptophan-rich sensory protein (TSPO), and the heat shock proteins. Collectively, the external application of acetic acid enhances drought avoidance in cassava through the upregulation of ABA signaling pathway genes and several stress responses- and tolerance-related genes. These data support the idea that adjustments of the acetic acid application to plants is useful to enhance drought tolerance, to minimize the growth inhibition in the agricultural field.

Asymmetric birth and death of type I and type II MADS-box gene subfamilies in the rubber tree facilitating laticifer development

The rubber tree (Hevea brasiliensis Muell. Arg.) is a rubber producing crop and contains specialized laticifers. MADS-box genes are a family of transcription factor genes that regulate plant development, especially floral organ and gametophyte development. 97 MADS-box genes were identified in the rubber tree through transcriptomes and genome mining. 93.8% of the genes were mapped onto the genome scaffolds in correspondence to the coverage (93.8%) of current version of sequenced genome. Phylogenetic analysis indicates that type II MADS-box genes have been more actively duplicated than their orthologous genes in Arabidopsis and rice, so that most (70, 72.2%) of the MADS-box genes in the rubber tree belong to type II subfamily. This is a high percentage compared to those in Arabidopsis (43.7%) and rice (56.8%). Moreover, 69 out of 70 type II genes in the rubber tree are transcribed, and they are mostly predominantly expressed in flowers, but some genes are predominantly expressed in laticifers, suggesting their roles in both flower and laticifer development. The number of type I genes in the rubber tree is only 27 (27.8%), a much smaller number compared to their orthologous genes in Arabidopsis (56.3%) and rice (43.2%). At the same time, most of the type I genes (55.6%, 15) in the rubber tree are silent and are probably pseudogenes. The high birth rate and low death rate of type II genes and low birth rate and high death rate of type I genes may corresponds to special developmental requirements in the rubber tree, e.g. the development of laticifer system for biosynthesis of cis-polyisoprene, the rubber. Moreover, atypical MIKC* factors (e.g. HbMADS1 in S-clade, and HbMADS20 in P-clade) are identified. These genes are diverged to typical MIKC* genes in sequences and facilitate functions required in laticifer development and rubber biosynthesis, which is not necessary in Arabidopsis and rice.

Extensive Post-Transcriptional Regulation Revealed by Transcriptomic and Proteomic Integrative Analysis in Cassava under Drought

Cassava is a major tropical/subtropical food crop and its yield is greatly restrained by drought; however, the mechanism underlying the drought stress remains largely unknown. In this study, totally 1242 and 715 differentially expressed genes (DEGs), together with 237 and 307 differentially expressed proteins (DEPs), were respectively identified in cassava leaves and roots through RNA-seq and iTRAQ techniques. The majority of DEGs and DEPs were exclusively regulated at the mRNA and protein level, respectively, whereas only a few were commonly regulated, indicating the major involvement of post-transcriptional regulation under drought. Subsequently, the functions of these specifically or commonly regulated DEGs and DEPs were analyzed, and the post-transcriptional regulation of genes involved in heat shock protein, secondary metabolism biosynthesis, and hormone biosynthesis was extensively discussed. This is the first report on an integration of transcriptomic and proteomic analysis in cassava, and it provides new insights into the post-transcriptional regulation of cassava drought stress.

Strand-specific RNA-seq based identification and functional prediction of drought-responsive lncRNAs in cassava

Background

Long noncoding RNAs (lncRNAs) have emerged as playing crucial roles in abiotic stress responsive regulation, however, the mechanism of lncRNAs underlying drought-tolerance remains largely unknown in cassava, an important tropical and sub-tropical root crop of remarkable drought tolerance.

Results

In this study, a total of 833 high-confidence lncRNAs, including 652 intergenic and 181 anti-sense lncRNAs, were identified in cassava leaves and root using strand-specific RNA-seq technology, of which 124 were drought-responsive. Trans-regulatory co-expression network revealed that lncRNAs exhibited tissue-specific expression patterns and they preferred to function differently in distinct tissues: e.g., cell-related metabolism, cell wall, and RNA regulation of transcription in folded leaf (FL); degradation of major carbohydrate (CHO) metabolism, calvin cycle and light reaction, light signaling, and tetrapyrrole synthesis in full expanded leaf (FEL); synthesis of major CHO metabolism, nitrogen-metabolism, photosynthesis, and redox in bottom leaf (BL); and hormone metabolism, secondary metabolism, calcium signaling, and abiotic stress in root (RT). In addition, 27 lncRNA-mRNA pairs referred to cis-acting regulation were identified, and these lncRNAs regulated the expression of their neighboring genes mainly through hormone metabolism, RNA regulation of transcription, and signaling of receptor kinase. Besides, 11 lncRNAs were identified acting as putative target mimics of known miRNAs in cassava. Finally, five drought-responsive lncRNAs and 13 co-expressed genes involved in trans-acting, cis-acting, or target mimic regulation were selected and confirmed by qRT-PCR.

Conclusions

These findings provide a comprehensive view of cassava lncRNAs in response to drought stress, which will enable in-depth functional analysis in the future.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5585-5) contains supplementary material, which is available to authorized users.

Transcriptome profiling of coriander: a dual purpose crop unravels stem gall resistance genes

Stem gall (Protomyces macrosporus Unger), a serious disease that affects leaves, petioles, stems and fruits of coriander (Coriandrum sativum L.) causing heavy loss in yield. Genetic improvement of coriander for stem gall disease is indispensable. Coriander cultivars of stem gall resistance (ACr-1) and susceptible (CS-6) leaf samples were utilized and transcriptome sequenced using Illumina NextSeq500 platform. After trimming low-quality reads and adapter sequences, a total of 49,163,108 and 43,746,120 high-quality reads were retained and further assembly resulted validated transcripts of 59,933 and 56,861. We have predicted 52,506 and 48,858 coding sequences (CDS) ofwhich 50,506 and 46,945 were annotated using NCBInr database. Gene ontology analysis annotated 19,099 and 17,625 terms; pathway analysis obtained 24 different functional pathway categories; signal transduction, transport, catabolism, translation and carbohydrate metabolism pathways etc. were dominated. Differentially expressed genes analysis predicted 13,123 CDS commonly expressed of which 431 and 400 genes were significantly upregulated and downregulated, respectively, in which Rgenes, stress inducible transcription factors such as ERF, NAC, bZIP, MYB, DREB and WRKY and antifungal related genes were predicted. The real-time PCR analysis of HSP20 gene expression in resistance showed upregulation by 10-fold over susceptible sample and 18s used as a housekeeping gene for normalization. The present results provide an insights into various aspects underlying the development of resistance to stem gall in coriander.

Transcriptomic signature reveals mechanism of flower bud distortion in witches'-broom disease of soybean (Glycine max)

BACKGROUND

Soybean (Glycine max L. Merril) crop is major source of edible oil and protein for human and animals besides its various industrial uses including biofuels. Phytoplasma induced floral bud distortion syndrome (FBD), also known as witches' broom syndrome (WBS) has been one of the major biotic stresses adversely affecting its productivity. Transcriptomic approach can be used for knowledge discovery of this disease manifestation by morpho-physiological key pathways.

RESULTS

We report transcriptomic study using Illumina HiSeq NGS data of FBD in soybean, revealing 17,454 differentially expressed genes, 5561 transcription factors, 139 pathways and 176,029 genic region putative markers single sequence repeats, single nucleotide polymorphism and Insertion Deletion. Roles of PmbA, Zn-dependent protease, SAP family and auxin responsive system are described revealing mechanism of flower bud distortion having abnormalities in pollen, stigma development. Validation of 10 randomly selected genes was done by qPCR. Our findings describe the basic mechanism of FBD disease, right from sensing of phytoplasma infection by host plant triggering molecular signalling leading to mobilization of carbohydrate and protein, phyllody, abnormal pollen development, improved colonization of insect in host plants to spread the disease. Study reveals how phytoplasma hijacks metabolic machinery of soybean manifesting FBD.

CONCLUSIONS

This is the first report of transcriptomic signature of FBD or WBS disease of soybean revealing morphological and metabolic changes which attracts insect for spread of disease. All the genic region putative markers may be used as genomic resource for variety improvement and new agro-chemical development for disease control to enhance soybean productivity.

Soybean leaves transcriptomic data dissects the phenylpropanoid pathway genes as a defence response against Phakopsora pachyrhizi

Asian soybean rust (ASR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, is responsible for severe yield losses of up to 90% in all soybean producing countries. Till today, eight resistance to Phakopsora pachyrhizi (Rpp) loci have been mapped in soybean. Their resistance mechanism is race specific but largely unknown. The transcriptomes of susceptible BRS184 and Rpp3 with ASR isolates T1-2 at 24 h after inoculation (hai) and without ASR inoculation (mock) were annotated by similarity searching with different databases. A total of 4518 differentially expressed genes were identified. We found 70.89%, 56.61%, 32.13%, and 56.04% genes in the protein family databases (PFAM), Gene Ontology (GO), Eukaryotic clusters of Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG), respectively. KEGG disclosed that 52% of the phenylpropanoid pathway related genes were up-regulated. The relative gene expression study for selected genes of that pathway was conducted by RT-qPCR using Rpp1-Rpp4 carrying lines with T1-2 infection. The RT-qPCR results revealed that the Rpp lines utilized these genes in a rate limiting manner as a defence response. With the exception of glycinol 4-dimethylallyltransferase (G4DT) and chalcone reductase (CHR), all the genes showed the greatest expression at 12 hai, but the gene expressions which occur between 24 and 96 hai make these Rpp lines unique to their respective ASR isolates. Moreover, functional coordination of arogenate dehydratase 6 (ADT6) and 4-hydroxy-3-methylbut-2-enyl diphosphate synthase (ispG), chalcone synthase (CHS) and CHR, and G4DT and phytyltransferase 3 (PT3) may have a great impact on soybean resistance against ASR.

The Late Embryogenesis Abundant Protein Family in Cassava (Manihot esculenta Crantz): Genome-Wide Characterization and Expression during Abiotic Stress

Late embryogenesis abundant (LEA) proteins, as a highly diverse group of polypeptides, play an important role in plant adaptation to abiotic stress; however, LEAs from cassava have not been studied in cassava. In this study, 26 LEA members were genome-wide identified from cassava, which were clustered into seven subfamily according to evolutionary relationship, protein motif, and gene structure analyses. Chromosomal location and duplication event analyses suggested that 26 MeLEAs distributed in 10 chromosomes and 11 MeLEA paralogues were subjected to purifying selection. Transcriptomic analysis showed the expression profiles of MeLEAs in different tissues of stem, leaves, and storage roots of three accessions. Comparative transcriptomic analysis revealed that the function of MeLEAs in response to drought may be differentiated in different accessions. Compared with the wild subspecies W14, more MeLEA genes were activated in cultivated varieties Arg7 and SC124 after drought treatment. Several MeLEA genes showed induction under various stresses and related signaling treatments. Taken together, this study demonstrates the transcriptional control of MeLEAs in tissue development and the responses to abiotic stress in cassava and identifies candidate genes for improving crop resistance to abiotic stress.

Influence of cadmium stress on root exudates of high cadmium accumulating rice line (Oryza sativa L.)

A hydroponic experiment with two different cadmium (Cd) accumulating rice lines of Lu527-8 (the high Cd accumulating rice line) and Lu527-4 (the normal rice line) was carried out to explore the links among Cd stress, root exudates and Cd accumulation. The results showed that (1) Cd stress increased quantities of organic acids, but had no effect on composition in root exudates of the two rice lines. In Cd treatments, the contents of every detected organic acid in root exudates of Lu527-8 were 1.76-2.43 times higher than those of Lu527-4. Significant positive correlations between organic acids contents and Cd contents in plants were observed in both rice lines, except that malic acid was only highly relevant to Lu527-8, but not to Lu527-4. (2) Both composition and quantities of amino acids in root exudates changed a lot under Cd stress and this change differed in two rice lines. In control, four amino acids (glutamic acid, glycine, tyrosine and histidine) were detected in two rice lines. Under Cd stress, eight amino acids in Lu527-8 and seven amino acids in Lu527-4 could be detected, among which phenylalanine was only secreted by Lu527-8 and alanine, methionine and lysine were secreted by both rice lines. The contents of those four newly secreted amino acids from Lu527-8 increased significantly with the increase of Cd dose and each had a high-positive correlation with Cd contents, but the same change did not appear in Lu527-4. The difference between two rice lines in secretion of organic acids and amino acids may be related to their different Cd uptake properties.

Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources

Pearl millet, (Pennisetum glaucum L.), an efficient (C4) crop of arid/semi-arid regions is known for hardiness. Crop is valuable for bio-fortification combating malnutrition and diabetes, higher caloric value and wider climatic resilience. Limited studies are done in pot-based experiments for drought response at gene-expression level, but field-based experiment mimicking drought by withdrawal of irrigation is still warranted. We report de novo assembly-based transcriptomic signature of drought response induced by irrigation withdrawal in pearl millet. We found 19983 differentially expressed genes, 7595 transcription factors, gene regulatory network having 45 hub genes controlling drought response. We report 34652 putative markers (4192 simple sequence repeats, 12111 SNPs and 6249 InDels). Study reveals role of purine and tryptophan metabolism in ABA accumulation mediating abiotic response in which MAPK acts as major intracellular signal sensing drought. Results were validated by qPCR of 13 randomly selected genes. We report the first web-based genomic resource ( http://webtom.cabgrid.res.in/pmdtdb/ ) which can be used for candidate genes-based SNP discovery programs and trait-based association studies. Looking at climatic change, nutritional and pharmaceutical importance of this crop, present investigation has immense value in understanding drought response in field condition. This is important in germplasm management and improvement in endeavour of pearl millet productivity.

The Discrepant and Similar Responses of Genome-Wide Transcriptional Profiles between Drought and Cold Stresses in Cassava

Background: Cassava, an important tropical crop, has remarkable drought tolerance, but is very sensitive to cold. The growth, development, and root productivity of cassava are all adversely affected under cold and drought. Methods: To profile the transcriptional response to cold and drought stresses, cassava seedlings were respectively subjected to 0, 6, 24, and 48 h of cold stress and 0, 4, 6, and 10 days of drought stress. Their folded leaves, fully extended leaves, and roots were respectively investigated using RNA-seq. Results: Many genes specifically and commonly responsive to cold and drought were revealed: genes related to basic cellular metabolism, tetrapyrrole synthesis, and brassinosteroid metabolism exclusively responded to cold; genes related to abiotic stress and ethylene metabolism exclusively responded to drought; and genes related to cell wall, photosynthesis, and carbohydrate metabolism, DNA synthesis/chromatic structure, abscisic acid and salicylic acid metabolism, and calcium signaling commonly responded to both cold and drought. Discussion: Combined with cold- and/or drought-responsive transcription factors, the regulatory networks responding to cold and drought in cassava were constructed. All these findings will improve our understanding of the specific and common responses to cold and drought in cassava, and shed light on genetic improvement of cold and drought tolerance in cassava.

Kiwifruit R2R3-MYB transcription factors and contribution of the novel AcMYB75 to red kiwifruit anthocyanin biosynthesis

Red kiwifruit (Actinidia chinensis) is a popular fresh fruit with a high market value due to its unique color, caused by anthocyanin accumulation. The R2R3-MYB transcription factors (TFs) have important roles in plant development and anthocyanin metabolism. In this first comprehensive study of R2R3-MYBs in kiwifruit, a total of 93 R2R3-MYB genes, including five novel previously unannotated AcMYBs, were identified. Their phylogenic relationship, exon-intron structures, and conserved motifs were analyzed. Based on transcriptome data, 60 AcMYBs were expressed (FPKM > 1) across seven developmental stages of kiwifruit, revealing five expression patterns. One of the 5 newly identified R2R3 TFs, AcMYB75, showed an anthocyanin accumulation-linked expression pattern during fruit development. AcMYB75 localized to the nucleus and has an active transactivation domain, verifying it as a transcription factor. AcMYB75 protein specifically bound the promoter of the anthocyanin biosynthesis gene ANS in yeast one-hybrid system and in vivo. In 35 S:AcMYB75 Arabidopsis plants, anthocyanin significantly accumulated in leaves, and the expression of anthocyanin biosynthetic genes was greatly up-regulated. Together, these results suggest that AcMYB75 is involved in anthocyanin biosynthesis in kiwifruit. These findings will increase our understanding of AcMYBs involved in anthocyanin biosynthesis, and also benefit further functional characterization of R2R3-MYB genes in kiwifruit.

Genome-wide analysis of aquaporin gene family and their responses to water-deficit stress conditions in cassava

Cassava (Manihot esculenta Crantz) is an important economic crop in tropical countries. Although cassava is considered a drought-tolerant crop that can grow in arid areas, the impact of drought can significantly reduce the growth and yield of cassava storage roots. The discovery of aquaporin molecules (AQPs) in plants has resulted in a paradigm shift in the understanding of plant-water relationships, whereas the relationship between aquaporin and drought resistance in cassava still remains elusive. To investigate the potential role of aquaporin in cassava under water-deficit conditions, 45 putative MeAQPs were identified in the cassava genome. Six members of MeAQPs, containing high numbers of water stress-responsive motifs in their promoter regions, were selected for a gene expression study. Two cassava cultivars, which showed different degrees of responses to water-deficit stress, were used to test in in vitro and potted plant systems. The differential expression of all candidate MeAQPs were found in only leaves from the potted plant system were consistent with the relative water content and with the stomatal closure profile of the two cultivars. MePIP2-1 and MePIP2-10 were up-regulated and this change in their expression might regulate a special signal for water efflux out of guard cells, thus inducing stomatal closure under water-deficit conditions. In addition, the expression profiles of genes in the ABA-dependent pathway revealed an essential correlation with stomatal closure. The potential functions of MeAQPs and candidate ABA-dependent pathway genes in response to water deficit in the more tolerant cassava cultivar were discussed.

Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava

Cold and drought stresses seriously affect cassava (Manihot esculenta) plant growth and yield. Recently, long noncoding RNAs (lncRNAs) have emerged as key regulators of diverse cellular processes in mammals and plants. To date, no systematic screening of lncRNAs under abiotic stress and their regulatory roles in cassava has been reported. In this study, we present the first reference catalog of 682 high-confidence lncRNAs based on analysis of strand-specific RNA-seq data from cassava shoot apices and young leaves under cold, drought stress and control conditions. Among them, 16 lncRNAs were identified as putative target mimics of cassava known miRNAs. Additionally, by comparing with small RNA-seq data, we found 42 lncNATs and sense gene pairs can generate nat-siRNAs. We identified 318 lncRNAs responsive to cold and/or drought stress, which were typically co-expressed concordantly or discordantly with their neighboring genes. Trans-regulatory network analysis suggested that many lncRNAs were associated with hormone signal transduction, secondary metabolites biosynthesis, and sucrose metabolism pathway. The study provides an opportunity for future computational and experimental studies to uncover the functions of lncRNAs in cassava.

Genome-wide characterization and expression profiling of HD-Zip gene family related to abiotic stress in cassava

Homeodomain-leucine zipper (HD-Zip) gene family plays important roles in various abiotic stresses and hormone signaling in plants. However, no information is currently available regarding this family in cassava (Manihot esculenta), an important drought-tolerant crop in tropical and sub-tropical areas. Here, 57 HD-Zip genes (MeHDZ01-57) were identified in the cassava genome, and they were classified into four subfamilies based on phylogenetic analysis, which was further supported by their gene structure and conserved motif characteristics. Of which five gene pairs were involved in segmental duplication but none for tandem duplication, suggesting that segmental duplication was the main cause for the expansion of MeHDZ gene family in cassava. Global expression profiles revealed that MeHDZ genes were constitutively expressed, or not expressed, or tissue-specific expressed in examined tissues in both cultivated and wild subspecies. Transcriptomic analysis of three genotypes showed that most of MeHDZ genes responded differently to drought and polyethylene glycol treatments. Subsequently, quantitative RT-PCR analysis revealed comprehensive responses of twelve selected MeHDZ genes to various stimuli including cold, salt, and ABA treatments. These findings will increase our understanding of HD-Zip gene family involved in abiotic stresses and signaling transduction, and will provide a solid base for further functional characterization of MeHDZ genes in cassava.