Global analysis of gene expression profiles in physic nut (Jatropha curcas L.) seedlings exposed to drought stress

Multigenic regulation in the ethylene biosynthesis pathway during coffee flowering

Ethylene regulates different aspects of the plant's life cycle, such as flowering, and acts as a defense signal in response to environmental stresses. Changes induced by water deficit (WD) in gene expression of the main enzymes involved in ethylene biosynthesis, 1-aminocyclopropane-1-carboxylic acid synthase (ACS) and oxidase (ACO), are frequently reported in plants. In this study, coffee (Coffea arabica) ACS and ACO family genes were characterized and their expression profiles were analyzed in leaves, roots, flower buds, and open flowers from plants under well-watered (WW) and water deficit (WD) conditions. Three new ACS genes were identified. Water deficit did not affect ACS expression in roots, however soil drying strongly downregulated ACO expression, indicating a transcriptional constraint in the biosynthesis pathway during the drought that can suppress ethylene production in roots. In floral buds, ACO expression is water-independent, suggesting a higher mechanism of control in reproductive organs during the final flowering stages. Leaves may be the main sites for ethylene precursor (1-aminocyclopropane-1-carboxylic acid, ACC) production in the shoot under well-watered conditions, contributing to an increase in the ethylene levels required for anthesis. Given these results, we suggest a possible regulatory mechanism for the ethylene biosynthesis pathway associated with coffee flowering with gene regulation in leaves being a key point in ethylene production and ACO genes play a major regulatory role in roots and the shoots. This mechanism may constitute a regulatory model for flowering in other woody species.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01235-y.

Genome-wide characterization and expression analysis of bHLH gene family in physic nut (Jatropha curcas L.)

The basic helix loop helix (bHLH) transcription factor perform essential roles in plant development and abiotic stress. Here, a total of 122 bHLH family members were identified from the physic nut (Jatropha curcas L.) genomic database. Chromosomal localization results showed that 120 members were located on 11 chromosomes. The phylogenetic tree manifested that the JcbHLHs could be grouped into 28 subfamilies. Syntenic analysis showed that there were 10 bHLH collinear genes among the physic nut, Arabidopsis thaliana and Oryza sativa. These genes, except JcbHLH84, were highly expressed in various tissues of the physic nut, implying a key role in plant development. Gene expression profiles showed that ten genes (especially JcbHLH33, JcbHLH45 and JcbHLH55) correspond to both salinity and drought stresses; while eight genes only respond to salinity and another eight genes only respond to drought stress. Moreover, the protein interaction network revealed that the JcbHLHs are involved in growth, development and stress signal transduction pathways. These discoveries will help to excavate several key genes may involve in salt or drought stresses and seed development, elucidate the complex transcriptional regulation mechanism of JcbHLH genes and provide the theoretical basis for stress response and genetic improvement of physic nut.

Role of ethylene in ER stress and the unfolded protein response in tomato (Solanum lycopersicum L.) plants

The unfolded protein response (UPR) plays a significant role in the maintenance of cellular homeostasis under endoplasmic reticulum (ER) stress, which is highly dependent on the regulation of defense-related phytohormones. In this study, the role of ethylene (ET) in ER stress and UPR was investigated in the leaves of intact tomato (Solanum lycopersicum) plants. Exogenous application of the ET precursor 1-aminocyclopropane-1-carboxylic acid not only resulted in higher ET emission from leaves but also increased the expression of the UPR marker gene SlBiP and the transcript levels of the ER stress sensor SlIRE1, as well as the levels of SlbZIP60, after 24 h in tomato leaves. Using ET receptor Never ripe (Nr) mutants, a significant role of ET in tunicamycin (Tm)-induced ER stress sensing and signaling was confirmed based on the changes in the expression levels of SlIRE1b and SlBiP. Furthermore, the analysis of other defense-related phytohormones showed that the Tm-induced ET can affect positively the levels of and response to salicylic acid. Additionally, it was found that nitric oxide production and lipid peroxidation, as well as the electrolyte leakage induced by Tm, is regulated by ET, whereas the levels of H₂O₂ and proteolytic activity seemed to be independent of ET under ER stress in the leaves of tomato plants.

Genome-Wide Identification, Expression Patterns and Sugar Transport of the Physic Nut SWEET Gene Family and a Functional Analysis of JcSWEET16 in Arabidopsis

The Sugars Will Eventually be Exported Transporters (SWEET) family is a class of sugar transporters that play key roles in phloem loading, seed filling, pollen development and the stress response in plants. Here, a total of 18 JcSWEET genes were identified in physic nut (Jatropha curcas L.) and classified into four clades by phylogenetic analysis. These JcSWEET genes share similar gene structures, and alternative splicing of messenger RNAs was observed for five of the JcSWEET genes. Three (JcSWEET1/4/5) of the JcSWEETs were found to possess transport activity for hexose molecules in yeast. Real-time quantitative PCR analysis of JcSWEETs in different tissues under normal growth conditions and abiotic stresses revealed that most are tissue-specifically expressed, and 12 JcSWEETs responded to either drought or salinity. The JcSWEET16 gene responded to drought and salinity stress in leaves, and the protein it encodes is localized in both the plasma membrane and the vacuolar membrane. The overexpression of JcSWEET16 in Arabidopsis thaliana modified the flowering time and saline tolerance levels but not the drought tolerance of the transgenic plants. Together, these results provide insights into the characteristics of SWEET genes in physic nut and could serve as a basis for cloning and further functional analysis of these genes.

Genotypic variation in 9-Cis-Epoxycarotenoid Dioxygenase3 gene expression and abscisic acid accumulation in relation to drought tolerance of Hevea brasiliensis

Abscisic acid (ABA) is a stress-related plant hormone, which is reported to confer drought tolerance. A key enzyme in ABA biosynthesis is 9-cis-epoxycarotenoid dioxygenase. In this study, changes in morphological, physiological response, HbNCED3, and ABA accumulation of RRIM 623 and PB 5/51 rubber clones were observed at different time points of water deficit conditions (0, 3, 5, 7, and 9 days of withholding water). During water deficit, the relative water content (RWC), photosynthetic rate (Pn), and stomatal conductance (Gs) decreased, whereas the electro leakage (EL) increased. The magnitudes of the changes in these parameters were greater for PB 5/51 than for RRIM 623. Therefore, RRIM 623 was designated as representative of drought-tolerant clone and PB 5/51 as a drought-sensitive clone. The HbNCED3 transcription level of RRIM 623 showed lower expression compared with that of PB 5/51, which corresponded to the accumulation of ABA. RRIM 623 accumulated less ABA than PB 5/51. The ABA in RRIM 623 gradually increased, especially on the 7th day of withholding water, whereas that in PB 5/51 rapidly increased during the early periods of drought conditions. Additionally, the sensitivity of stomatal response to ABA showed that RRIM 623 had a higher sensitivity than PB 5/51. These results demonstrate that the drought-tolerant rubber clone, RRIM 623, was characterized by lower ABA accumulation during drought stress than the drought-sensitive clone, PB 5/51. The drought tolerance mechanism of the RRIM 623 might be associated with stomatal sensitivity to ABA accumulation under drought stress.

Genome-wide characterization of bZIP transcription factors and their expression patterns in response to drought and salinity stress in Jatropha curcas

The basic leucine zipper (bZIP) family is one of the largest families of transcription factors (TFs) in plants and is responsible for various functions, including regulating development and responses to abiotic/biotic stresses. However, the roles of bZIPs in the regulation of responses to drought stress and salinity stress remain poorly understood in Jatropha curcas L., a biodiesel crop. In the present study, 50 JcbZIP genes were identified and classified into ten groups. Cis-element analysis indicated that JcbZIP genes are associated with abiotic stress. Gene expression patterns and quantitative real-time PCR (qRT-PCR) showed that four JcbZIP genes (JcbZIPs 34, 36, 49 and 50) are key resistance-related genes under both drought and salinity stress conditions. On the basis of the results of cis-element and phylogenetic analyses, JcbZIP49 and JcbZIP50 are likely involved in responses to drought and salinity stress; moreover, JcbZIP34 and JcbZIP36 might also play important roles in seed development and response to abiotic stress. These findings advance our understanding of the comprehensive characteristics of JcbZIP genes and provide new insights for functional validation in the further.

Aging, stress, and senescence in plants: what can biological diversity teach us?

Aging, stress, and senescence in plants are interconnected processes that determine longevity. We focus here on compiling and discussing our current knowledge on the mechanisms of development that long-lived perennial plants have evolved to prevent and delay senescence. Clonal and nonclonal perennial herbs of various life forms and longevities will be particularly considered to illustrate what biological diversity can teach us about aging as a universal phenomenon. Source-sink relations and redox signaling will also be discussed as examples of regulatory mechanisms of senescence at the organ level. Whether or not effective mechanisms that biological diversity has evolved to completely prevent the wear and tear of aging will be applicable to human aging in the near future ultimately depends on ethical aspects.

Rhizobacteria and Arbuscular Mycorrhizal Fungi of Oil Crops (Physic Nut and Sacha Inchi): A Cultivable-Based Assessment for Abundance, Diversity, and Plant Growth-Promoting Potentials

Nowadays, oil crops are very attractive both for human consumption and biodiesel production; however, little is known about their commensal rhizosphere microbes. In this study, rhizosphere samples were collected from physic nut and sacha inchi plants grown in several areas of Thailand. Rhizobacteria, cultivable in nitrogen-free media, and arbuscular mycorrhizal (AM) fungi were isolated and examined for abundance, diversity, and plant growth-promoting activities (indole-3-acetic acid (IAA) and siderophore production, nitrogen fixation, and phosphate solubilization). Results showed that only the AM spore amount was affected by plant species and soil features. Considering rhizobacterial diversity, two classes—Alphaproteobacteria (Ensifer sp. and Agrobacterium sp.) and Gammaproteobacteria (Raoultella sp. and Pseudomonas spp.)—were identified in physic nut rhizosphere, and three classes; Actinobacteria (Microbacterium sp.), Betaproteobacteria (Burkholderia sp.) and Gammaproteobacteria (Pantoea sp.) were identified in the sacha inchi rhizosphere. Considering AM fungal diversity, four genera were identified (Acaulospora, Claroideoglomus, Glomus, and Funneliformis) in sacha inchi rhizospheres and two genera (Acaulospora and Glomus) in physic nut rhizospheres. The rhizobacteria with the highest IAA production and AM spores with the highest root-colonizing ability were identified, and the best ones (Ensifer sp. CM1-RB003 and Acaulospora sp. CM2-AMA3 for physic nut, and Pantoea sp. CR1-RB056 and Funneliformis sp. CR2-AMF1 for sacha inchi) were evaluated in pot experiments alone and in a consortium in comparison with a non-inoculated control. The microbial treatments increased the length and the diameter of stems and the chlorophyll content in both the crops. CM1-RB003 and CR1-RB056 also increased the number of leaves in sacha inchi. Interestingly, in physic nut, the consortium increased AM fungal root colonization and the numbers of offspring AM spores in comparison with those observed in sacha inchi. Our findings proved that AM fungal abundance and diversity likely rely on plant species and soil features. In addition, pot experiments showed that rhizosphere microorganisms were the key players in the development and growth of physic nut and sacha inchi.

Genome-wide analysis and expression profiling of the heat shock transcription factor gene family in Physic Nut (Jatropha curcas L.)

The heat shock transcription factor (Hsf) family, identified as one of the important gene families, participates in plant development process and some stress response. So far, there have been no reports on the research of the Hsf transcription factors in physic nut. In this study, seventeen putative Hsf genes identified from physic nut genome. Phylogenetic analysis manifested these genes classified into three groups: A, B and C. Chromosomal location showed that they distributed eight out of eleven linkage groups. Expression profiling indicated that fourteen JcHsf genes highly expressed in different tissues except JcHsf1, JcHsf6 and JcHsf13. In addition, induction of six and twelve JcHsf genes noted against salt stress and drought stress, respectively, which demonstrated that the JcHsf genes are involved in abiotic stress responses. Our results contribute to a better understanding of the JcHsf gene family and further study of its function.

Light-harvesting chlorophyll a/b-binding protein-coding genes in jatropha and the comparison with castor, cassava and arabidopsis

The Lhc (light-harvesting chlorophyll a/b-binding protein) superfamily represents a class of antennae proteins that play indispensable roles in capture of solar energy as well as photoprotection under stress conditions. Despite their importance, little information has been available beyond model plants. In this study, we presents a first genome-wide analysis of Lhc superfamily genes in jatropha (Jatropha curcas L., Euphorbiaceae), an oil-bearing plant for biodiesel purpose. A total of 27 members were identified from the jatropha genome, which were shown to distribute over nine out of the 11 chromosomes. The superfamily number is comparable to 28 present in castor (Ricinus communis, Euphorbiaceae), but relatively less than 35 in cassava (Manihot esculenta, Euphorbiaceae) and 34 in arabidopsis (Arabidopsis thaliana) that experienced one or two recent whole-genome duplications (WGDs), respectively. In contrast to a high number of paralogs present in cassava and arabidopsis, few duplicates were found in jatropha as observed in castor, corresponding to no recent WGD occurred in these two species. Nevertheless, 26 orthologous groups representing four defined families were found in jatropha, and nearly one-to-one orthologous relationship was observed between jatropha and castor. By contrast, a novel group named SEP6 was shown to have been lost in arabidopsis. Global transcriptome profiling revealed a predominant expression pattern of most JcLhc superfamily genes in green tissues, reflecting their key roles in photosynthesis. Moreover, their expression profiles upon hormones, drought, and salt stresses were also investigated. These findings not only improve our knowledge on species-specific evolution of the Lhc supergene family, but also provide valuable information for further studies in jatropha.

JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants

Background

Jatropha curcas is an oil-bearing plant, and has seeds with high oil content (~ 40%). Several advantages, such as easy genetic transformation and short generation duration, have led to the emergence of J. curcas as a model for woody energy plants. With the development of high-throughput sequencing, the genome of Jatropha curcas has been sequenced by different groups and a mass of transcriptome data was released. How to integrate and analyze these omics data is crucial for functional genomics research on J. curcas.

Results

By establishing pipelines for processing novel gene identification, gene function annotation, and gene network construction, we systematically integrated and analyzed a series of J. curcas transcriptome data. Based on these data, we constructed a J. curcas database (JCDB), which not only includes general gene information, gene functional annotation, gene interaction networks, and gene expression matrices but also provides tools for browsing, searching, and downloading data, as well as online BLAST, the JBrowse genome browser, ID conversion, heatmaps, and gene network analysis tools.

Conclusions

JCDB is the most comprehensive and well annotated knowledge base for J. curcas. We believe it will make a valuable contribution to the functional genomics study of J. curcas. The database is accessible at http://jcdb.xtbg.ac.cn.

Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae)

Environmental variation along the geographical space can shape populations by natural selection. In the context of global warming and changing precipitation regimes, it is crucial to understand the role of environmental heterogeneity in tropical trees adaptation, given their disproportional contribution to water and carbon biogeochemical cycles. Here, we investigated how heterogeneity in freshwater availability along tropical wetlands has influenced molecular variations of the black mangrove (Avicennia germinans). A total of 57 trees were sampled at seven sites differing markedly in precipitation regime and riverine freshwater inputs. Using 2,297 genome-wide single nucleotide polymorphic markers, we found signatures of natural selection by the association between variations in allele frequencies and environmental variables, including the precipitation of the warmest quarter and the annual precipitation. Additionally, we found candidate loci for selection based on statistical deviations from neutral expectations of interpopulation differentiation. Most candidate loci within transcribed sequences were functionally associated with central aspects of drought tolerance or plant response to drought. Moreover, our results suggest the occurrence of the rapid evolution of a population, probably in response to sudden and persistent limitations in plant access to soil water, following a road construction in 1974. Observations supporting rapid evolution included the reduction in tree size and changes in allele frequencies and in transcript expression associated with increased drought tolerance through the accumulation of osmoprotectants and antioxidants, biosynthesis of cuticles, protection against protein degradation, stomatal closure, photorespiration and photosynthesis. We describe a major role of spatial heterogeneity in freshwater availability in the specialization of this typically tropical tree.

Insights into Barley Root Transcriptome under Mild Drought Stress with an Emphasis on Gene Expression Regulatory Mechanisms

Root systems play a pivotal role in coupling with drought stress, which is accompanied with a substantial transcriptome rebuilding in the root tissues. Here, we present the results of global gene expression profiling of roots of two barley genotypes with contrasting abilities to cope with drought that were subjected to a mild level of the stress. We concentrate our analysis on gene expression regulation processes, which allowed the identification of 88 genes from 39 families involved in transcriptional regulation in roots upon mild drought. They include 13 genes encoding transcription factors (TFs) from AP2 family represented by ERFs, DREB, or B3 domain-containing TFs, eight WRKYs, six NACs, five of the HD-domain, MYB or MYB-related, bHLH and bZIP TFs. Also, the representatives of C3H, CPP, GRAS, LOB-domain, TCP, Tiffy, Tubby, and NF-Ys TFs, among others were found to be regulated by the mild drought in barley roots. We found that drought tolerance is accompanied with a lower number of gene expression changes than the amount observed in a susceptible genotype. The better drought acclimation may be related to the activation of transcription factors involved in the maintenance of primary root growth and in the epigenetic control of chromatin and DNA methylation. In addition, our analysis pointed to fives TFs from ERF, LOB, NAC, WRKY and bHLH families that may be important in the mild but not the severe drought response of barley roots.

Microarray analysis of transcriptional responses to salt and drought stress in Arabidopsis thaliana

Microarray expression profile analysis is a useful approach to increase our knowledge about genes involved in regulatory networks and signal transduction pathways related to abiotic stress tolerance. Salt and drought, as two important abiotic stresses, adversely affect plant productivity in the world every year. To understand stress response mechanisms and identify genes and proteins which play critical roles in these mechanisms, the study of individual genes and proteins cannot be considered as an effective approach. On the other hand, the availability of new global data provides us an effective way to shed some light on the central role of molecules involved in stress response mechanisms in the plant. A meta-analysis of salt and drought stress responses was carried out using 38 samples of different experiments from leaves and roots of Arabidopsis plants exposed to drought and salt stresses. We figured out the number of differentially expressed genes (DEGs) was higher in roots under both stresses. Also, we found that the number of common DEGs under both stresses was more in roots and also the number of common DEGs in both tissues under salt stress was more than drought stress. The highest percent of DEGs was related to cell and cell part (about 87%). Around 9% and 7% of DEGs in roots and leaves encoded transcription factors, respectively. Network analysis revealed that three transcription factor families HSF, AP2/ERF and C2H2, may have critical roles in salt and drought stress response mechanisms in Arabidopsis ​and some proteins like STZ may be introduced as a new candidate gene for enhancing salt and drought tolerance in crop plants.

Transcriptomic analysis of Eruca vesicaria subs. sativa lines with contrasting tolerance to polyethylene glycol-simulated drought stress

BACKGROUND

Eruca vesicaria subsp. sativa is one of the Cruciferae species most tolerant to drought stress. In our previous study some extremely drought-tolerant/sensitive Eruca lines were obtained. However little is known about the mechanism for drought tolerance in Eruca.

METHODS

In this study two E. vesicaria subs. sativa lines with contrasting drought tolerance were treated with liquid MS/PEG solution. Total RNA was isolated from 7-day old whole seedlings and then applied to Illumina sequencing platform for high-throughput transcriptional sequencing.

RESULTS

KEGG pathway analysis indicated that differentially expressed genes (DEGs) involved in alpha-Linolenic acid metabolism, Tyrosine metabolism, Phenylalanine, Tyrosine and tryptophan biosynthesis, Galactose metabolism, Isoquinoline alkaloid biosynthesis, Tropane, Piperidine and pyridine alkaloid biosynthesis, Mineral absorption, were all up-regulated specifically in drought-tolerant (DT) Eruca line under drought stress, while DEGs involved in ribosome, ribosome biogenesis, Pyrimidine metabolism, RNA degradation, Glyoxylate and dicarboxylate metabolism, Aminoacyl-tRNA biosynthesis, Citrate cycle, Methane metabolism, Carbon fixation in photosynthetic organisms, were all down-regulated. 51 DEGs were found to be most significantly up-regulated (log₂ ratio ≥ 8) specifically in the DT line under PEG treatment, including those for ethylene-responsive transcription factors, WRKY and bHLH transcription factors, calmodulin-binding transcription activator, cysteine-rich receptor-like protein kinase, mitogen-activated protein kinase kinase, WD repeat-containing protein, OPDA reductase, allene oxide cyclase, aquaporin, O-acyltransferase WSD1, C-5 sterol desaturase, sugar transporter ERD6-like 12, trehalose-phosphate phosphatase and galactinol synthase 4. Eight of these 51 DEGs wre enriched in 8 COG and 17 KEGG pathways.

CONCLUSIONS

DEGs that were found to be most significantly up-regulated specifically in the DT line under PEG treatment, up-regulation of DEGs involved in Arginine and proline metabolism, alpha-linolenic acid metabolism and down-regulation of carbon fixation and protein synthesis might be critical for the drought tolerance in Eruca. These results will be valuable for revealing mechanism of drought tolerance in Eruca and also for genetic engineering to improve drought tolerance in crops.

Genomics analysis of genes encoding respiratory burst oxidase homologs (RBOHs) in jatropha and the comparison with castor bean

Respiratory burst oxidase homologs (RBOHs), which catalyze the production of superoxide from oxygen and NADPH, play key roles in plant growth and development, hormone signaling, and stress responses. Compared with extensive studies in model plants arabidopsis and rice, little is known about RBOHs in other species. This study presents a genome-wide analysis of Rboh family genes in jatropha (Jatropha curcas) as well as the comparison with castor bean (Ricinus communis), another economically important non-food oilseed crop of the Euphorbiaceae family. The family number of seven members identified from the jatropha genome is equal to that present in castor bean, and further phylogenetic analysis assigned these genes into seven groups named RBOHD, -C, -B, -E, -F, -N, and -H. In contrast to a high number of paralogs present in arabidopsis and rice that experienced several rounds of recent whole-genome duplications, no duplicate was identified in both jatropha and castor bean. Conserved synteny and one-to-one orthologous relationship were observed between jatropha and castor bean Rboh genes. Although exon-intron structures are usually highly conserved between orthologs, loss of certain introns was observed for JcRbohB, JcRbohD, and RcRbohN, supporting their divergence. Global gene expression profiling revealed diverse patterns of JcRbohs over various tissues. Moreover, expression patterns of JcRbohs during flower development as well as various stresses were also investigated. These findings will not only improve our knowledge on species-specific evolution of the Rboh gene family, but also provide valuable information for further functional analysis of Rboh genes in jatropha.

A Novel Sweetpotato Transcription Factor Gene IbMYB116 Enhances Drought Tolerance in Transgenic Arabidopsis

Several members of the MYB transcription factor family have been found to regulate growth, developmental processes, metabolism, and biotic and abiotic stress responses in plants. However, the role of MYB116 in plants is still unclear. In this study, a MYB transcription factor gene IbMYB116 was cloned and characterized from the sweetpotato [Ipomoea batatas (L.) Lam.] line Xushu55-2, a line that is considered to be drought resistant. We show here that IbMYB116 is a nuclear protein and that it possesses a transactivation domain at the C terminus. This gene exhibited a high expression level in the leaf tissues of Xushu55-2 and was strongly induced by PEG6000 and methyl-jasmonate (MeJA). The IbMYB116-overexpressing Arabidopsis plants showed significantly enhanced drought tolerance, increased MeJA content, and a decreased H₂O₂ level under drought stress. The overexpression of IbMYB116 in Arabidopsis systematically upregulated jasmonic acid (JA) biosynthesis genes and activated the JA signaling pathway as well as reactive oxygen species (ROS)-scavenging system genes under drought stress conditions. The overall results suggest that the IbMYB116 gene might enhance drought tolerance by activating a ROS-scavenging system through the JA signaling pathway in transgenic Arabidopsis. These findings reveal, for the first time, the crucial role of IbMYB116 in the drought tolerance of plants.

Elucidation and analyses of the regulatory networks of upland and lowland ecotypes of switchgrass in response to drought and salt stresses

Switchgrass is an important bioenergy crop typically grown in marginal lands, where the plants must often deal with abiotic stresses such as drought and salt. Alamo is known to be more tolerant to both stress types than Dacotah, two ecotypes of switchgrass. Understanding of their stress response and adaptation programs can have important implications to engineering more stress tolerant plants. We present here a computational study by analyzing time-course transcriptomic data of the two ecotypes to elucidate and compare their regulatory systems in response to drought and salt stresses. A total of 1,693 genes (target genes or TGs) are found to be differentially expressed and possibly regulated by 143 transcription factors (TFs) in response to drought stress together in the two ecotypes. Similarly, 1,535 TGs regulated by 110 TFs are identified to be involved in response to salt stress. Two regulatory networks are constructed to predict their regulatory relationships. In addition, a time-dependent hidden Markov model is derived for each ecotype responding to each stress type, to provide a dynamic view of how each regulatory network changes its behavior over time. A few new insights about the response mechanisms are predicted from the regulatory networks and the time-dependent models. Comparative analyses between the network models of the two ecotypes reveal key commonalities and main differences between the two regulatory systems. Overall, our results provide new information about the complex regulatory mechanisms of switchgrass responding to drought and salt stresses.

Genome-wide identification and expression profiling of the auxin response factor (ARF) gene family in physic nut

Auxin response factors (ARF) are important transcription factors which mediate the transcription of auxin responsive genes by binding directly to auxin response elements (AuxREs) found in the promoter regions of these genes. To date, no information has been available about the genome-wide organization of the ARF transcription factor family in physic nut. In this study, 17 ARF genes (JcARFs) are identified in the physic nut genome. A detailed investigation into the physic nut ARF gene family is performed, including analysis of the exon-intron structure, conserved domains, conserved motifs, phylogeny, chromosomal locations, potential small RNA targets and expression profiles under various conditions. Phylogenetic analysis suggests that the 17 JcARF proteins are clustered into 6 groups, and most JcARF proteins from the physic nut reveal closer relationships with those from Arabidopsis than those from rice. Of the 17 JcARF genes, eight are predicted to be the potential targets of small RNAs; most of the genes show differential patterns of expression among four tissues (root, stem cortex, leaf, and seed); and qRT-PCR indicates that the expression of all JcARF genes is inhibited or induced in response to exogenous auxin. Expression profile analysis based on RNA-seq data shows that in leaves, 11 of the JcARF genes respond to at least one abiotic stressor (drought and/or salinity) at, as a minimum, at least one time point. Our results provide valuable information for further studies on the roles of JcARF genes in regulating physic nut's growth, development and responses to abiotic stress.

Genome-Wide Screening and Characterization of the Dof Gene Family in Physic Nut (Jatropha curcas L.)

Physic nut (Jatropha curcas L.) is a species of flowering plant with great potential for biofuel production and as an emerging model organism for functional genomic analysis, particularly in the Euphorbiaceae family. DNA binding with one finger (Dof) transcription factors play critical roles in numerous biological processes in plants. Nevertheless, the knowledge about members, and the evolutionary and functional characteristics of the Dof gene family in physic nut is insufficient. Therefore, we performed a genome-wide screening and characterization of the Dof gene family within the physic nut draft genome. In total, 24 JcDof genes (encoding 33 JcDof proteins) were identified. All the JcDof genes were divided into three major groups based on phylogenetic inference, which was further validated by the subsequent gene structure and motif analysis. Genome comparison revealed that segmental duplication may have played crucial roles in the expansion of the JcDof gene family, and gene expansion was mainly subjected to positive selection. The expression profile demonstrated the broad involvement of JcDof genes in response to various abiotic stresses, hormonal treatments and functional divergence. This study provides valuable information for better understanding the evolution of JcDof genes, and lays a foundation for future functional exploration of JcDof genes.

Long non-coding RNAs of switchgrass (Panicum virgatum L.) in multiple dehydration stresses

BACKGROUND

Long non-coding RNAs (lncRNAs) play important roles in plant growth and stress responses. Studies of lncRNAs in non-model plants are quite limited, especially those investigating multiple dehydration stresses. In this study, we identified novel lncRNAs and analyzed their functions in dehydration stress memory in switchgrass, an excellent biofuel feedstock and soil-conserving plant in the Gramineae family.

RESULTS

We analyzed genome-wide transcriptional profiles of leaves of 5-week-old switchgrass plantlets grown via tissue culture after primary and secondary dehydration stresses (D1 and D2) and identified 16,551 novel lncRNAs, including 4554 annotated lncRNAs (targeting 3574 genes), and 11,997 unknown lncRNAs. Gene ontology and pathway enrichment analysis of annotated genes showed that the differentially expressed lncRNAs were related to abscisic acid (ABA) and ethylene (ETH) biosynthesis and signal transduction, and to starch and sucrose metabolism. The upregulated lncRNAs and genes were related to ABA synthesis and its signal transduction, and to trehalose synthesis. Meanwhile, lncRNAs and genes related to ETH biosynthesis and signal transduction were suppressed. LncRNAs and genes involved in ABA metabolism were verified using quantitative real-time PCR, and the endogenous ABA content was determined via high performance liquid chromatography mass spectrometry (HPLC-MS). These results showed that ABA accumulated significantly during dehydration stress, especially in D2. Furthermore, we identified 307 dehydration stress memory lncRNAs, and the ratios of different memory types in switchgrass were similar to those in Arabidopsis and maize.

CONCLUSIONS

The molecular responses of switchgrass lncRNAs to multiple dehydration stresses were researched systematically, revealing novel information about their transcriptional regulatory behavior. This study provides new insights into the response mechanism to dehydration stress in plants. The lncRNAs and pathways identified in this study provide valuable information for genetic modification of switchgrass and other crops.

Comparison of GWAS models to identify non-additive genetic control of flowering time in sunflower hybrids

This study compares five models of GWAS, to show the added value of non-additive modeling of allelic effects to identify genomic regions controlling flowering time of sunflower hybrids. Genome-wide association studies are a powerful and widely used tool to decipher the genetic control of complex traits. One of the main challenges for hybrid crops, such as maize or sunflower, is to model the hybrid vigor in the linear mixed models, considering the relatedness between individuals. Here, we compared two additive and three non-additive association models for their ability to identify genomic regions associated with flowering time in sunflower hybrids. A panel of 452 sunflower hybrids, corresponding to incomplete crossing between 36 male lines and 36 female lines, was phenotyped in five environments and genotyped for 2,204,423 SNPs. Intra-locus effects were estimated in multi-locus models to detect genomic regions associated with flowering time using the different models. Thirteen quantitative trait loci were identified in total, two with both model categories and one with only non-additive models. A quantitative trait loci on LG09, detected by both the additive and non-additive models, is located near a GAI homolog and is presented in detail. Overall, this study shows the added value of non-additive modeling of allelic effects for identifying genomic regions that control traits of interest and that could participate in the heterosis observed in hybrids.

Transcriptional and physiological data reveal the dehydration memory behavior in switchgrass (Panicum virgatum L.)

BACKGROUND

Switchgrass (Panicum virgatum L.) is a model biofuel plant because of its high biomass, cellulose-richness, easy degradation to ethanol, and the availability of extensive genomic information. However, a little is currently known about the molecular responses of switchgrass plants to dehydration stress, especially multiple dehydration stresses.

RESULTS

Studies on the transcriptional profiles of 35-day-old tissue culture plants revealed 741 dehydration memory genes. Gene Ontology and pathway analysis showed that these genes were enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction. Further analysis of specific pathways combined with physiological data suggested that switchgrass improved its dehydration resistance by changing various aspects of its responses to secondary dehydration stress (D2), including the regulation of abscisic acid (ABA) and jasmonic acid (JA) biosynthesis and signal transduction, the biosynthesis of osmolytes (l-proline, stachyose and trehalose), energy metabolism (i.e., metabolic process relating to photosynthetic systems, glycolysis, and the TCA cycle), and lignin biosynthesis. The transcriptional data and chemical substance assays showed that ABA was significantly accumulated during both primary (D1) and secondary (D2) dehydration stresses, whereas JA accumulated during D1 but became significantly less abundant during D2. This suggests the existence of a complicated signaling network of plant hormones in response to repeated dehydration stresses. A homology analysis focusing on switchgrass, maize, and Arabidopsis revealed the conservation and species-specific distribution of dehydration memory genes.

CONCLUSIONS

The molecular responses of switchgrass plants to successive dehydration stresses have been systematically characterized, revealing a previously unknown transcriptional memory behavior. These results provide new insights into the mechanisms of dehydration stress responses in plants. The genes and pathways identified in this study will be useful for the genetic improvement of switchgrass and other crops.

Global gene expression analysis of the response of physic nut (Jatropha curcas L.) to medium- and long-term nitrogen deficiency

Jatropha curcas L. is an important biofuel plant with excellent tolerance of barren environments. However, studies on the regulatory mechanisms that operate in this plant in response to nitrogen (N) shortage are scarce. In this study, genome-wide transcriptional profiles of the roots and leaves of 8-week old physic nut seedlings were analyzed after 2 and 16 days of N starvation. Enrichment results showed that genes associated with N metabolism, processing and regulation of RNA, and transport predominated among those showing alterations in expression. Genes encoding transporter families underwent major changes in expression in both roots and leaves; in particular, those with roles in ammonia, amino acid and peptide transport were generally up-regulated after long-term starvation, while AQUAPORIN genes, whose products function in osmoregulation, were down-regulated. We also found that ASPARA−GINASE B1 and SARCOSINE OXIDASE genes were up-regulated in roots and leaves after 2 and 16 d N starvation. Genes associated with ubiquitination-mediated protein degradation were significantly up-regulated. In addition, genes in the JA biosynthesis pathway were strongly activated while expression of those in GA signaling was inhibited in leaves. We showed that four major classes of genes, those with roles in N uptake, N reutilization, C/N ratio balance, and cell structure and synthesis, were particularly influenced by long-term N limitation. Our discoveries may offer clues to the molecular mechanisms that regulate N reallocation and reutilization so as to maintain or increase plant performance even under adverse environmental conditions.

Genome-Wide Identification of Jatropha curcas Aquaporin Genes and the Comparative Analysis Provides Insights into the Gene Family Expansion and Evolution in Hevea brasiliensis

Aquaporins (AQPs) are channel-forming integral membrane proteins that transport water and other small solutes across biological membranes. Despite the vital role of AQPs, to date, little is known in physic nut (Jatropha curcas L., Euphorbiaceae), an important non-edible oilseed crop with great potential for the production of biodiesel. In this study, 32 AQP genes were identified from the physic nut genome and the family number is relatively small in comparison to 51 in another Euphorbiaceae plant, rubber tree (Hevea brasiliensis Muell. Arg.). Based on the phylogenetic analysis, the JcAQPs were assigned to five subfamilies, i.e., nine plasma membrane intrinsic proteins (PIPs), nine tonoplast intrinsic proteins (TIPs), eight NOD26-like intrinsic proteins (NIPs), two X intrinsic proteins (XIPs), and four small basic intrinsic proteins (SIPs). Like rubber tree and other plant species, functional prediction based on the aromatic/arginine selectivity filter, Froger's positions, and specificity-determining positions showed a remarkable difference in substrate specificity among subfamilies of JcAQPs. Genome-wide comparative analysis revealed the specific expansion of PIP and TIP subfamilies in rubber tree and the specific gene loss of the XIP subfamily in physic nut. Furthermore, by analyzing deep transcriptome sequencing data, the expression evolution especially the expression divergence of duplicated HbAQP genes was also investigated and discussed. Results obtained from this study not only provide valuable information for future functional analysis and utilization of Jc/HbAQP genes, but also provide a useful reference to survey the gene family expansion and evolution in Euphorbiaceae plants and other plant species.

Genome-Wide Analysis of the AP2/ERF Gene Family in Physic Nut and Overexpression of the JcERF011 Gene in Rice Increased Its Sensitivity to Salinity Stress

The AP2/ERF transcription factors play crucial roles in plant growth, development and responses to biotic and abiotic stresses. A total of 119 AP2/ERF genes (JcAP2/ERFs) have been identified in the physic nut genome; they include 16 AP2, 4 RAV, 1 Soloist, and 98 ERF genes. Phylogenetic analysis indicated that physic nut AP2 genes could be divided into 3 subgroups, while ERF genes could be classed into 11 groups or 43 subgroups. The AP2/ERF genes are non-randomly distributed across the 11 linkage groups of the physic nut genome and retain many duplicates which arose from ancient duplication events. The expression patterns of several JcAP2/ERF duplicates in the physic nut showed differences among four tissues (root, stem, leaf, and seed), and 38 JcAP2/ERF genes responded to at least one abiotic stressor (drought, salinity, phosphate starvation, and nitrogen starvation) in leaves and/or roots according to analysis of digital gene expression tag data. The expression of JcERF011 was downregulated by salinity stress in physic nut roots. Overexpression of the JcERF011 gene in rice plants increased its sensitivity to salinity stress. The increased expression levels of several salt tolerance-related genes were impaired in the JcERF011-overexpressing plants under salinity stress.

Transcriptomics and physiological analyses reveal co-ordinated alteration of metabolic pathways in Jatropha curcas drought tolerance

Jatropha curcas, a multipurpose plant attracting a great deal of attention due to its high oil content and quality for biofuel, is recognized as a drought-tolerant species. However, this drought tolerance is still poorly characterized. This study aims to contribute to uncover the molecular background of this tolerance, using a combined approach of transcriptional profiling and morphophysiological characterization during a period of water-withholding (49 d) followed by rewatering (7 d). Morphophysiological measurements showed that J. curcas plants present different adaptation strategies to withstand moderate and severe drought. Therefore, RNA sequencing was performed for samples collected under moderate and severe stress followed by rewatering, for both roots and leaves. Jatropha curcas transcriptomic analysis revealed shoot- and root-specific adaptations across all investigated conditions, except under severe stress, when the dramatic transcriptomic reorganization at the root and shoot level surpassed organ specificity. These changes in gene expression were clearly shown by the down-regulation of genes involved in growth and water uptake, and up-regulation of genes related to osmotic adjustments and cellular homeostasis. However, organ-specific gene variations were also detected, such as strong up-regulation of abscisic acid synthesis in roots under moderate stress and of chlorophyll metabolism in leaves under severe stress. Functional validation further corroborated the differential expression of genes coding for enzymes involved in chlorophyll metabolism, which correlates with the metabolite content of this pathway.

Abiotic Stresses: Insight into Gene Regulation and Protein Expression in Photosynthetic Pathways of Plants

Global warming and climate change intensified the occurrence and severity of abiotic stresses that seriously affect the growth and development of plants,especially, plant photosynthesis. The direct impact of abiotic stress on the activity of photosynthesis is disruption of all photosynthesis components such as photosystem I and II, electron transport, carbon fixation, ATP generating system and stomatal conductance. The photosynthetic system of plants reacts to the stress differently, according to the plant type, photosynthetic systems (C₃ or C₄), type of the stress, time and duration of the occurrence and several other factors. The plant responds to the stresses by a coordinate chloroplast and nuclear gene expression. Chloroplast, thylakoid membrane, and nucleus are the main targets of regulated proteins and metabolites associated with photosynthetic pathways. Rapid responses of plant cell metabolism and adaptation to photosynthetic machinery are key factors for survival of plants in a fluctuating environment. This review gives a comprehensive view of photosynthesis-related alterations at the gene and protein levels for plant adaptation or reaction in response to abiotic stress.

Genome-Wide Analysis of the NAC Gene Family in Physic Nut (Jatropha curcas L.)

The NAC proteins (NAM, ATAF1/2 and CUC2) are plant-specific transcriptional regulators that have a conserved NAM domain in the N-terminus. They are involved in various biological processes, including both biotic and abiotic stress responses. In the present study, a total of 100 NAC genes (JcNAC) were identified in physic nut (Jatropha curcas L.). Based on phylogenetic analysis and gene structures, 83 JcNAC genes were classified as members of, or proposed to be diverged from, 39 previously predicted orthologous groups (OGs) of NAC sequences. Physic nut has a single intron-containing NAC gene subfamily that has been lost in many plants. The JcNAC genes are non-randomly distributed across the 11 linkage groups of the physic nut genome, and appear to be preferentially retained duplicates that arose from both ancient and recent duplication events. Digital gene expression analysis indicates that some of the JcNAC genes have tissue-specific expression profiles (e.g. in leaves, roots, stem cortex or seeds), and 29 genes differentially respond to abiotic stresses (drought, salinity, phosphorus deficiency and nitrogen deficiency). Our results will be helpful for further functional analysis of the NAC genes in physic nut.