Transcriptome analysis of leaf and root of rice seedling to acute dehydration

The tuber-specific StbHLH93 gene regulates proplastid-to-amyloplast development during stolon swelling in potato

In potato, stolon swelling is a complex and highly regulated process, and much more work is needed to fully understand the underlying mechanisms. We identified a novel tuber-specific basic helix-loop-helix (bHLH) transcription factor, StbHLH93, based on the high-resolution transcriptome of potato tuber development. StbHLH93 is predominantly expressed in the subapical and perimedullary region of the stolon and developing tubers. Knockdown of StbHLH93 significantly decreased tuber number and size, resulting from suppression of stolon swelling. Furthermore, we found that StbHLH93 directly binds to the plastid protein import system gene TIC56 promoter, activates its expression, and is involved in proplastid-to-amyloplast development during the stolon-to-tuber transition. Knockdown of the target TIC56 gene resulted in similarly problematic amyloplast biogenesis and tuberization. Taken together, StbHLH93 functions in the differentiation of proplastids to regulate stolon swelling. This study highlights the critical role of proplastid-to-amyloplast interconversion during potato tuberization.

Transcriptomic analysis reveals the gene regulatory networks involved in leaf and root response to osmotic stress in tomato

Introduction

Tomato (Solanum lycopersicum L.) is a major horticultural crop that is cultivated worldwide and is characteristic of the Mediterranean agricultural system. It represents a key component of the diet of billion people and an important source of vitamins and carotenoids. Tomato cultivation in open field often experiences drought episodes, leading to severe yield losses, since most modern cultivars are sensitive to water deficit. Water stress leads to changes in the expression of stress-responsive genes in different plant tissues, and transcriptomics can support the identification of genes and pathways regulating this response.

Methods

Here, we performed a transcriptomic analysis of two tomato genotypes, M82 and Tondo, in response to a PEG-mediated osmotic treatment. The analysis was conducted separately on leaves and roots to characterize the specific response of these two organs.

Results

A total of 6,267 differentially expressed transcripts related to stress response was detected. The construction of gene co-expression networks defined the molecular pathways of the common and specific responses of leaf and root. The common response was characterized by ABA-dependent and ABA-independent signaling pathways, and by the interconnection between ABA and JA signaling. The root-specific response concerned genes involved in cell wall metabolism and remodeling, whereas the leaf-specific response was principally related to leaf senescence and ethylene signaling. The transcription factors representing the hubs of these regulatory networks were identified. Some of them have not yet been characterized and can represent novel candidates for tolerance.

Discussion

This work shed new light on the regulatory networks occurring in tomato leaf and root under osmotic stress and set the base for an in-depth characterization of novel stress-related genes that may represent potential candidates for improving tolerance to abiotic stress in tomato.

Integration of transcriptomic and metabolomic analyses provides insights into response mechanisms to nitrogen and phosphorus deficiencies in soybean

Nitrogen (N) and phosphorus (P) are two essential plant macronutrients that can limit plant growth by different mechanisms. We aimed to shed light on how soybean respond to low nitrogen (LN), low phosphorus (LP) and their combined deficiency (LNP). Generally, these conditions triggered changes in gene expression of the same processes, including cell wall organization, defense response, response to oxidative stress, and photosynthesis, however, response was different in each condition. A typical primary response to LN and LP was detected also in soybean, i.e., the enhanced uptake of N and P, respectively, by upregulation of genes for the corresponding transporters. The regulation of genes involved in cell wall organization showed that in LP roots tended to produce more casparian strip, in LN more secondary wall biosynthesis occurred, and in LNP reduction in expression of genes involved in secondary wall production accompanied by cell wall loosening was observed. Flavonoid biosynthesis also showed distinct pattern of regulation in different conditions: more anthocyanin production in LP, and more isoflavonoid production in LN and LNP, which we confirmed also on the metabolite level. Interestingly, in soybean the nutrient deficiencies reduced defense response by lowering expression of genes involved in defense response, suggesting a role of N and P nutrition in plant disease resistance. In conclusion, we provide detailed information on how LN, LP, and LNP affect different processes in soybean roots on the molecular and physiological levels.

Suppressed ABA signal transduction in the spike promotes sucrose use in the stem and reduces grain number in wheat under water stress

Water stress is a primary trigger for reducing grain number per spike in wheat during the reproductive period. However, under stress conditions, the responses of plant organs and the interactions between them at the molecular and physiological levels remain unclear. In this study, when water stress occurred at the young microspore stage, RNA-seq data indicated that the spike had 970 differentially expressed genes, while the stem, comprising the two internodes below the spike (TIS), had 382. Abscisic acid (ABA) signal transduction genes were down-regulated by water stress in both these tissues, although to a greater extent in the TIS than in the spike. A reduction in sucrose was observed, and was accompanied by increases in cell wall invertase (CWIN) and sucrose:sucrose 1-fructosyl-transferase (1-SST) activities. Hexose and fructan were increased in the TIS but decreased in the spike. ABA was increased in the spike and TIS, and showed significant positive correlation with CWIN and 1-SST activities in the TIS. Overall, our results suggest that water stress induces the conversion of sucrose to hexose by CWIN, and to fructan by 1-SST, due to increased down-regulation of ABA signal transduction related-genes in the TIS; this leads to deficient sucrose supply to the spike and a decrease in grain number.

Temporal transcriptomic differences between tolerant and susceptible genotypes contribute to rice drought tolerance

BACKGROUND

Drought-tolerance ensures a crop to maintain life activities and protect cell from damages under dehydration. It refers to diverse mechanisms temporally activated when the crop adapts to drought. However, knowledge about the temporal dynamics of rice transcriptome under drought is limited.

RESULTS

Here, we investigated temporal transcriptomic dynamics in 12 rice genotypes, which varied in drought tolerance (DT), under a naturally occurred drought in fields. The tolerant genotypes possess less differentially expressed genes (DEGs) while they have higher proportions of upregulated DEGs. Tolerant and susceptible genotypes have great differences in temporally activated biological processes (BPs) during the drought period and at the recovery stage based on their DEGs. The DT-featured BPs, which are activated specially (e.g. raffinose, fucose, and trehalose metabolic processes, etc.) or earlier in the tolerant genotypes (e.g. protein and histone deacetylation, protein peptidyl-prolyl isomerization, transcriptional attenuation, ferric iron transport, etc.) shall contribute to DT. Meanwhile, the tolerant genotypes and the susceptible genotypes also present great differences in photosynthesis and cross-talks among phytohormones under drought. A certain transcriptomic tradeoff between DT and productivity is observed. Tolerant genotypes have a better balance between DT and productivity under drought by activating drought-responsive genes appropriately. Twenty hub genes in the gene coexpression network, which are correlated with DT but without potential penalties in productivity, are recommended as good candidates for DT.

CONCLUSIONS

Findings of this study provide us informative cues about rice temporal transcriptomic dynamics under drought and strengthen our system-level understandings in rice DT.

Genome wide identification of the trihelix transcription factors and overexpression of Gh_A05G2067 (GT-2), a novel gene contributing to increased drought and salt stresses tolerance in cotton

We identified 102, 51 and 51 proteins encoded by the trihelix genes in Gossypium hirsutum, Gossypium arboreum and Gossypium raimondii, respectively. RNA sequence data and real-time quantitative polymerase chain reaction analysis showed that Gh_A05G2067 (GT-2) was highly upregulated under drought and salt stress conditions. Transient expression of GT-2-green fluorescent protein fusion protein in protoplast showed that GT-2 was localized in the nucleus. The overexpression of GT-2 conferred an enhanced drought tolerance to cotton, with lower malondialdehyde, hydrogen peroxide contents and higher reactive oxygen scavenging enzyme activities. Moreover, chlorophyll content, relative leaf water content (RLWC), excised leaf water loss (ELWL) and cell membrane stability (CMS) were relatively stable in the GT-2-overexpressed lines compared to wild-type (WT). Similarly, stress-responsive genes RD29A, SOS1, ABF4 and CBL1 were highly upregulated in the GT-2-overexpressed lines but were significantly downregulated in WT. In addition, the GT-2-silenced cotton plants exhibited a high level of oxidation injury, due to high levels of oxidant enzymes, in addition to negative effects on CMS, ELWL, RLWC and chlorophyll content. These results mark the foundation for future exploration of the trihelix genes in cotton, with an aim of developing more resilient, versatile and highly tolerant cotton genotypes.

Strigolactone Signaling Genes Showing Differential Expression Patterns in Arabidopsis max Mutants

Strigolactone (SL) is a recently discovered class of phytohormone that inhibits shoot branching. The molecular mechanism underlying SL biosynthesis, perception, and signal transduction is vital to the plant branching phenotype. Some aspects of their biosynthesis, perception, and signaling include the role of four MORE AXILLARY GROWTH genes, MAX3, MAX4, MAX1, and MAX2. It is important to identify downstream genes that are involved in SL signaling. To achieve this, we studied the genomic aspects of the strigolactone biosynthesis pathway using microarray analysis of four max mutants. We identified SL signaling candidate genes that showed differential expression patterns in max mutants. More specifically, 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 4 (ACC4) and PROTEIN KINASE 3 (PKS3) displayed contrasting expression patterns, indicating a regulatory mechanism in SL signaling pathway to control different phenotypes apart from branching phenotype.

A WUSCHEL Homeobox Transcription Factor, OsWOX13, Enhances Drought Tolerance and Triggers Early Flowering in Rice

Plants have evolved strategies to cope with drought stress by maximizing physiological capacity and adjusting developmental processes such as flowering time. The WOX13 orthologous group is the most conserved among the clade of WOX homeodomain-containing proteins and is found to function in both drought stress and flower development. In this study, we isolated and characterized OsWOX13 from rice. OsWOX13 was regulated spatially in vegetative organs but temporally in flowers and seeds. Overexpression of OsWOX13 (OsWOX13-ov) in rice under the rab21 promoter resulted in drought resistance and early flowering by 7-10 days. Screening of gene expression profiles in mature leaf and panicles of OsWOX13-ov showed a broad spectrum of effects on biological processes, such as abiotic and biotic stresses, exerting a cross-talk between responses. Protein binding microarray and electrophoretic mobility shift assay analyses supported ATTGATTG as the putative cis-element binding of OsWOX13. OsDREB1A and OsDREB1F, drought stress response transcription factors, contain ATTGATTG motif(s) in their promoters and are preferentially expressed in OsWOX13-ov. In addition, Heading date 3a and OsMADS14, regulators in the flowering pathway and development, were enhanced in OsWOX13-ov. These results suggest that OsWOX13 mediates the stress response and early flowering and, thus, may be a regulator of genes involved in drought escape.

No Time to Waste: Transcriptome Study Reveals that Drought Tolerance in Barley May Be Attributed to Stressed-Like Expression Patterns that Exist before the Occurrence of Stress

Plant survival in adverse environmental conditions requires a substantial change in the metabolism, which is reflected by the extensive transcriptome rebuilding upon the occurrence of the stress. Therefore, transcriptomic studies offer an insight into the mechanisms of plant stress responses. Here, we present the results of global gene expression profiling of roots and leaves of two barley genotypes with contrasting ability to cope with drought stress. Our analysis suggests that drought tolerance results from a certain level of transcription of stress-influenced genes that is present even before the onset of drought. Genes that predispose the plant to better drought survival play a role in the regulatory network of gene expression, including several transcription factors, translation regulators and structural components of ribosomes. An important group of genes is involved in signaling mechanisms, with significant contribution of hormone signaling pathways and an interplay between ABA, auxin, ethylene and brassinosteroid homeostasis. Signal transduction in a drought tolerant genotype may be more efficient through the expression of genes required for environmental sensing that are active already during normal water availability and are related to actin filaments and LIM domain proteins, which may function as osmotic biosensors. Better survival of drought may also be attributed to more effective processes of energy generation and more efficient chloroplasts biogenesis. Interestingly, our data suggest that several genes involved in a photosynthesis process are required for the establishment of effective drought response not only in leaves, but also in roots of barley. Thus, we propose a hypothesis that root plastids may turn into the anti-oxidative centers protecting root macromolecules from oxidative damage during drought stress. Specific genes and their potential role in building up a drought-tolerant barley phenotype is extensively discussed with special emphasis on processes that take place in barley roots. When possible, the interconnections between particular factors are emphasized to draw a broader picture of the molecular mechanisms of drought tolerance in barley.

Transcriptome Analysis of ABA/JA-Dual Responsive Genes in Rice Shoot and Root

Abstract: The phytohormone abscisic acid (ABA) enables plants to adapt to adverse environmental conditions through the modulation of metabolic pathways and of growth and developmental programs. We used comparative microarray analysis to identify genes exhibiting ABA-dependent expression and other hormone-dependent expression among them in Oryza sativa shoot and root. We identified 854 genes as significantly up- or down-regulated in root or shoot under ABA treatment condition. Most of these genes had similar expression profiles in root and shoot under ABA treatment condition, whereas 86 genes displayed opposite expression responses in root and shoot. To examine the crosstalk between ABA and other hormones, we compared the expression profiles of the ABA-dependently regulated genes under several different hormone treatment conditions. Interestingly, around half of the ABA-dependently expressed genes were also regulated by jasmonic acid based on microarray data analysis. We searched the promoter regions of these genes for cis-elements that could be responsible for their responsiveness to both hormones, and found that ABRE and MYC2 elements, among others, were common to the promoters of genes that were regulated by both ABA and JA. These results show that ABA and JA might have common gene expression regulation system and might explain why the JA could function for both abiotic and biotic stress tolerance.

Novel mechanisms for organic acid-mediated aluminium tolerance in roots and leaves of two contrasting soybean genotypes

Aluminium (Al) toxicity is one of the most important limiting factors for crop yield in acidic soils. However, the mechanisms that confer Al tolerance still remain largely unknown. To understand the molecular mechanism that confers different tolerance to Al, we performed global transcriptome analysis to the roots and leaves of two contrasting soybean genotypes, BX10 (Al-tolerant) and BD2 (Al-sensitive) under 0 and 50 μM Al3+ treatments, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that the expression levels of the genes involved in lipid/carbohydrate metabolism and jasmonic acid (JA)-mediated signalling pathway were highly induced in the roots and leaves of both soybean genotypes. The gene encoding enzymes, including pyruvate kinase, phosphoenolpyruvate carboxylase, ATP-citrate lyase and glutamate-oxaloacetate transaminase 2, associated with organic acid metabolism were differentially expressed in the BX10 roots. In addition, the genes involved in citrate transport were differentially expressed. Among these genes, FRD3b was down-regulated only in BD2, whereas the other two multidrug and toxic compound extrusion genes were up-regulated in both soybean genotypes. These findings confirmed that BX10 roots secreted more citrate than BD2 to withstand Al stress. The gene encoding enzymes or regulators, such as lipoxygenase, 12-oxophytodienoate reductase, acyl-CoA oxidase and jasmonate ZIM-domain proteins, involved in JA biosynthesis and signalling were preferentially induced in BD2 leaves. This finding suggests that the JA defence response was activated, possibly weakening the growth of aerial parts because of excessive resource consumption and ATP biosynthesis deficiency. Our results suggest that the Al sensitivity in some soybean varieties could be attributed to the low level of citrate metabolism and exudation in the roots and the high level of JA-mediated defence response in the leaves.

Analysis of Genes with Alternatively Spliced Transcripts in the Leaf, Root, Panicle and Seed of Rice Using a Long Oligomer Microarray and RNA-Seq

Pre-mRNA splicing further increases protein diversity acquired through evolution. The underlying driving forces for this phenomenon are unknown, especially in terms of gene expression. A rice alternatively spliced transcript detection microarray (ASDM) and RNA sequencing (RNA-Seq) were applied to differentiate the transcriptome of 4 representative organs of Oryza sativa L. cv. Ilmi: leaves, roots, 1-cm-stage panicles and young seeds at 21 days after pollination. Comparison of data obtained by microarray and RNA-Seq showed a bell-shaped distribution and a co-lineation for highly expressed genes. Transcripts were classified according to the degree of organ enrichment using a coefficient value (CV, the ratio of the standard deviation to the mean values): highly variable (CVI), variable (CVII), and constitutive (CVIII) groups. A higher index of the portion of loci with alternatively spliced transcripts in a group (IAST) value was observed for the constitutive group. Genes of the highly variable group showed the characteristics of the examined organs, and alternatively spliced transcripts tended to exhibit the same organ specificity or less organ preferences, with avoidance of 'organ distinctness'. In addition, within a locus, a tendency of higher expression was found for transcripts with a longer coding sequence (CDS), and a spliced intron was the most commonly found type of alternative splicing for an extended CDS. Thus, pre-mRNA splicing might have evolved to retain maximum functionality in terms of organ preference and multiplicity.

Reference genes for accurate gene expression analyses across different tissues, developmental stages and genotypes in rice for drought tolerance

BACKGROUND

Quantitative reverse transcription PCR (qRT-PCR) has been routinely used to quantify gene expression level. This technique determines the expression of a target gene by comparison to an internal control gene uniformly expressed among the samples analyzed. The reproducibility and reliability of the results depend heavily on the reference genes used. To achieve successful gene expression analyses for drought tolerance studies in rice, reference gene selection should be based on consistency in expression across variables. We aimed to provide reference genes that would be consistent across different tissues, developmental stages and genotypes of rice and hence improve the quality of data in qRT-PCR analysis.

FINDINGS

Ten candidate reference genes were screened from four ubiquitously expressed gene families by analyzing public microarray data sets that included profiles of multiple organs, developmental stages, and water availability status in rice. These genes were evaluated through qRT-PCR experiments with a rigorous statistical analysis to determine the best reference genes. A ubiquitin isogene showed the best gene expression stability as a single reference gene, while a 3-gene combination of another ubiquitin and two cyclophilin isogenes was the best reference gene combination. Comparison between the qRT-PCR and in-house microarray data on roots demonstrated reliability of the identified reference genes to monitor the differential expression of drought-related candidate genes.

CONCLUSIONS

Specific isogenes from among the regularly used gene families were identified for use in qRT-PCR-based analyses for gene expression in studies on drought tolerance in rice. These were stable across variables of treatment, genotype, tissue and growth stage. A single gene and/or a three gene set analysis is recommended, based on the resources available.

Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress

BACKGROUND

Rice (Oryza sativa L.) is one of the most important crops cultivated in both tropical and temperate regions and is characterized by a low water-use efficiency and a high sensitivity to a water deficit, with yield reductions occurring at lower stress levels compared to most other crops. To identify genes and pathways involved in the tolerant response to dehydration, a powerful approach consists in the genome-wide analysis of stress-induced expression changes by comparing drought-tolerant and drought-sensitive genotypes.

RESULTS

The physiological response to osmotic stress of 17 japonica rice genotypes was evaluated. A clear differentiation of the most tolerant and the most sensitive phenotypes was evident, especially after 24 and 48 h of treatment. Two genotypes, which were characterized by a contrasting response (tolerance/sensitivity) to the imposed stress, were selected. A parallel transcriptomic analysis was performed on roots and leaves of these two genotypes at 3 and 24 h of stress treatment. RNA-Sequencing data showed that the tolerant genotype Eurosis and the sensitive genotype Loto mainly differed in the early response to osmotic stress in roots. In particular, the tolerant genotype was characterized by a prompt regulation of genes related to chromatin, cytoskeleton and transmembrane transporters. Moreover, a differential expression of transcription factor-encoding genes, genes involved in hormone-mediate signalling and genes involved in the biosynthesis of lignin was observed between the two genotypes.

CONCLUSIONS

Our results provide a transcriptomic characterization of the osmotic stress response in rice and identify several genes that may be important players in the tolerant response.

Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice

Plants show a high degree of developmental plasticity in response to external cues, including day length and environmental stress. Water scarcity in particular can interfere with photoperiodic flowering, resulting in the acceleration of the switch to reproductive growth in several species, a process called drought escape. However, other strategies are possible and drought stress can also delay flowering, albeit the underlying mechanisms have never been addressed at the molecular level. We investigated these interactions in rice, a short day species in which drought stress delays flowering. A protocol that allows the synchronization of drought with the floral transition was set up to profile the transcriptome of leaves subjected to stress under distinct photoperiods. We identified clusters of genes that responded to drought differently depending on day length. Exposure to drought stress under floral-inductive photoperiods strongly reduced transcription of EARLY HEADING DATE 1 (Ehd1), HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1), primary integrators of day length signals, providing a molecular connection between stress and the photoperiodic pathway. However, phenotypic and transcriptional analyses suggested that OsGIGANTEA (OsGI) does not integrate drought and photoperiodic signals as in Arabidopsis, highlighting molecular differences between long and short day model species.

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.

Complex molecular mechanisms underlying seedling salt tolerance in rice revealed by comparative transcriptome and metabolomic profiling

To understand the physiological and molecular mechanisms underlying seedling salt tolerance in rice (Oryza sativa L.), the phenotypic, metabolic, and transcriptome responses of two related rice genotypes, IR64 and PL177, with contrasting salt tolerance were characterized under salt stress and salt+abscisic acid (ABA) conditions. PL177 showed significantly less salt damage, lower Na(+)/K(+) ratios in shoots, and Na(+) translocation from roots to shoots, attributed largely to better salt exclusion from its roots and salt compartmentation of its shoots. Exogenous ABA was able to enhance the salt tolerance of IR64 by selectively decreasing accumulation of Na(+) in its roots and increasing K(+) in its shoots. Salt stress induced general and organ-specific increases of many primary metabolites in both rice genotypes, with strong accumulation of several sugars plus proline in shoots and allantoin in roots. This was due primarily to ABA-mediated repression of genes for degradation of these metabolites under salt. In PL177, salt specifically up-regulated genes involved in several pathways underlying salt tolerance, including ABA-mediated cellular lipid and fatty acid metabolic processes and cytoplasmic transport, sequestration by vacuoles, detoxification and cell-wall remodeling in shoots, and oxidation-reduction reactions in roots. Combined genetic and transcriptomic evidence shortlisted relatively few candidate genes for improved salt tolerance in PL177.

OsMADS26 Negatively Regulates Resistance to Pathogens and Drought Tolerance in Rice

Functional analyses of MADS-box transcription factors in plants have unraveled their role in major developmental programs (e.g. flowering and floral organ identity) as well as stress-related developmental processes, such as abscission, fruit ripening, and senescence. Overexpression of the rice (Oryza sativa) MADS26 gene in rice has revealed a possible function related to stress response. Here, we show that OsMADS26-down-regulated plants exhibit enhanced resistance against two major rice pathogens: Magnaporthe oryzae and Xanthomonas oryzae. Despite this enhanced resistance to biotic stresses, OsMADS26-down-regulated plants also displayed enhanced tolerance to water deficit. These phenotypes were observed in both controlled and field conditions. Interestingly, alteration of OsMADS26 expression does not have a strong impact on plant development. Gene expression profiling revealed that a majority of genes misregulated in overexpresser and down-regulated OsMADS26 lines compared with control plants are associated to biotic or abiotic stress response. Altogether, our data indicate that OsMADS26 acts as an upstream regulator of stress-associated genes and thereby, a hub to modulate the response to various stresses in the rice plant.

Genome-wide transcriptional and physiological responses to drought stress in leaves and roots of two willow genotypes

BACKGROUND

Drought is a major environmental stress that can have severe impacts on plant productivity and survival. Understanding molecular mechanisms of drought responses is crucial in order to breed for drought adapted plant cultivars. The aim of the present study was to investigate phenotypic and transcriptional drought responses in two willow genotypes (520 and 592) originating from an experimental cross between S. viminalis × (S. viminalis × S. schwerinii). Willows are woody perennials in the Salicaceae plant family that are grown as bioenergy crops worldwide.

METHODS

An experiment was conducted where plants were exposed to drought and different eco-physiological parameters were assessed. RNA-seq data was furthermore generated with the Illumina technology from root tips and leaves from plants grown in drought and well-watered (WW) conditions. The RNA-seq data was assembled de novo with the Trinity assembler to create a reference gene set to which the reads were mapped in order to obtain differentially expressed genes (DEGs) between the drought and WW conditions. To investigate molecular mechanisms involved in the drought response, GO enrichment analyses were conducted. Candidate genes with a putative function in the drought response were also identified.

RESULTS

A total of 52,599 gene models were obtained and after filtering on gene expression (FPKM ≥ 1), 35,733 gene models remained, of which 24,421 contained open reading frames. A total of 5,112 unique DEGs were identified between drought and WW conditions, of which the majority were found in the root tips. Phenotypically, genotype 592 displayed less growth reduction in response to drought compared to genotype 520. At the transcriptional level, genotype 520 displayed a greater response in the leaves as more DEGs were found in genotype 520 compared to genotype 592. In contrast, the transcriptional responses in the root tips were rather similar between the two genotypes. A core set of candidate genes encoding proteins with a putative function in drought response was identified, for example MYBs and bZIPs as well as chlorophyll a/b binding proteins.

DISCUSSION

We found substantial differences in drought responses between the genotypes, both at the phenotypic and transcriptional levels. In addition to the genotypic variation in several traits, we also found indications for genotypic variation in trait plasticity, which could play a role in drought adaptation. Furthermore, the two genotypes displayed overall similar transcriptional responses in the root tips, but more variation in the leaves. It is thus possible that the observed phenotypic differences could be a result of transcriptional differences mostly at the leaf level.

CONCLUSIONS

This study has contributed to a better general understanding of drought responses in woody plants, specifically in willows, and has implications for breeding research towards more drought adapted plants.

De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic Data

Background

The perennial O. rufipogon (common wild rice), which is considered to be the ancestor of Asian cultivated rice species, contains many useful genetic resources, including drought resistance genes. However, few studies have identified the drought resistance and tissue-specific genes in common wild rice.

Results

In this study, transcriptome sequencing libraries were constructed, including drought-treated roots (DR) and control leaves (CL) and roots (CR). Using Illumina sequencing technology, we generated 16.75 million bases of high-quality sequence data for common wild rice and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 119,332 unigenes with an average length of 715 bp. A total of 88,813 distinct sequences (74.42% of unigenes) significantly matched known genes in the NCBI NT database. Differentially expressed gene (DEG) analysis showed that 3617 genes were up-regulated and 4171 genes were down-regulated in the CR library compared with the CL library. Among the DEGs, 535 genes were expressed in roots but not in shoots. A similar comparison between the DR and CR libraries showed that 1393 genes were up-regulated and 315 genes were down-regulated in the DR library compared with the CR library. Finally, 37 genes that were specifically expressed in roots were screened after comparing the DEGs identified in the above-described analyses.

Conclusion

This study provides a transcriptome sequence resource for common wild rice plants and establishes a digital gene expression profile of wild rice plants under drought conditions using the assembled transcriptome data as a reference. Several tissue-specific and drought-stress-related candidate genes were identified, representing a fully characterized transcriptome and providing a valuable resource for genetic and genomic studies in plants.

Profiling gene expression in citrus fruit calyx abscission zone (AZ-C) treated with ethylene

On-tree storage and harvesting of mature fruit account for a large proportion of cost in the production of citrus, and a reduction of the cost would not be achieved without a thorough understanding of the mechani sm of the mature fruit abscission. Genome-wide gene expression changes in ethylene-treated fruit calyx abscission zone (AZ-C) of Citrus sinensis cv. Olinda were therefore investigated using a citrus genome array representing up to 33,879 citrus transcripts. In total, 1313 and 1044 differentially regulated genes were identified in AZ-C treated with ethylene for 4 and 24 h, respectively. The results showed that mature citrus fruit abscission commenced with the activation of ethylene signal transduction pathway that led to the activation of ethylene responsive transcription factors and the subsequent transcriptional regulation of a large set of ethylene responsive genes. Significantly down-regulated genes included those of starch/sugar biosynthesis, transportation of water and growth promoting hormone synthesis and signaling, whereas significantly up-regulated genes were those involved in defense, cell wall degradation, and secondary metabolism. Our data unraveled the underlying mechanisms of some known important biochemical events occurring at AZ-C and should provide informative suggestions for future manipulation of the events to achieve a controllable abscission for mature citrus fruit.

Rice GROWTH UNDER DROUGHT KINASE is required for drought tolerance and grain yield under normal and drought stress conditions

Rice (Oryza sativa) is the primary food source for more than one-half of the world's population. Because rice cultivation is dependent on water availability, drought during flowering severely affects grain yield. Here, we show that the function of a drought-inducible receptor-like cytoplasmic kinase, named GROWTH UNDER DROUGHT KINASE (GUDK), is required for grain yield under drought and well-watered conditions. Loss-of-function gudk mutant lines exhibit sensitivity to salinity, osmotic stress, and abscisic acid treatment at the seedling stage, and a reduction in photosynthesis and plant biomass under controlled drought stress at the vegetative stage. The gudk mutants interestingly showed a significant reduction in grain yield, both under normal well-watered conditions and under drought stress at the reproductive stage. Phosphoproteome profiling of the mutant followed by in vitro assays identified the transcription factor APETALA2/ETHYLENE RESPONSE FACTOR OsAP37 as a phosphorylation target of GUDK. The involvement of OsAP37 in regulating grain yield under drought through activation of several stress genes was previously shown. Our transactivation assays confirmed that GUDK is required for activation of stress genes by OsAP37. We propose that GUDK mediates drought stress signaling through phosphorylation and activation of OsAP37, resulting in transcriptional activation of stress-regulated genes, which impart tolerance and improve yield under drought. Our study reveals insights around drought stress signaling mediated by receptor-like cytoplasmic kinases, and also identifies a primary regulator of grain yield in rice that offers the opportunity to improve and stabilize rice grain yield under normal and drought stress conditions.

Overexpression of a Calcium-Dependent Protein Kinase Confers Salt and Drought Tolerance in Rice by Preventing Membrane Lipid Peroxidation

The OsCPK4 gene is a member of the complex gene family of calcium-dependent protein kinases in rice (Oryza sativa). Here, we report that OsCPK4 expression is induced by high salinity, drought, and the phytohormone abscisic acid. Moreover, a plasma membrane localization of OsCPK4 was observed by transient expression assays of green fluorescent protein-tagged OsCPK4 in onion (Allium cepa) epidermal cells. Overexpression of OsCPK4 in rice plants significantly enhances tolerance to salt and drought stress. Knockdown rice plants, however, are severely impaired in growth and development. Compared with control plants, OsCPK4 overexpressor plants exhibit stronger water-holding capability and reduced levels of membrane lipid peroxidation and electrolyte leakage under drought or salt stress conditions. Also, salt-treated OsCPK4 seedlings accumulate less Na⁺ in their roots. We carried out microarray analysis of transgenic rice overexpressing OsCPK4 and found that overexpression of OsCPK4 has a low impact on the rice transcriptome. Moreover, no genes were found to be commonly regulated by OsCPK4 in roots and leaves of rice plants. A significant number of genes involved in lipid metabolism and protection against oxidative stress appear to be up-regulated by OsCPK4 in roots of overexpressor plants. Meanwhile, OsCPK4 overexpression has no effect on the expression of well-characterized abiotic stress-associated transcriptional regulatory networks (i.e. ORYZA SATIVA DEHYDRATION-RESPONSIVE ELEMENT BINDING PROTEIN1 and ORYZA SATIVA No Apical Meristem, Arabidopsis Transcription Activation Factor1-2, Cup-Shaped Cotyledon6 genes) and LATE EMBRYOGENESIS ABUNDANT genes in their roots. Taken together, our data show that OsCPK4 functions as a positive regulator of the salt and drought stress responses in rice via the protection of cellular membranes from stress-induced oxidative damage.