Global transcriptome profile of rice root in response to essential macronutrient deficiency

A major genetic locus in neighbours controls changes of gene expression and susceptibility in intraspecific rice mixtures

Reports indicate that intraspecific neighbours alter the physiology of focal plants, and with a few exceptions, their molecular responses to neighbours are unknown. Recently, changes in susceptibility to pathogen resulting from such interactions were demonstrated, a phenomenon called neighbour-modulated susceptibility (NMS). However, the genetics of NMS and the associated molecular responses are largely unexplored. Here, we analysed in rice the modification of biomass and susceptibility to the blast fungus pathogen in the Kitaake focal genotype in the presence of 280 different neighbours. Using genome-wide association studies, we identified the loci in the neighbour that determine the response in Kitaake. Using a targeted transcriptomic approach, we characterized the molecular responses in focal plants co-cultivated with various neighbours inducing a reduction in susceptibility. Our study demonstrates that NMS is controlled by one major locus in the rice genome of its neighbour. Furthermore, we show that this locus can be associated with characteristic patterns of gene expression in focal plant. Finally, we propose an hypothesis where Pi could play a role in explaining this case of NMS. Our study sheds light on how plants affect the physiology in their neighbourhood and opens perspectives for understanding plant-plant interactions.

Transcriptome and hyperspectral profiling allows assessment of phosphorus nutrient status in rice under field conditions

Phosphorus (P) is one of the macronutrients indispensable for crop production, and therefore it is important to understand the potential of plants to adapt to low P conditions. We compared growth and leaf genome-wide transcriptome of four rice cultivars during growth between two fields with different amount of available phosphate and further analysed the acceptable range of P levels for normal growth from the view of both appearance traits and internal P nutrient status, which was measured by profiling the expression of the P indicator gene. This demonstrated that rice plants have a robustness to moderate P-deficient conditions expressing a system for P acquisition and usage without any effects on yield potential and that P indicator gene expression could be a useful index for early diagnosis of P status in plants. To develop a simple method for assessment of P status, we tried to predict the expression level using reflectance spectroscopy and hyperspectral imaging, thereby providing models with good performance. Our findings suggest that rice plants have the potential to adapt to moderate low P conditions in the field and showed that the hyperspectral technique is one of the useful tools for simple measurement of molecular-level dynamics reflecting internal nutrient conditions.

Genomic variation reveals demographic history and biological adaptation of the ancient relictual, lotus (Nelumbo Adans)

Lotus (Nelumbo Adans.), a relict plant, is the testimony of long-term sustained ecological success, but the underlying genetic changes related to its survival strategy remains unclear. Here, we assembled the high-quality lotus genome, investigated genome variation of lotus mutation accumulation (MA) lines and reconstructed the demographic history of wild Asian lotus, respectively. We identified and validated 43 base substitutions fixed in MA lines, implying a spontaneous mutation rate of 1.4 × 10-9 base/generation in lotus shoot stem cells. The past history of lotus revealed that the ancestors of lotus in eastern and southern Asia could be traced back ~20 million years ago (Mya) and experienced twice significant bottlenecks and population splits. We further identified the selected genes among three lotus groups in different habitats, suggesting that 453 genes between tropical and temperate group and 410 genes between two subgroups from Northeastern China and the Yangtze River - Yellow River Basin might play important roles in natural selection in lotus's adaptation and resilience. Our findings not only improve an understanding of the lotus evolutionary history and the genetic basis of its survival advantages, but also provide valuable data for addressing various questions in evolution and protection for the relict plants.

The Divergent Roles of the Rice bcl-2 Associated Athanogene (BAG) Genes in Plant Development and Environmental Responses

Bcl-2-associated athanogene (BAG), a group of proteins evolutionarily conserved and functioned as co-chaperones in plants and animals, is involved in various cell activities and diverse physiological processes. However, the biological functions of this gene family in rice are largely unknown. In this study, we identified a total of six BAG members in rice. These genes were classified into two groups, OsBAG1, -2, -3, and -4 are in group I with a conserved ubiquitin-like structure and OsBAG5 and -6 are in group Ⅱ with a calmodulin-binding domain, in addition to a common BAG domain. The BAG genes exhibited diverse expression patterns, with OsBAG4 showing the highest expression level, followed by OsBAG1 and OsBAG3, and OsBAG6 preferentially expressed in the panicle, endosperm, and calli. The co-expression analysis and the hierarchical cluster analysis indicated that the OsBAG1 and OsBAG3 were co-expressed with primary cell wall-biosynthesizing genes, OsBAG4 was co-expressed with phytohormone and transcriptional factors, and OsBAG6 was co-expressed with disease and shock-associated genes. β-glucuronidase (GUS) staining further indicated that OsBAG3 is mainly involved in primary young tissues under both primary and secondary growth. In addition, the expression of the BAG genes under brown planthopper (BPH) feeding, N, P, and K deficiency, heat, drought and plant hormones treatments was investigated. Our results clearly showed that OsBAGs are multifunctional molecules as inferred by their protein structures, subcellular localizations, and expression profiles. BAGs in group I are mainly involved in plant development, whereas BAGs in group II are reactive in gene regulations and stress responses. Our results provide a solid basis for the further elucidation of the biological functions of plant BAG genes.

Expression dynamics indicate the role of Jasmonic acid biosynthesis pathway in regulating macronutrient (N, P and K+) deficiency tolerance in rice (Oryza sativa L.)

Expression pattern indicates that JA biosynthesis pathway via regulating JA levels might control root system architecture to improve nutrient use efficiency (NUE) and N, P, K⁺ deficiency tolerance in rice. Deficiencies of macronutrients (N, P and K⁺) and consequent excessive use of fertilizers have dramatically reduced soil fertility. It calls for development of nutrient use efficient plants. Plants combat nutrient deficiencies by altering their root system architecture (RSA) to enhance the acquisition of nutrients from the soil. Amongst various phytohormones, Jasmonic acid (JA) is known to regulate plant root growth and modulate RSA. Therefore, to understand the role of JA in macronutrient deficiency in rice, expression pattern of JA biosynthesis genes was analyzed under N, P and K⁺ deficiencies. Several members belonging to different families of JA biosynthesis genes (PLA1, LOX, AOS, AOC, OPR, ACX and JAR1) showed differential expression exclusively in one nutrient deficiency or in multiple nutrient deficiencies. Expression analysis during developmental stages showed that several genes expressed significantly in vegetative tissues, particularly in root. In addition, JA biosynthesis genes were found to have significant expression under the treatment of different phytohormones, including Auxin, cytokinin, gibberellic acid (GA), abscisic acid (ABA), JA and abiotic stresses, such as drought, salinity and cold. Analysis of promoters of these genes revealed various cis-regulatory elements associated with hormone response, plant development and abiotic stresses. These findings suggest that JA biosynthesis pathway by regulating the level of JA might control the RSA thus, it may help rice plant in combating macronutrient deficiency.

Isolation and screening of potassium solubilizing bacteria from saxicolous habitat and their impact on tomato growth in different soil types

Bacteria that solubilize nutrients in the soil are commonly used as bio-inoculants for promoting the growth of different crop species. However, the influence of potassium (K) solubilizing bacteria (KSB) originating from saxicolous habitat (rock-dwelling) on plant growth has not been frequently examined. In this study, we isolated KSB from saxicolous habitats and estimated their ability to produce plant growth hormone, organic acids, and siderophore that may facilitate plant growth. Fifteen culturable saxicolous bacterial isolates with varied K solubilizing ability were isolated from two sites. Of these, four potential K solubilizers were selected and identified by 16S rRNA gene sequencing. The four bacterial isolates resembled Bacillus subtilis, Bacillus cereus, Bacillus licheniformis, and Burkholderia cenocepacia and produced different organic acids, indole acetic acid, and siderophore under in vitro conditions. Potassium solubilization differed among the bacterial isolates and was significantly influenced by K sources. Inoculation of KSB improved the tomato plant growth parameters like plant height, leaf area, total root length, root/shoot ratio, and tissue K content in sterilized and unsterilized Alfisol, and Vertisol soils under greenhouse conditions. We also observed higher residual K content in the KSB inoculated post-harvest soils. Among the four KSB isolates screened, B. licheniformis and B. cenocepacia presents an excellent prospect as bio-inoculants for improving tomato growth in different soil types. Besides these, the enriched K content in the post-harvest soils may help the growth of subsequent crops in sustainable agriculture.

Transcriptome Analysis Unravels Key Factors Involved in Response to Potassium Deficiency and Feedback Regulation of K+ Uptake in Cotton Roots

To properly understand cotton responses to potassium (K+) deficiency and how its shoot feedback regulates K+ uptake and root growth, we analyzed the changes in root transcriptome induced by low K+ (0.03 mM K+, lasting three days) in self-grafts of a K+ inefficient cotton variety (CCRI41/CCRI41, scion/rootstock) and its reciprocal grafts with a K+ efficient variety (SCRC22/CCRI41). Compared with CCRI41/CCRI41, the SCRC22 scion enhanced the K+ uptake and root growth of CCRI41 rootstock. A total of 1968 and 2539 differently expressed genes (DEGs) were identified in the roots of CCRI41/CCRI41 and SCRC22/CCRI41 in response to K+ deficiency, respectively. The overlapped and similarly (both up- or both down-) regulated DEGs in the two grafts were considered the basic response to K+ deficiency in cotton roots, whereas the DEGs only found in SCRC22/CCRI41 (1954) and those oppositely (one up- and the other down-) regulated in the two grafts might be the key factors involved in the feedback regulation of K+ uptake and root growth. The expression level of four putative K+ transporter genes (three GhHAK5s and one GhKUP3) increased in both grafts under low K+, which could enable plants to cope with K+ deficiency. In addition, two ethylene response factors (ERFs), GhERF15 and GhESE3, both down-regulated in the roots of CCRI41/CCRI41 and SCRC22/CCRI41, may negatively regulate K+ uptake in cotton roots due to higher net K+ uptake rate in their virus-induced gene silencing (VIGS) plants. In terms of feedback regulation of K+ uptake and root growth, several up-regulated DEGs related to Ca2+ binding and CIPK (CBL-interacting protein kinases), one up-regulated GhKUP3 and several up-regulated GhNRT2.1s probably play important roles. In conclusion, these results provide a deeper insight into the molecular mechanisms involved in basic response to low K+ stress in cotton roots and feedback regulation of K+ uptake, and present several low K+ tolerance-associated genes that need to be further identified and characterized.

Down regulation of transcripts involved in selective metabolic pathways as an acclimation strategy in nitrogen use efficient genotypes of rice under low nitrogen

To understand the molecular mechanism of nitrogen use efficiency (NUE) in rice, two nitrogen (N) use efficient genotypes and two non-efficient genotypes were characterized using transcriptome analyses. The four genotypes were evaluated for 3 years under low and recommended N field conditions for 12 traits/parameters of yield, straw, nitrogen content along with NUE indices and 2 promising donors for rice NUE were identified. Using the transcriptome data generated from GS FLX 454 Roche and Illumina HiSeq 2000 of two efficient and two non-efficient genotypes grown under field conditions of low N and recommended N and their de novo assembly, differentially expressed transcripts and pathways during the panicle development were identified. Down regulation was observed in 30% of metabolic pathways in efficient genotypes and is being proposed as an acclimation strategy to low N. Ten sub metabolic pathways significantly enriched with additional transcripts either in the direction of the common expression or contra-regulated to the common expression were found to be critical for NUE in rice. Among the up-regulated transcripts in efficient genotypes, a hypothetical protein OsI_17904 with 2 alternative forms suggested the role of alternative splicing in NUE of rice and a potassium channel SKOR transcript (LOC_Os06g14030) has shown a positive correlation (0.62) with single plant yield under low N in a set of 16 rice genotypes. From the present study, we propose that the efficient genotypes appear to down regulate several not so critical metabolic pathways and divert the thus conserved energy to produce seed/yield under long-term N starvation.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02631-5.

Transcriptome-based approaches for clarification of nutritional responses and improvement of crop production

Genome-wide transcriptome profiling is a powerful tool for identifying key genes and pathways involved in plant development and physiological processes. This review summarizes studies that have used transcriptome profiling mainly in rice to focus on responses to macronutrients such as nitrogen, phosphorus and potassium, and spatio-temporal root profiling in relation to the regulation of root system architecture as well as nutrient uptake and transport. We also discuss strategies based on meta- and co-expression analyses with different attributed transcriptome data, which can be used for investigating the regulatory mechanisms and dynamics of nutritional responses and adaptation, and speculate on further advances in transcriptome profiling that could have potential application to crop breeding and cultivation.

OsJAZ9 overexpression modulates jasmonic acid biosynthesis and potassium deficiency responses in rice

Enhanced bioactive JA (JA-Ile) accumulation in OsJAZ9 overexpressing rice helps plants tolerate K deficiency. Potassium (K) represents up to 10% of the plant's total dry biomass, and its deficiency makes plants highly susceptible to both abiotic and biotic stresses. K shortage results in the inhibition of root and shoots growth, but the underlying mechanism of this response is unclear. Our RNA-Seq and qPCR analysis suggested leading roles for JA pathway genes under K deficiency in rice. Notably, K deficiency and JA application produced similar phenotypic and transcriptional responses. Here, we integrated molecular, physiological and morphological studies to analyze the role of OsJAZ9 in JA homeostasis and K deficiency responses. We raised OsJAZ9 over-expression, knockdown, transcriptional reporter, translational reporter and C-terminal deleted translational reporter lines in rice to establish the role of JA signaling in K ion homeostasis. JA profiling revealed significantly increased JA-Ile levels in OsJAZ9 OE lines under K deficiency. Furthermore, we established that OsJAZ9 overexpression and knockdown result in K deficiency tolerance and sensitivity, respectively, by modulating various K transporters and root system architecture. Our data provide evidence on the crucial roles of OsJAZ9 for improving K deficiency tolerance in rice by altering JA levels and JA responses.

Orange Leafhopper Cicadulina bipunctata Feeding Induces Gall Formation Nitrogen Dependently and Regulates Gibberellin Signaling

Orange leafhopper Cicadulina bipunctata feeding induces wallaby ear symptoms, namely growth suppression and gall formation characterized by severe swelling of leaf veins, on various Poaceae, thereby leading to low crop yields. Here, we investigated the development of wallaby ear symptoms on rice seedlings due to C. bipunctata feeding. After confirming that C. bipunctata feeding induces growth suppression and gall formation on rice seedlings, we further demonstrated that gall formation score decreased with decreasing levels of nitrogen in the medium and that C. bipunctata feeding induces the expression levels of nitrogen transporter genes. These gene expression changes may participate in the nutrient accumulation observed in galled tissues and in gall formation. In addition, these expression changes should induce growth promotion but the inhibition of gibberellin signaling by C. bipunctata feeding might be the reason why growth is suppressed. Treatment with plant growth regulators did not affect gall formation, suggesting the existence of a complex gall formation mechanism by C. bipunctata feeding.

Effect of Seedling Nitrogen Condition on Subsequent Vegetative Growth Stages and Its Relationship to the Expression of Nitrogen Transporter Genes in Rice

Nitrogen (N) deficiency is one of the most common problems in soils, limiting crop growth and production. However, the effects of N limitation in seedlings on vegetative growth remain poorly understood. Here, we show that N limitation in rice seedlings restricted vegetative growth but not yield. Aboveground parts were affected mainly during the period of tillering, but belowground parts were sensitive throughout vegetative growth, especially during panicle development. At the tillering stage, N-limited plants had a significantly lower N content in shoots, but not in roots. On the other hand, N content in roots during the panicle development stage was significantly lower in N-limited plants. This distinct response was driven by significant changes in expression of N transporter genes during growth. Under N limitation, N translocation from roots to shoots was greatly sped up by systemic expression of N transporter genes to obtain balanced growth. N limitation during the seedling stage did not reduce any yield components. We conclude that the N condition during the seedling stage affects physiological responses such as N translocation through the expression of N transporter genes.

Comparative analysis of tissue-specific transcriptomic responses to nitrogen stress in spinach (Spinacia oleracea)

Nitrogen (N) is critical to the growth and productivity of crops. To understand the molecular mechanisms influenced by N stress, we used RNA-Sequencing (RNA-Seq) to analyze differentially expressed genes (DEGs) in root and leaf tissues of spinach. N stress negatively influenced photosynthesis, biomass accumulation, amino acid profiles, and partitioning of N across tissues. RNA-seq analysis revealed that N stress caused most transcriptomic changes in roots, identifying 1,346 DEGs. High-affinity nitrate transporters (NRT2.1, NRT2.5) and glutamine amidotransferase (GAT1) genes were strongly induced in roots in response to N deplete and replete conditions, respectively. GO and KEGG analyses revealed that the functions associated with metabolic pathways and nutrient reservoir activity were enriched due to N stress. Whereas KEGG pathway enrichment analysis indicated the upregulation of DEGs associated with DNA replication, pyrimidine, and purine metabolism in the presence of high N in leaf tissue. A subset of transcription factors comprising bHLH, MYB, WRKY, and AP2/ERF family members was over-represented in both tissues in response to N perturbation. Interesting DEGs associated with N uptake, amino acid metabolism, hormonal pathway, carbon metabolism, along with transcription factors, were highlighted. The results provide valuable information about the underlying molecular processes in response to N stress in spinach and; could serve as a resource for functional analysis of candidate genes/pathways and enhancement of nitrogen use efficiency.

PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens

Physcomitrella patens is a bryophyte model plant that is often used to study plant evolution and development. Its resources are of great importance for comparative genomics and evo-devo approaches. However, expression data from Physcomitrella patens were so far generated using different gene annotation versions and three different platforms: CombiMatrix and NimbleGen expression microarrays and RNA sequencing. The currently available P. patens expression data are distributed across three tools with different visualization methods to access the data. Here, we introduce an interactive expression atlas, Physcomitrella Expression Atlas Tool (PEATmoss), that unifies publicly available expression data for P. patens and provides multiple visualization methods to query the data in a single web-based tool. Moreover, PEATmoss includes 35 expression experiments not previously available in any other expression atlas. To facilitate gene expression queries across different gene annotation versions, and to access P. patens annotations and related resources, a lookup database and web tool linked to PEATmoss was implemented. PEATmoss can be accessed at https://peatmoss.online.uni-marburg.de.

Transcriptome analysis of rice (Oryza sativa L.) in response to ammonium resupply reveals the involvement of phytohormone signaling and the transcription factor OsJAZ9 in reprogramming of nitrogen uptake and metabolism

NH₄⁺ is not only the primary nitrogen for rice, a well-known NH₄⁺ specialist, but is also the chief limiting factor for its production. Limiting NH₄⁺ triggers a series of physiological and biochemical responses that help rice optimise its nitrogen acquisition. However, the dynamic nature and spatial distribution of the adjustments at the whole plant level during this response are still unknown. Here, nitrogen-starved rice seedlings were treated with 0.1 mM (NH₄)₂SO₄ for 4 or 12 h, and then the shoots and roots were harvested for RNA-Seq analysis. We identified 138 and 815 differentially expressed genes (DEGs) in shoots, and 597 and 1074 in roots following 4 and 12 h treatment, respectively. Up-regulated DEGs mainly participated in phenylpropanoid, sugar, and amino acid metabolism, which was confirmed by chemical content analysis. The transcription factor OsJAZ9 was the most pronouncedly induced component under low NH₄⁺ in roots, and a significant increase in root growth, NH₄⁺ absorption, amino acid, and sugar metabolism in response to resupplied NH₄⁺ following nitrogen starvation was identified in JAZ9ox (OsJAZ9-overexpressed) and coi1 (OsCOI1-RNAi). Our data provide comprehensive insight into the whole-plant transcriptomic response in terms of metabolic processes and signaling transduction to a low-NH₄⁺ signal, and identify the transcription factor OsJAZ9 and its involvement in the regulation of carbon/nitrogen metabolism as central to the response to low NH₄⁺.

Transcriptomic Analysis Reveals the Molecular Adaptation of Three Major Secondary Metabolic Pathways to Multiple Macronutrient Starvation in Tea (Camellia sinensis)

Tea (Camellia sinensis (L.) O. Kuntze) is a widely consumed beverage. Lack of macronutrients is a major cause of tea yield and quality losses. Though the effects of macronutrient starvation on tea metabolism have been studied, little is known about their molecular mechanisms. Hence, we investigated changes in the gene expression of tea plants under nitrogen (N), phosphate (P), and potassium (K) deficient conditions by RNA-sequencing. A total of 9103 differentially expressed genes (DEG) were identified. Function enrichment analysis showed that many biological processes and pathways were common to N, P, and K starvation. In particular, cis-element analysis of promoter of genes uncovered that members of the WRKY, MYB, bHLH, NF-Y, NAC, Trihelix, and GATA families were more likely to regulate genes involved in catechins, l-theanine, and caffeine biosynthetic pathways. Our results provide a comprehensive insight into the mechanisms of responses to N, P, and K starvation, and a global basis for the improvement of tea quality and molecular breeding.

Nitrogen Starvation Differentially Influences Transcriptional and Uptake Rate Profiles in Roots of Two Maize Inbred Lines with Different NUE

Nitrogen use efficiency (NUE) of crops is estimated to be less than 50%, with a strong impact on environment and economy. Genotype-dependent ability to cope with N shortage has been only partially explored in maize and, in this context, the comparison of molecular responses of lines with different NUE is of particular interest in order to dissect the key elements underlying NUE. Changes in root transcriptome and NH₄⁺/NO₃^- uptake rates during growth (after 1 and 4 days) without N were studied in high (Lo5) and low (T250) NUE maize inbred lines. Results suggests that only a small set of transcripts were commonly modulated in both lines in response to N starvation. However, in both lines, transcripts linked to anthocyanin biosynthesis and lateral root formation were positively affected. On the contrary, those involved in root elongation were downregulated. The main differences between the two lines reside in the ability to modulate the transcripts involved in the transport, distribution and assimilation of mineral nutrients. With regard to N mineral forms, only the Lo5 line responded to N starvation by increasing the NH₄⁺ fluxes as supported by the upregulation of a transcript putatively involved in its transport.

Unraveling the Genetic Elements Involved in Shoot and Root Growth Regulation by Jasmonate in Rice Using a Genome-Wide Association Study

BACKGROUND

Due to their sessile life style, plant survival is dependent on the ability to build up fast and highly adapted responses to environmental stresses by modulating defense response and organ growth. The phytohormone jasmonate plays an essential role in regulating these plant responses to stress.

RESULTS

To assess variation of plant growth responses and identify genetic determinants associated to JA treatment, we conducted a genome-wide association study (GWAS) using an original panel of Vietnamese rice accessions. The phenotyping results showed a high natural genetic variability of the 155 tested rice accessions in response to JA for shoot and root growth. The level of growth inhibition by JA is different according to the rice varieties tested. We conducted genome-wide association study and identified 28 significant associations for root length (RTL), shoot length (SHL), root weight (RTW), shoot weight (SHW) and total weight (TTW) in response to JA treatment. Three common QTLs were found for RTL, RTW and SHL. Among a list of 560 candidate genes found to co-locate with the QTLs, a transcriptome analysis from public database for the JA response allows us to identify 232 regulated genes including several JA-responsive transcription factors known to play a role in stress response.

CONCLUSION

Our genome-wide association study shows that common and specific genetic elements are associated with inhibition of shoot and root growth under JA treatment suggesting the involvement of a complex JA-dependent genetic control of rice growth inhibition at the whole plant level. Besides, numerous candidate genes associated to stress and JA response are co-located with the association loci, providing useful information for future studies on genetics and breeding to optimize the growth-defense trade-off in rice.

Root Branching and Nutrient Efficiency: Status and Way Forward in Root and Tuber Crops

Plants are immobile organisms that require roots to efficiently and cost-effectively exploit their habitat for water and nutrients. Plant root systems are dynamic structures capable of altering root branching, root angle, and root growth rates determining overall architecture. This plasticity involves belowground plant-root mediated synergies coupled through a continuum of environmental interactions and endogenous developmental processes facilitating plants to adapt to favorable or adverse soil conditions. Plant root branching is paramount to ensure adequate access to soil water and nutrients. Although substantial resources have been devoted toward this goal, significant knowledge gaps exist. In well-studied systems such as rice and maize, it has become evident that root branching plays a significant role in the acquisition of nutrients and other soil-based resources. In these crop species, specific root branching traits that confer enhanced nutrient acquisition are well-characterized and are already being incorporated into breeding populations. In contrast, the understanding of root branching in root and tuber crop productivity has lagged behind. In this review article, we highlight what is known about root branching in root and tuber crops (RTCs) and mark new research directions, such as the use novel phenotyping methods, examining the changes in root morphology and anatomy under nutrient stress, and germplasm screening with enhanced root architecture for more efficient nutrient capture. These directions will permit a better understanding of the interaction between root branching and nutrient acquisition in these globally important crop species.

Transcriptome monitoring visualizes growth stage-dependent nutrient status dynamics in rice under field conditions

Crop plants undergo morpho-physiological changes throughout the growth process in response to both the internal and the external environment, and that eventually determine the yield. The system-level adjustment of the morpho-physiological changes has remained largely unclear, however, especially in field conditions. Here, we reveal changes in nutrient status associated with tiller development and soil conditions based on the leaf transcriptome profile of rice (Oryza sativa) throughout the entire period of growth. We performed gene co-expression network analysis and identified three gene sets as indicators for monitoring the internal nitrogen and phosphorus status. Expression profiling reveals that the phosphorus starvation response is expressed during the tillering stage and is then switched off with the transition to nitrogen deficiency. Coincident with phosphorus status dynamics, the level of phosphate in the leaf is demonstrated to be low during the tillering stage and subsequently increases drastically. The phosphorus dynamics are genetically validated by analysing mutants with a defect in phosphorus homeostasis. Notably, we show that nitrogen limitation directly suppresses the phosphorus starvation response. Finally, the phosphorus starvation response is demonstrated to be activated in soil with a high phosphate retention capacity, without the visible phenotypes associated with phosphorus starvation. Our results reveal a growth stage- and soil condition-dependent reaction that requires phosphorus, which is expressed to promote the phosphorus uptake required for developing tillers and is directly adjusted by nitrogen status. A molecular framework for elucidating nutrient status dynamics under field conditions would provide insights into improving crop productivity.

The controversies of silicon's role in plant biology

Contents Summary 67 I. Introduction 68 II. Silicon transport in plants: to absorb or not to absorb 69 III. The role of silicon in plants: not just a matter of semantics 71 IV. Silicon and biotic stress: beyond mechanical barriers and defense priming 76 V. Silicon and abiotic stress: a proliferation of proposed mechanisms 78 VI. The apoplastic obstruction hypothesis: a working model 79 VII. Perspectives and conclusions 80 Acknowledgements 81 References 81 SUMMARY: Silicon (Si) is not classified as an essential plant nutrient, and yet numerous reports have shown its beneficial effects in a variety of species and environmental circumstances. This has created much confusion in the scientific community with respect to its biological roles. Here, we link molecular and phenotypic data to better classify Si transport, and critically summarize the current state of understanding of the roles of Si in higher plants. We argue that much of the empirical evidence, in particular that derived from recent functional genomics, is at odds with many of the mechanistic assertions surrounding Si's role. In essence, these data do not support reports that Si affects a wide range of molecular-genetic, biochemical and physiological processes. A major reinterpretation of Si's role is therefore needed, which is critical to guide future studies and inform agricultural practice. We propose a working model, which we term the 'apoplastic obstruction hypothesis', which attempts to unify the various observations on Si's beneficial influences on plant growth and yield. This model argues for a fundamental role of Si as an extracellular prophylactic agent against biotic and abiotic stresses (as opposed to an active cellular agent), with important cascading effects on plant form and function.

Interactive effects of Magnaporthe inoculation and nitrogen doses on the plant enzyme machinery and phyllosphere microbiome of resistant and susceptible rice cultivars

Severity of plant diseases is often influenced by the availability of nutrients, particularly N; however, its effect on the phyllosphere microbiome in foliar pathogen challenged plants is less investigated in rice. The tripartite interaction among the fungal pathogen (Magnaporthe oryzae), rice cultivars (basmati and non-basmati, blast resistant or susceptible) and nitrogen (N) fertilization (0, 120 and 180 N) was investigated. Plant growth, elicitation of defense responses and abundance of microbial members in the rice phyllosphere were monitored using biochemical and molecular methods. In general, photosynthetic pigments were distinct for each cultivar, and optimal N doses led to higher values. The susceptible var. CO-39 and resistant CO-39I exhibited higher contents of photosynthetic pigments and micronutrients such as zinc in leaves in response to N doses. Elicitation of defense and hydrolytic enzymes was significantly influenced by pathogen inoculation and modulated by N doses, but varietal effects were distinct. Scoring indices emphasized the pathogen susceptibility of var. CO-39 and PB-1, which showed almost 40-60% higher values than the resistant cultivars; the interactions of cultivars and N doses was also significant. Characteristic changes were recorded in the abundances of the gene copies, particularly, with an overall increase in the number of cyanobacterial 16S rRNA, and bacterial amoA in pathogen-challenged treatments, while nifH gene copies exhibited a reducing trend with increasing N doses, in the presence or absence of pathogen. The varietal differences in the cause and effect relationships can be valuable in crop protection for more effective foliar application of pesticides or biocontrol agents.

Transcriptome Analysis of Two Rice Varieties Contrasting for Nitrogen Use Efficiency under Chronic N Starvation Reveals Differences in Chloroplast and Starch Metabolism-Related Genes

The nitrogen use efficiency (NUE) of crop plants is limited and enhancing it in rice, a major cereal crop, would be beneficial for farmers and the environment alike. Here we report the genome-wide transcriptome analysis of two rice genotypes, IR 64 (IR64) and Nagina 22 (N22) under optimal (N+) and chronic starvation (N−) of nitrogen (N) from 15-day-old root and shoot tissues. The two genotypes were found to be contrasting in their response to N−; IR64 root architecture and root dry weight remained almost equivalent to that under N+ conditions, while N22 showed high foraging ability but a substantial reduction in biomass under N−. Similarly, the photosynthetic pigments showed a drastic reduction in N22 under low N, while IR64 was more resilient. Nitrate reductase showed significantly low specific activity under N− in both genotypes. Glutamate synthase (GOGAT) and citrate synthase CS activity were highly reduced in N22 but not in IR64. Transcriptome analysis of these genotypes revealed nearly double the number of genes to be differentially expressed (DEGs) in roots (1016) compared to shoots (571). The response of the two genotypes to N starvation was distinctly different reflecting their morphological/biochemical response with just two and eight common DEGs in the root and shoot tissues. There were a total of 385 nitrogen-responsive DEGs (106 in shoots and 279 in roots) between the two genotypes. Fifty-two of the 89 DEGs identified as specific to N22 root tissues were also found to be differentially expressed between the two genotypes under N−. Most of these DEGs belonged to starch and chloroplast metabolism, followed by membrane and signaling proteins. Physical mapping of DEGs revealed 95 DEGs in roots and 76 in shoots to be present in quantitative trait loci (QTL) known for NUE.

Transporter genes identified in landraces associated with high zinc in polished rice through panicle transcriptome for biofortification

Polished rice is poor source of micronutrients, however wide genotypic variability exists for zinc uptake and remobilization and zinc content in brown and polished grains in rice. Two landraces (Chittimutyalu and Kala Jeera Joha) and one popular improved variety (BPT 5204) were grown under zinc sufficient soil and their analyses showed high zinc in straw of improved variety, but high zinc in polished rice in landraces suggesting better translocation ability of zinc into the grain in landraces. Transcriptome analyses of the panicle tissue showed 41182 novel transcripts across three samples. Out of 1011 differentially expressed exclusive transcripts by two landraces, 311 were up regulated and 534 were down regulated. Phosphate transporter-exporter (PHO), proton-coupled peptide transporters (POT) and vacuolar iron transporter (VIT) showed enhanced and significant differential expression in landraces. Out of 24 genes subjected to quantitative real time analyses for confirmation, eight genes showed significant differential expression in landraces. Through mapping, six rice microsatellite markers spanning the genomic regions of six differentially expressed genes were validated for their association with zinc in brown and polished rice using recombinant inbred lines (RIL) of BPT 5204/Chittimutyalu. Thus, this study reports repertoire of genes associated with high zinc in polished rice and a proof concept for deployment of transcriptome information for validation in mapping population and its use in marker assisted selection for biofortification of rice with zinc.

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.

Improvement in phosphate acquisition and utilization by a secretory purple acid phosphatase (OsPAP21b) in rice

Phosphate (Pi) deficiency in soil system is a limiting factor for rice growth and yield. Majority of the soil phosphorus (P) is organic in nature, not readily available for root uptake. Low Pi-inducible purple acid phosphatases (PAPs) are hypothesized to enhance the availability of Pi in soil and cellular system. However, information on molecular and physiological roles of rice PAPs is very limited. Here, we demonstrate the role of a novel rice PAP, OsPAP21b in improving plant utilization of organic-P. OsPAP21b was found to be under the transcriptional control of OsPHR2 and strictly regulated by plant Pi status at both transcript and protein levels. Biochemically, OsPAP21b showed hydrolysis of several organophosphates at acidic pH and possessed sufficient thermostability befitting for high-temperature rice ecosystems with acidic soils. Interestingly, OsPAP21b was revealed to be a secretory PAP and encodes a distinguishable major APase (acid phosphatase) isoform under low Pi in roots. Further, OsPAP21b-overexpressing transgenics showed increased biomass, APase activity and P content in both hydroponics supplemented with organic-P sources and soil containing organic manure as sole P source. Additionally, overexpression lines depicted increased root length, biomass and lateral roots under low Pi while RNAi lines showed reduced root length and biomass as compared to WT. In the light of these evidences, present study strongly proposes OsPAP21b as a useful candidate for improving Pi acquisition and utilization in rice.

Transcriptome Analysis of Differentially Expressed Genes Induced by Low and High Potassium Levels Provides Insight into Fruit Sugar Metabolism of Pear

Potassium (K) deficiency is a common abiotic stress that can inhibit the growth of fruit and thus reduce crop yields. Little research has been conducted on pear transcriptional changes under low and high K conditions. Here, we performed an experiment with 7-year-old pot-grown "Huangguan" pear trees treated with low, Control or high K levels (0, 0.4, or 0.8 g·K2O/kg soil, respectively) during fruit enlargement and mature stages. We identified 36,444 transcripts from leaves and fruit using transcriptome sequencing technology. From 105 days after full blooming (DAB) to 129 DAB, the number of differentially expressed genes (DEGs) in leaves and fruit in response to low K increased, while in response to high K, the number of DEGs in leaves and fruit decreased. We selected 17 of these DEGs for qRT-PCR analysis to confirm the RNA sequencing results. Based on GO enrichment and KEGG pathway analysis, we found that low-K treatment significantly reduced K nutrient and carbohydrate metabolism of the leaves and fruit compared with the Control treatment. During the fruit development stages, AKT1 (gene39320) played an important role on K+ transport of the leaves and fruit response to K stress. At maturity, sucrose and acid metabolic pathways were inhibited by low K. The up-regulation of the expression of three SDH and two S6PDH genes involved in sorbitol metabolism was induced by low K, promoting the fructose accumulation. Simultaneously, higher expression was found for genes encoding amylase under low K, promoting the decomposition of the starch and leading the glucose accumulation. High K could enhance leaf photosynthesis, and improve the distribution of the nutrient and carbohydrate from leaf to fruit. Sugar components of the leaves and fruit under low K were regulated by the expression of genes encoding 8 types of hormone signals and reactive oxygen species (ROS). Our data revealed the gene expression patterns of leaves and fruit in response to different K levels during the middle and late stages of fruit development as well as the molecular mechanism of improvement of fruit sugar levels by K and provided a scientific basis for improving fruit quality with supplemental K fertilizers.

Growth Stimulatory Effects and Genome-Wide Transcriptional Changes Produced by Protein Hydrolysates in Maize Seedlings

Protein hydrolysates are an emerging class of crop management products utilized for improving nutrient assimilation and mitigating crop stress. They generally consist of a mixture of peptides and free amino acids derived from the hydrolysis of plant or animal sources. The present work was aimed at studying the effects and the action mechanisms of a protein hydrolysate derived from animal residues on maize root growth and physiology in comparison with the effects induced by either free amino acids or inorganic N supply. The application of the protein hydrolysate caused a remarkable enhancement of root growth. In particular, in the protein hydrolysate-treated plants the length and surface area of lateral roots were about 7 and 1.5 times higher than in plants treated with inorganic N or free amino acids, respectively. The root growth promoting effect of the protein hydrolysate was associated with an increased root accumulation of K, Zn, Cu, and Mn when compared with inorganic N and amino acids treatments. A microarray analysis allowed to dissect the transcriptional changes induced by the different treatments demonstrating treatment-specific effects principally on cell wall organization, transport processes, stress responses and hormone metabolism.

Transcriptomic Analysis of Soil Grown T. aestivum cv. Root to Reveal the Changes in Expression of Genes in Response to Multiple Nutrients Deficiency

Deficiency of necessary macronutrients, i.e., Potassium (K), Magnesium (Mg), Nitrogen (N), Phosphorus (P), and Sulfate (S) in the soil leads to a reduction in plant growth and yield, which is a result of changes in expression level of various genes. This study was performed to identify the differentially expressed genes and its associated metabolic pathways occurred in soil grown wheat root samples excavated from the control and treated fields. To identify the difference in gene expression levels due to deficiency of the said nutrients, a transcriptomic, meta-analysis was performed on array expression profile data. A set of 435 statistically significant probes encoding 398 Nutrient Deficiency Response Genes (NRGs) responding at-least one nutrients deficiency (ND) were identified. Out of them 55 NRGs were found to response to minimum two ND. Singular Enrichment Analysis (SEA) predicts ontological based classifications and functional analysis of NRGs in different cellular/molecular pathways involved in root development and growth. Functional annotation and reaction mechanism of differentially expressed genes, proteins/enzymes in the different metabolic pathway through MapMan analysis were explored. Further the meta-analysis was performed to revels the active involvement each NRGs in distinct tissues and their comparative potential expression analysis in different stress conditions. The study results in exploring the role of major acting candidate genes such as Non-specific serine/threonine protein kinase, Xyloglucan endotransglucosylase/hydrolase, Peroxides, Glycerophosphoryl diester phosphodiesterase, S-adenosylmethionine decarboxylase proenzyme, Dehydrin family proteins, Transcription factors, Membrane Proteins, Metal binding proteins, Photosystem proteins, Transporter and Transferase associated in different metabolic pathways. Finally, the differences of transcriptional responses in the soil-grown root of T. aestivum cv. and in-vitro grown model plants under nutrients deficiency were summarized.

Understanding Plant Nitrogen Metabolism through Metabolomics and Computational Approaches

A comprehensive understanding of plant metabolism could provide a direct mechanism for improving nitrogen use efficiency (NUE) in crops. One of the major barriers to achieving this outcome is our poor understanding of the complex metabolic networks, physiological factors, and signaling mechanisms that affect NUE in agricultural settings. However, an exciting collection of computational and experimental approaches has begun to elucidate whole-plant nitrogen usage and provides an avenue for connecting nitrogen-related phenotypes to genes. Herein, we describe how metabolomics, computational models of metabolism, and flux balance analysis have been harnessed to advance our understanding of plant nitrogen metabolism. We introduce a model describing the complex flow of nitrogen through crops in a real-world agricultural setting and describe how experimental metabolomics data, such as isotope labeling rates and analyses of nutrient uptake, can be used to refine these models. In summary, the metabolomics/computational approach offers an exciting mechanism for understanding NUE that may ultimately lead to more effective crop management and engineered plants with higher yields.

Genome-wide transcriptome analysis of expression in rice seedling roots in response to supplemental nitrogen

Nitrogen (N) is the most important macronutrient for plant growth and grain yields. For rice crops, nitrate and ammonium are the major N sources. To explore the genomic responses to ammonium supplements in rice roots, we used 17-day-old seedlings grown in the absence of external N that were then exposed to 0.5mM (NH4)2SO4 for 3h. Transcriptomic profiles were examined by microarray experiments. In all, 634 genes were up-regulated at least two-fold by the N-supplement when compared with expression in roots from untreated control plants. Gene Ontology (GO) enrichment analysis revealed that those upregulated genes are associated with 23 GO terms. Among them, metabolic processes for diverse amino acids (i.e., aspartate, threonine, tryptophan, glutamine, l-phenylalanine, and thiamin) as well as nitrogen compounds are highly over-represented, demonstrating that our selected genes are suitable for studying the N-response in roots. This enrichment analysis also indicated that nitrogen is closely linked to diverse transporter activities by primary metabolites, including proteins (amino acids), lipids, and carbohydrates, and is associated with carbohydrate catabolism and cell wall organization. Integration of results from omics analysis of metabolic pathways and transcriptome data using the MapMan tool suggested that the TCA cycle and pathway for mitochondrial electron transport are co-regulated when rice roots are exposed to ammonium. We also investigated the expression of N-responsive marker genes by performing a comparative analysis with root samples from plants grown under different NH4(+) treatments. The diverse responses to such treatment provide useful insight into the global changes related to the shift from an N-deficiency to an enhanced N-supply in rice, a model crop plant.

OsCHX14 is Involved in the K+ Homeostasis in Rice (Oryza sativa) Flowers

Previously we showed in the osjar1 mutants that the lodicule senescence which controls the closing of rice flowers was delayed. This resulted in florets staying open longer when compared with the wild type. The gene OsJAR1 is silenced in osjar1 mutants and is a key member of the jasmonic acid (JA) signaling pathway. We found that K concentrations in lodicules and flowers of osjar1-2 were significantly elevated compared with the wild type, indicating that K⁺ homeostasis may play a role in regulating the closure of rice flowers. The cation/H⁺ exchanger (CHX) family from rice was screened for potential K⁺ transporters involved as many members of this family in Arabidopsis were exclusively or preferentially expressed in flowers. Expression profiling confirmed that among 17 CHX genes in rice, OsCHX14 was the only member that showed an expression polymorphism, not only in osjar1 mutants but also in RNAi (RNA interference) lines of OsCOI1, another key member of the JA signaling pathway. This suggests that the expression of OsCHX14 is regulated by the JA signaling pathway. Green fluorescent protein (GFP)-tagged OsCHX14 protein was preferentially localized to the endoplasmic reticulum. Promoter-β-glucuronidase (GUS) analysis of transgenic rice revealed that OsCHX14 is mainly expressed in lodicules and the region close by throughout the flowering process. Characterization in yeast and Xenopus laevis oocytes verified that OsCHX14 is able to transport K⁺, Rb⁺ and Cs⁺ in vivo. Our data suggest that OsCHX14 may play an important role in K⁺ homeostasis during flowering in rice.

Jasmonate signaling is activated in the very early stages of iron deficiency responses in rice roots

Under low iron availability, plants induce the expression of various genes involved in iron uptake and translocation at the transcriptional level. This iron deficiency response is affected by various plant hormones, but the roles of jasmonates in this response are not well-known. We investigated the involvement of jasmonates in rice iron deficiency responses. High rates of jasmonate-inducible genes were induced during the very early stages of iron deficiency treatment in rice roots. Many jasmonate-inducible genes were also negatively regulated by the ubiquitin ligases OsHRZ1 and OsHRZ2 and positively regulated by the transcription factor IDEF1. Ten out of 35 genes involved in jasmonate biosynthesis and signaling were rapidly induced at 3 h of iron deficiency treatment, and this induction preceded that of known iron deficiency-inducible genes involved in iron uptake and translocation. Twelve genes involved in jasmonate biosynthesis and signaling were also upregulated in HRZ-knockdown roots. Endogenous concentrations of jasmonic acid and jasmonoyl isoleucine tended to be rapidly increased in roots in response to iron deficiency treatment, whereas these concentrations were higher in HRZ-knockdown roots under iron-sufficient conditions. Analysis of the jasmonate-deficient cpm2 mutant revealed that jasmonates repress the expression of many iron deficiency-inducible genes involved in iron uptake and translocation under iron sufficiency, but this repression is partly canceled under an early stage of iron deficiency. These results indicate that jasmonate signaling is activated during the very early stages of iron deficiency, which is partly regulated by IDEF1 and OsHRZs.

Comparative RNA-Seq Analysis Reveals That Regulatory Network of Maize Root Development Controls the Expression of Genes in Response to N Stress

Nitrogen (N) is an essential nutrient for plants, and it directly affects grain yield and protein content in cereal crops. Plant root systems are not only critical for anchorage in the soil, but also for N acquisition. Therefore, genes controlling root development might also affect N uptake by plants. In this study, the responses of nitrogen on root architecture of mutant rtcs and wild-type of maize were investigated by morphological and physiological analysis. Subsequently, we performed a comparative RNA-Seq analysis to compare gene expression profiles between mutant rtcs roots and wild-type roots under different N conditions. We identified 786 co-modulated differentially expressed genes (DEGs) related to root development. These genes participated in various metabolic processes. A co-expression cluster analysis and a cis-regulatory motifs analysis revealed the importance of the AP2-EREBP transcription factor family in the rtcs-dependent regulatory network. Some genotype-specific DEGs contained at least one LBD motif in their promoter region. Further analyses of the differences in gene transcript levels between rtcs and wild-type under different N conditions revealed 403 co-modulated DEGs with distinct functions. A comparative analysis revealed that the regulatory network controlling root development also controlled gene expression in response to N-deficiency. Several AP2-EREBP family members involved in multiple hormone signaling pathways were among the DEGs. These transcription factors might play important roles in the rtcs-dependent regulatory network related to root development and the N-deficiency response. Genes encoding the nitrate transporters NRT2-1, NAR2.1, NAR2.2, and NAR2.3 showed much higher transcript levels in rtcs than in wild-type under normal-N conditions. This result indicated that the LBD gene family mainly functions as transcriptional repressors, as noted in other studies. In summary, using a comparative RNA-Seq-based approach, we identified DEGs related to root development that also participated in the N-deficiency response in maize. These findings will increase our understanding of the molecular regulatory networks controlling root development and N-stress responses.

Comparison between Arabidopsis and Rice for Main Pathways of K(+) and Na(+) Uptake by Roots

K(+) is an essential macronutrient for plants. It is acquired by specific uptake systems located in roots. Although the concentrations of K(+) in the soil solution are widely variable, K(+) nutrition is secured by uptake systems that exhibit different affinities for K(+). Two main systems have been described for root K(+) uptake in several species: the high-affinity HAK5-like transporter and the inward-rectifier AKT1-like channel. Other unidentified systems may be also involved in root K(+) uptake, although they only seem to operate when K(+) is not limiting. The use of knock-out lines has allowed demonstrating their role in root K(+) uptake in Arabidopsis and rice. Plant adaptation to the different K(+) supplies relies on the finely tuned regulation of these systems. Low K(+)-induced transcriptional up-regulation of the genes encoding HAK5-like transporters occurs through a signal cascade that includes changes in the membrane potential of root cells and increases in ethylene and reactive oxygen species concentrations. Activation of AKT1 channels occurs through phosphorylation by the CIPK23/CBL1 complex. Recently, activation of the Arabidopsis HAK5 by the same complex has been reported, pointing to CIPK23/CBL as a central regulator of the plant's adaptation to low K(+). Na(+) is not an essential plant nutrient but it may be beneficial for some plants. At low concentrations, Na(+) improves growth, especially under K(+) deficiency. Thus, high-affinity Na(+) uptake systems have been described that belong to the HKT and HAK families of transporters. At high concentrations, typical of saline environments, Na(+) accumulates in plant tissues at high concentrations, producing alterations that include toxicity, water deficit and K(+) deficiency. Data concerning pathways for Na(+) uptake into roots under saline conditions are still scarce, although several possibilities have been proposed. The apoplast is a significant pathway for Na(+) uptake in rice grown under salinity conditions, but in other plant species different mechanisms involving non-selective cation channels or transporters are under discussion.

Microarray: gateway to unravel the mystery of abiotic stresses in plants

Environmental factors, such as drought, salinity, extreme temperature, ozone poisoning, metal toxicity etc., significantly affect crops. To study these factors and to design a possible remedy, biological experimental data concerning these crops requires the quantification of gene expression and comparative analyses at high throughput level. Development of microarrays is the platform to study the differential expression profiling of the targeted genes. This technology can be applied to gene expression studies, ranging from individual genes to whole genome level. It is now possible to perform the quantification of the differential expression of genes on a glass slide in a single experiment. This review documents recently published reports on the use of microarrays for the identification of genes in different plant species playing their role in different cellular networks under abiotic stresses. The regulation pattern of differentially-expressed genes, individually or in group form, may help us to study different pathways and functions at the cellular and molecular level. These studies can provide us with a lot of useful information to unravel the mystery of abiotic stresses in important crop plants.

Coexpression Network Analysis of Macronutrient Deficiency Response Genes in Rice

BACKGROUND

Macronutrients are pivotal elements for proper plant growth and development. Although extensive gene expression profiling revealed a large number of genes differentially expressed under various nutrient deprivation, characterization of these genes has never been fully explored especially in rice. Coexpression network analysis is a useful tool to elucidate the functional relationships of genes based on common expression. Therefore, we performed microarray analysis of rice shoot under nitrogen (N), phosphorus (P), and potassium (K) deficiency conditions. Moreover, we conducted a large scale coexpression analysis by integrating the data with previously generated gene expression profiles of organs and tissues at different developmental stages to obtain a global view of gene networks associated with plant response to nutrient deficiency.

RESULTS

We statistically identified 5400 differentially expressed genes under the nutrient deficiency treatments. Subsequent coexpression analysis resulted in the extraction of 6 modules (groups of highly interconnected genes) with distinct gene expression signatures. Three of these modules comprise mostly of downregulated genes under N deficiency associated with distinct functions such as development of immature organs, protein biosynthesis and photosynthesis in chloroplast of green tissues, and fundamental cellular processes in all organs and tissues. Furthermore, we identified one module containing upregulated genes under N and K deficiency conditions, and a number of genes encoding protein kinase, kinase-like domain containing protein and nutrient transporters. This module might be particularly involved in adaptation to nutrient deficiency via phosphorylation-mediated signal transduction and/or post-transcriptional regulation.

CONCLUSIONS

Our study demonstrated that large scale coexpression analysis is an efficient approach in characterizing the nutrient response genes based on biological functions and could provide new insights in understanding plant response to nutrient deficiency.

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.

JAZ Repressors: Potential Involvement in Nutrients Deficiency Response in Rice and Chickpea

Jasmonates (JA) are well-known phytohormones which play important roles in plant development and defense against pathogens. Jasmonate ZIM domain (JAZ) proteins are plant-specific proteins and act as transcriptional repressors of JA-responsive genes. JA regulates both biotic and abiotic stress responses in plants; however, its role in nutrient deficiency responses is very elusive. Although, JA is well-known for root growth inhibition, little is known about behavior of JAZ genes in response to nutrient deficiencies, under which root architectural alteration is an important adaptation. Using protein sequence homology and a conserved-domains approach, here we identify 10 novel JAZ genes from the recently sequenced Chickpea genome, which is one of the most nutrient efficient crops. Both rice and chickpea JAZ genes express in tissue- and stimuli-specific manners. Many of which are preferentially expressed in root. Our analysis further showed differential expression of JAZ genes under macro (NPK) and micronutrients (Zn, Fe) deficiency in rice and chickpea roots. While both rice and chickpea JAZ genes showed a certain level of specificity toward type of nutrient deficiency, generally majority of them showed induction under K deficiency. Generally, JAZ genes showed an induction at early stages of stress and expression declined at later stages of macro-nutrient deficiency. Our results suggest that JAZ genes might play a role in early nutrient deficiency response both in monocot and dicot roots, and information generated here can be further used for understanding the possible roles of JA in root architectural alterations for nutrient deficiency adaptations.

Role of ethylene in responses of plants to nitrogen availability

Ethylene is a plant hormone involved in several physiological processes and regulates the plant development during the whole life. Stressful conditions usually activate ethylene biosynthesis and signaling in plants. The availability of nutrients, shortage or excess, influences plant metabolism and ethylene plays an important role in plant adaptation under suboptimal conditions. Among the plant nutrients, the nitrogen (N) is one the most important mineral element required for plant growth and development. The availability of N significantly influences plant metabolism, including ethylene biology. The interaction between ethylene and N affects several physiological processes such as leaf gas exchanges, roots architecture, leaf, fruits, and flowers development. Low plant N use efficiency (NUE) leads to N loss and N deprivation, which affect ethylene biosynthesis and tissues sensitivity, inducing cell damage and ultimately lysis. Plants may respond differently to N availability balancing ethylene production through its signaling network. This review discusses the recent advances in the interaction between N availability and ethylene at whole plant and different organ levels, and explores how N availability induces ethylene biology and plant responses. Exogenously applied ethylene seems to cope the stress conditions and improves plant physiological performance. This can be explained considering the expression of ethylene biosynthesis and signaling genes under different N availability. A greater understanding of the regulation of N by means of ethylene modulation may help to increase NUE and directly influence crop productivity under conditions of limited N availability, leading to positive effects on the environment. Moreover, efforts should be focused on the effect of N deficiency or excess in fruit trees, where ethylene can have detrimental effects especially during postharvest.

Metabolic and co-expression network-based analyses associated with nitrate response in rice

BACKGROUND

Understanding gene expression and metabolic re-programming that occur in response to limiting nitrogen (N) conditions in crop plants is crucial for the ongoing progress towards the development of varieties with improved nitrogen use efficiency (NUE). To unravel new details on the molecular and metabolic responses to N availability in a major food crop, we conducted analyses on a weighted gene co-expression network and metabolic profile data obtained from leaves and roots of rice plants adapted to sufficient and limiting N as well as after shifting them to limiting (reduction) and sufficient (induction) N conditions.

RESULTS

A gene co-expression network representing clusters of rice genes with similar expression patterns across four nitrogen conditions and two tissue types was generated. The resulting 18 clusters were analyzed for enrichment of significant gene ontology (GO) terms. Four clusters exhibited significant correlation with limiting and reducing nitrate treatments. Among the identified enriched GO terms, those related to nucleoside/nucleotide, purine and ATP binding, defense response, sugar/carbohydrate binding, protein kinase activities, cell-death and cell wall enzymatic activity are enriched. Although a subset of functional categories are more broadly associated with the response of rice organs to limiting N and N reduction, our analyses suggest that N reduction elicits a response distinguishable from that to adaptation to limiting N, particularly in leaves. This observation is further supported by metabolic profiling which shows that several compounds in leaves change proportionally to the nitrate level (i.e. higher in sufficient N vs. limiting N) and respond with even higher levels when the nitrate level is reduced. Notably, these compounds are directly involved in N assimilation, transport, and storage (glutamine, asparagine, glutamate and allantoin) and extend to most amino acids. Based on these data, we hypothesize that plants respond by rapidly mobilizing stored vacuolar nitrate when N deficit is perceived, and that the response likely involves phosphorylation signal cascades and transcriptional regulation.

CONCLUSIONS

The co-expression network analysis and metabolic profiling performed in rice pinpoint the relevance of signal transduction components and regulation of N mobilization in response to limiting N conditions and deepen our understanding of N responses and N use in crops.

A low K+ signal is required for functional high-affinity K+ uptake through HAK5 transporters

The high-affinity K(+) transporter HAK5 is a key system for root K(+) uptake and, under very low external K(+), the only one capable of supplying K(+) to the plant. Functional HAK5-mediated K(+) uptake should be tightly regulated for plant adaptation to different environmental conditions. Thus, it has been described that the gene encoding the transporter is transcriptionally regulated, being highly induced under K(+) limitation. Here we show that environmental conditions, such as the lack of K(+), NO(3)(-) or P, that induced a hyperpolarization of the plasma membrane of root cells, induce HAK5 transcription. However, only the deprivation of K(+) produces functional HAK5-mediated K(+) uptake in the root. These results suggest on the one hand the existence of a posttranscriptional regulation of HAK5 elicited by the low K(+) signal and on the other that HAK5 may be involved in yet-unknown functions related to NO(3)(-) and P deficiencies. These results have been obtained here with Solanum lycopersicum (cv. Micro-Tom) as well as Arabidopsis thaliana plants, suggesting that the posttranscriptional regulation of high-affinity HAK transporters take place in all plant species.

The effects of fluctuations in the nutrient supply on the expression of five members of the AGL17 clade of MADS-box genes in rice

The ANR1 MADS-box gene in Arabidopsis is a key gene involved in regulating lateral root development in response to the external nitrate supply. There are five ANR1-like genes in Oryza sativa, OsMADS23, OsMADS25, OsMADS27, OsMADS57 and OsMADS61, all of which belong to the AGL17 clade. Here we have investigated the responsiveness of these genes to fluctuations in nitrogen (N), phosphorus (P) and sulfur (S) mineral nutrient supply. The MADS-box genes have been shown to have a range of responses to the nutrient supply. The expression of OsMADS61 was transiently induced by N deprivation but was not affected by re-supply with various N sources. The expression of OsMADS25 and OsMADS27 was induced by re-supplying with NO3(-) and NH4NO3, but downregulated by NH4(+). The expression of OsMADS57 was significantly downregulated by N starvation and upregulated by 3 h NO3(-) re-supply. OsMADS23 was the only gene that showed no response to either N starvation nor NO3(-) re-supply. OsMADS57 was the only gene not regulated by P fluctuation whereas the expression of OsMADS23, OsMADS25 and OsMADS27 was downregulated by P starvation and P re-supply. In contrast, all five ANR1-related genes were significantly upregulated by S starvation. Our results also indicated that there were interactions among nitrate, sulphate and phosphate transporters in rice.

Virus-induced gene silencing is a versatile tool for unraveling the functional relevance of multiple abiotic-stress-responsive genes in crop plants

Virus-induced gene silencing (VIGS) is an effective tool for gene function analysis in plants. Over the last decade, VIGS has been successfully used as both a forward and reverse genetics technique for gene function analysis in various model plants, as well as crop plants. With the increased identification of differentially expressed genes under various abiotic stresses through high-throughput transcript profiling, the application of VIGS is expected to be important in the future for functional characterization of a large number of genes. In the recent past, VIGS was proven to be an elegant tool for functional characterization of genes associated with abiotic stress responses. In this review, we provide an overview of how VIGS is used in different crop species to characterize genes associated with drought-, salt-, oxidative- and nutrient-deficiency-stresses. We describe the examples from studies where abiotic stress related genes are characterized using VIGS. In addition, we describe the major advantages of VIGS over other currently available functional genomics tools. We also summarize the recent improvements, limitations and future prospects of using VIGS as a tool for studying plant responses to abiotic stresses.

Molecular mechanisms involved in plant adaptation to low K(+) availability

Potassium is a major inorganic constituent of the living cell and the most abundant cation in the cytosol. It plays a role in various functions at the cell level, such as electrical neutralization of anionic charges, protein synthesis, long- and short-term control of membrane polarization, and regulation of the osmotic potential. Through the latter function, K(+) is involved at the whole-plant level in osmotically driven functions such as cell movements, regulation of stomatal aperture, or phloem transport. Thus, plant growth and development require that large amounts of K(+) are taken up from the soil and translocated to the various organs. In most ecosystems, however, soil K(+) availability is low and fluctuating, so plants have developed strategies to take up K(+) more efficiently and preserve vital functions and growth when K(+) availability is becoming limited. These strategies include increased capacity for high-affinity K(+) uptake from the soil, K(+) redistribution between the cytosolic and vacuolar pools, ensuring cytosolic homeostasis, and modification of root system development and architecture. Our knowledge about the mechanisms and signalling cascades involved in these different adaptive responses has been rapidly growing during the last decade, revealing a highly complex network of interacting processes. This review is focused on the different physiological responses induced by K(+) deprivation, their underlying molecular events, and the present knowledge and hypotheses regarding the mechanisms responsible for K(+) sensing and signalling.