Differential expression profiles and pathways of genes in sugarcane leaf at elongation stage in response to drought stress

Transgenic sugarcane overexpressing Glyoxalase III improved germination and biomass production at formative stage under salinity and water-deficit stress conditions

The glyoxalase system, involving Glyoxalase I (GlyI) and Glyoxalase II (Gly II), plays a vital role in abiotic stress tolerance in plants. A novel enzyme Glyoxalase III (Gly III) was found recently from bacteria, yeast, and plant species. This enzyme provides a new way to detoxify Methylglyoxal (MG), a cytotoxic α-oxoaldehyde, which, in excess, can cause complete cell destruction by forming Reactive Oxygen Species (ROS) and Advanced Glycation End products (AGEs) or DNA/RNA mutation. In this background, the current study examined sugarcane transgenic events that exhibit an increase in expression of EaGly III, to assess their performance in terms of germination and biomass production during formative stage under stress conditions. Southern blot analysis outcomes confirmed the integration of transgene in the transgenic plants. The results from quantitative RT-PCR analyses confirmed high expression levels of EaGly III in transgenic events compared to wild type (WT) under salinity (100 and 200 mM NaCl) and drought (withholding watering) conditions. Transgenic events exhibited enhanced biomass productivity ranged between 0.141 Kg/pot and 0.395 Kg/pot under 200 mM salinity and 0.262 Kg/pot and 0.666 Kg/pot under drought stress. Further, transgenic events observed significantly higher germination rates under salinity and drought conditions compared to that of WT. Subcellular localization prediction by EaGlyIII-GFP fusion expression in sugarcane callus showed that it is distributed across the cytoplasm, thus indicating its widespread activity within the cell. These results strongly suggest that enhancing EaGly III activity is a useful strategy to improve the salinity and drought-tolerance in sugarcane as well as other crops.

A Large-Scale Candidate-Gene Association Mapping for Drought Tolerance and Agronomic Traits in Sugarcane

Dissection of the genetic loci controlling drought tolerance traits with a complex genetic inheritance is important for drought-tolerant sugarcane improvement. In this study, we conducted a large-scale candidate gene association study of 649 candidate genes in a sugarcane diversity panel to identify genetic variants underlying agronomic traits and drought tolerance indices evaluated in plant cane and ratoon cane under water-stressed (WS) and non-stressed (NS) environments. We identified 197 significant marker-trait associations (MTAs) in 141 candidate genes associated with 18 evaluated traits with the Bonferroni correction threshold (α = 0.05). Out of the total, 95 MTAs in 78 candidate genes and 62 MTAs in 58 candidate genes were detected under NS and WS conditions, respectively. Most MTAs were found only in specific water regimes and crop seasons. These MTAs explained 7.93-30.52% of phenotypic variation. Association mapping results revealed that 34, 59, and 104 MTAs involved physiological and molecular adaptation, phytohormone metabolism, and drought-inducible genes. They identified 19 pleiotropic genes associated with more than one trait and many genes related to drought tolerance indices. The genetic and genomic resources identified in this study will enable the combining of yield-related traits and sugar-related traits with agronomic value to optimize the yield of sugarcane cultivars grown under drought-stressed and non-stressed environments.

Drought and salinity stresses induced physio-biochemical changes in sugarcane: an overview of tolerance mechanism and mitigating approaches

Sugarcane productivity is being hampered globally under changing environmental scenarios like drought and salinity. The highly complex nature of the plant responses against these stresses is determined by a variety of factors such as genotype, developmental phase of the plant, progression rate and stress, intensity, and duration. These factors influence plant responses and can determine whether mitigation approaches associated with acclimation are implemented. In this review, we attempt to summarize the effects of drought and salinity on sugarcane growth, specifically on the plant's responses at various levels, viz., physiological, biochemical, and metabolic responses, to these stresses. Furthermore, mitigation strategies for dealing with these stresses have been discussed. Despite sugarcane's complex genomes, conventional breeding approaches can be utilized in conjunction with molecular breeding and omics technologies to develop drought- and salinity-tolerant cultivars. The significant role of plant growth-promoting bacteria in sustaining sugarcane productivity under drought and salinity cannot be overlooked.

Transcriptomic and Proteomic Landscape of Sugarcane Response to Biotic and Abiotic Stressors

Sugarcane, a C₄ plant, provides most of the world's sugar, and a substantial amount of renewable bioenergy, due to its unique sugar-accumulating and feedstock properties. Brazil, India, China, and Thailand are the four largest sugarcane producers worldwide, and the crop has the potential to be grown in arid and semi-arid regions if its stress tolerance can be improved. Modern sugarcane cultivars which exhibit a greater extent of polyploidy and agronomically important traits, such as high sugar concentration, biomass production, and stress tolerance, are regulated by complex mechanisms. Molecular techniques have revolutionized our understanding of the interactions between genes, proteins, and metabolites, and have aided in the identification of the key regulators of diverse traits. This review discusses various molecular techniques for dissecting the mechanisms underlying the sugarcane response to biotic and abiotic stresses. The comprehensive characterization of sugarcane's response to various stresses will provide targets and resources for sugarcane crop improvement.

Transcriptome analysis reveals the molecular mechanisms of adaptation to high temperatures in Gracilaria bailinae

Global warming causes great thermal stress to macroalgae and those species that can adapt to it are thought to be better able to cope with warmer oceans. Gracilaria bailinae, a macroalgae with high economic and ecological values, can survive through the hot summer in the South China Sea, but the molecular mechanisms underlying its adaptation to high temperatures are unclear. To address this issue, the present study analyzed the growth and transcriptome of G. bailinae after a 7-day exposure to 15°C (LT: low temperature), 25°C (MT: middle temperature), and 35°C (HT: high temperature). Growth analysis showed that the HT group had the highest relative growth rate (RGR = 2.1%) with the maximum photochemical quantum yield of PSII (F _v/F _m = 0.62) remaining within the normal range. Transcriptome analysis showed more differentially expressed genes (DEGs) in the comparison between MT and HT groups than in that between MT and LT, and most of these DEGs tended to be downregulated at higher temperatures. The KEGG pathway enrichment analysis showed that the DEGs were mainly enriched in the carbohydrate, energy, and lipid metabolisms. In addition, the genes involved in NADPH and ATP synthesis, which are associated with photosynthesis, the Calvin cycle, pyruvate metabolism, and the citrate cycle, were downregulated. Downregulation was also observed in genes that encode enzymes involved in fatty acid desaturation and alpha-linolenic acid metabolism. In summary, G. bailinae regulated the synthesis of NADPH and ATP, which are involved in the above-mentioned processes, to reduce unnecessary energy consumption, and limited the synthesis of enzymes in the metabolism of unsaturated fatty acids and alpha-linolenic acid to adapt to high environmental temperatures. The results of this study improve our understanding of the molecular mechanisms underlying the adaptation of G. bailinae to high temperatures.

Field evaluation of TaDREB2B-ectopic expression sugarcane (Saccharum spp. hybrid) for drought tolerance

Sugarcane is one of the most crucial sugar crops globally that supplies the main raw material for sugar and ethanol production, but drought stress causes a severe decline in sugarcane yield worldwide. Enhancing sugarcane drought resistance and reducing yield and quality losses is an ongoing challenge in sugarcane genetic improvement. Here, we introduced a Tripidium arundinaceum dehydration-responsive element-binding transcription factor (TaDREB2B) behind the drought-responsible RD29A promoter into a commercial sugarcane cultivar FN95-1702 and subsequently conducted a series of drought tolerance experiments and investigation of agronomic and quality traits. Physiological analysis indicated that Prd29A: TaDREB2B transgenic sugarcane significantly confers drought tolerance in both the greenhouses and the field by enhancing water retention capacity and reducing membrane damage without compromising growth. These transgenic plants exhibit obvious improvements in yield performance and various physiological traits under the limited-irrigation condition in the field, such as increasing 41.9% yield and 44.4% the number of ratooning sugarcane seedlings. Moreover, Prd29A: TaDREB2B transgenic plants do not penalize major quality traits, including sucrose content, gravity purity, Brix, etc. Collectively, our results demonstrated that the Prd29A-TaDREB2B promoter-transgene combination will be a useful biotechnological tool for the increase of drought tolerance and the minimum of yield losses in sugarcane.

A short review on sugarcane: its domestication, molecular manipulations and future perspectives

Sugarcane (Saccharum spp.) is a special crop plant that underwent anthropogenic evolution from a wild grass species to an important food, fodder, and energy crop. Unlike any other grass species which were selected for their kernels, sugarcane was selected for its high stem sucrose accumulation. Flowering in sugarcane is not favored since flowering diverts the stored sugar resources for the reproductive and developmental energy needs. Cultivars are vegetatively propagated and sugarcane breeding is still essentially focused on conventional methods, since the knowledge of sugarcane genetics has lagged that of other major crops. Cultivar improvement has been extremely challenging due to its polyploidy and aneuploidy nature derived from a few interspecific hybridizations between Saccharum officinarum and Saccharum spontaneum, revealing the coexistence of two distinct genome organization modes in the modern variety. Alongside implementation of modern agricultural techniques, generation of hybrid clones, transgenics and genome edited events will help to meet the ever-growing bioenergy needs. Additionally, there are two common biotechnological approaches to improve plant stress tolerance, which includes marker-assisted selection (MAS) and genetic transformation. During the past two decades, the use of molecular approaches has contributed greatly to a better understanding of the genetic and biochemical basis of plant stress-tolerance and in some cases, it led to the development of plants with enhanced tolerance to abiotic stress. Hence, this review mainly intends on the events that shaped the sugarcane as what it is now and what challenges ahead and measures taken to further improve its yield, production and maximize utilization to beat the growing demands.

Leaf transcriptome profiling of contrasting sugarcane genotypes for drought tolerance under field conditions

Drought is the most detrimental abiotic stress to sugarcane production. Nevertheless, transcriptomic analyses remain scarce for field-grown plants. Here we performed comparative transcriptional profiling of two contrasting sugarcane genotypes, ‘IACSP97-7065’ (drought-sensitive) and ‘IACSP94-2094’ (drought-tolerant) grown in a drought-prone environment. Physiological parameters and expression profiles were analyzed at 42 (May) and 117 (August) days after the last rainfall. The first sampling was done under mild drought (soil water potential of −60 kPa), while the second one was under severe drought (soil water potential of −75 kPa). Microarray analysis revealed a total of 622 differentially expressed genes in both sugarcane genotypes under mild and severe drought stress, uncovering about 250 exclusive transcripts to ‘IACSP94-2094’ involved in oxidoreductase activity, transcriptional regulation, metabolism of amino acids, and translation. Interestingly, the enhanced antioxidant system of ‘IACSP94-2094’ may protect photosystem II from oxidative damage, which partially ensures stable photochemical activity even after 117 days of water shortage. Moreover, the tolerant genotype shows a more extensive set of responsive transcription factors, promoting the fine-tuning of drought-related molecular pathways. These results help elucidate the intrinsic molecular mechanisms of a drought-tolerant sugarcane genotype to cope with ever-changing environments, including prolonged water deficit, and may be useful for plant breeding programs.

Transcriptome Analysis Reveals a Gene Expression Pattern That Contributes to Sugarcane Bud Propagation Induced by Indole-3-Butyric Acid

Sugarcane is a cash crop that plays an integral part in the sugar industry. The Sustainable Sugarcane Initiative (SSI) has been adopted globally, ensuring enough and aiming for more yield, helping increase disease-free sugarcane cultivation. Single-bud seeds could be the best approach for sugarcane cultivation. Indole-3-butyric acid (IBA) is a rooting agent utilized significantly in seedling propagation. Greenhouse experiment results discovered the significant growth promotion in sugarcane seedlings and accumulation of plant hormones at 100 ppm IBA. Next, we performed transcriptomic analysis of sugarcane buds using RNA sequencing and compared their gene expression during root development due to affect of IBA (100 ppm). A total of 113,475 unigenes were annotated with an average length of 836 bp (N50 = 1,536). The comparative RNA-seq study between the control (CK) and IBA-treated (T) buds showed significant differentially expressed unigenes (494 upregulated and 2086 downregulated). The IBA influenced major biological processes including metabolic process, the cellular process, and single-organism process. For cellular component category, cell, cell part, organelle, membrane, and organelle part were mainly affected. In addition, catalytic activity and binding were primarily affected in the molecular function categories. Furthermore, the expression of genes related to plant hormones and signaling pathways was analyzed by qRT-PCR, which was consistent with the RNA-seq expression profile. This study provides new insights into the IBA response to the bud sprouting in sugarcane based on RNA sequencing, and generated information could help further research on breeding improvement of sugarcane.

Inferring the genetic responses to acute drought stress across an ecological gradient

BACKGROUND

How do xerophytic species thrive in environments that experience extreme annual drought? Although critical to the survival of many species, the genetic responses to drought stress in many non-model organisms has yet to be explored. We investigated this question in Mentzelia section Bartonia (Loasaceae), which occurs throughout western North America, including arid lands. To better understand the genetic responses to drought stress among species that occur in different habitats, the gene expression levels of three species from Mentzelia were compared across a precipitation gradient. Two de novo reference transcriptomes were generated and annotated. Leaf and root tissues were collected from control and drought shocked plants and compared to one another for differential expression. A target-gene approach was also implemented to better understand how drought-related genes from model and crop species function in non-model systems.

RESULTS

When comparing the drought-shock treatment plants to their respective control plants, we identified 165 differentially expressed clusters across all three species. Differentially expressed genes including those associated with water movement, photosynthesis, and delayed senescence. The transcriptome profiling approach was coupled with a target genes approach that measured expression of 90 genes associated with drought tolerance in model organisms. Comparing differentially expressed genes with a ≥ 2 log-fold value between species and tissue types showed significant differences in drought response. In pairwise comparisons, species that occurred in drier environments differentially expressed greater genes in leaves when drought shocked than those from wetter environments, but expression in the roots mostly produced opposite results.

CONCLUSIONS

Arid-adapted species mount greater genetic responses compared to the mesophytic species, which has likely evolved in response to consistent annual drought exposure across generations. Drought responses also depended on organ type. Xerophytes, for example, mounted a larger response in leaves to downregulate photosynthesis and senescence, while mobilizing carbon and regulating water in the roots. The complexity of drought responses in Mentzelia suggest that whole organism responses need to be considered when studying drought and, in particular, the physiological mechanisms in which plants regulate water, carbon, cell death, metabolism, and secondary metabolites.

Drought Stress Mitigating Morphological, Physiological, Biochemical, and Molecular Responses of Guava (Psidium guajava L.) Cultivars

Guava (Psidium guajava L.), a major fruit crop of the sub-tropical region, is facing a production decline due to drought stress. Morphophysiological responses to drought stress and underlying transcriptional regulations in guava are, largely, unknown. This study evaluated the drought stress tolerance of two guava cultivars, viz. "Gola" and "Surahi," at morphological and physiological levels regulated differentially by ESTs (Expressed Sequence Tags). The treatments comprises three moisture regimes, viz. T_o = 100% (control), T₁ = 75%, and T₂ = 50% of field capacity. There was an overall decrease in both morphological and physiological attributes of studied guava cultivars in response to drought stress. Nonetheless, the water use efficiency of the "Surahi" cultivar increased (41.86%) speculating its higher drought tolerance based on enhanced peroxidase (402%) and catalase (170.21%) activities under 50% field capacity (T₂). Moreover, higher proline and flavonoid contents reinforced drought stress retaliation of the "Surahi" cultivar. The differential expression of a significant number of ESTs in "Surahi" (234) as compared to "Gola" (117) cultivar, somehow, regulated its cellular, biological, and molecular functions to strengthen morphophysiological attributes against drought stress as indicated by the upregulation of ESTs related to peroxidase, sucrose synthase (SUS), alcohol dehydrogenase (ADH), and ubiquitin at morphological, biochemical, and physiological levels. In conclusion, the drought stress acclimation of pear-shaped guava cultivar "Surahi" is due to the increased activities of peroxidase (POD) and catalase (CAT) complimented by the upregulation of related ESTs.

Response of Sugarcane Rhizosphere Bacterial Community to Drought Stress

Sugarcane is an important sugar and energy crop, and its yield is greatly affected by drought. Although a large number of studies have shown that rhizosphere microorganisms can help improve the adaptability of plants to biotic or abiotic stresses, there is a lack of studies on the adaptability of sugarcane rhizosphere microbial communities to host plants. Therefore, we conducted drought stress treatment and normal irrigation treatment on three sugarcane varieties GT21, GT31, and GT42 widely cultivated in Guangxi. Using 16S rDNA sequencing technology to analyze the changes in abundance of the sugarcane rhizosphere bacterial community under different treatments, combined with the determination of soil enzyme activity, soil nutrient content, and sugarcane physiological characteristics, we explored the sugarcane rhizosphere bacterial community response to drought stress. In addition, we used the structural equation model to verify the response path of sugarcane rhizosphere bacteria. The results show that the bacterial community structure in the rhizosphere of sugarcane is stable under normal water conditions. The change in the bacterial community structure under drought stress has a 25.2% correlation with the drought adaptability of sugarcane, but the correlation with drought stress is as high as 42.17%. The changes in abundance of rhizosphere bacteria under drought stress are mainly concentrated in the phylum Rhizobiales and Streptomycetales. This change is directly related to the physiological state of the host plant under drought stress, soil available phosphorus, soil urease and soil acid protease. We investigated the response species of rhizosphere microorganisms and their response pathways under drought stress, providing a scientific basis for rhizosphere microorganisms to assist host plants to improve drought adaptability.

Foliar application of silicon boosts growth, photosynthetic leaf gas exchange, antioxidative response and resistance to limited water irrigation in sugarcane (Saccharum officinarum L.)

Plant cell and water relationship regulates morphological, physiological and biochemical characteristics to optimize carboxylation for enhanced biomass yield in sugarcane. Insufficient water irrigation is one of the serious problems to impair potential yield of agriculturally important sugarcane cash crop by loss in plant performance. Our study aims to reveal consequences of foliar spray of silicon (Si) using calcium metasilicate powder (Wollastonite, CaO.SiO₂) to alleviate the adverse effects of limited water irrigation in sugarcane. Silicon (0, 50, 100 and 500 ppm) was applied as foliar spray on normally grown 45 days old sugarcane plants. Further, these plants were raised at half field capacity (50%) using water irrigation precisely up to 90 days under open environmental variables. Consequently, restricted irrigation impaired plant growth-development, leaf relative water content (%), photosynthetic pigments, SPAD unit, photosynthetic performance, chlorophyll fluorescence variable yield (Fv/Fm) and biomass yield. Notably, it has enhanced values of proline, hydrogen peroxide (H₂O₂), malondialdehyde (MDA), antioxidative defense enzyme molecules viz., catalase (CAT), ascorbate peroxidase (APx) and superoxide dismutase (SOD). The foliar spray of Si defended sugarcane plants from limited water irrigation stress as Si quenched harmful effect of water-deficit and also enhanced the operation of antioxidant defense machinery for improved sugarcane plant performance suitably favored stomatal dynamics for photosynthesis and plant productivity.

Investigation of Defensive Role of Silicon during Drought Stress Induced by Irrigation Capacity in Sugarcane: Physiological and Biochemical Characteristics

Water stress may become one of the most inevitable factors in years to come regulating crop growth, development, and productivity globally. The application of eco-friendly stress mitigator may sustain physiological fitness of the plants as uptake and accumulation of silicon (Si) found to alleviate stress with plant performance. Our study focused on the mitigative effects of Si using calcium metasilicate (wollastonite powder, CaO·SiO₂) in sugarcane (Saccharum officinarum L.) prior to the exposure of water stress created by the retention of 50-45% soil moisture capacity. Si (0, 50, 100, and 500 ppm L^-1) was supplied through soil irrigation in S. officinarum L. grown at about half of the soil moisture capacity for a period of 90 days. Water stress impaired plant growth, biomass, leaf relative water content, SPAD value, photosynthetic pigments capacity, and photochemical efficiency (F _v/F _m) of photosystem II. The levels of antioxidative defense-induced enzymes, viz., catalase, ascorbate peroxidase, and superoxide dismutase, enhanced. Silicon-treated plants expressed positive correlation with their performance index. A quadratic nonlinear relation observed between loss and gain (%) in physiological and biochemical parameters during water stress upon Si application. Si was found to be effective in restoring the water stress injuries integrated to facilitate the operation of antioxidant defense machinery in S. officinarum L. with improved plant performance index and photosynthetic carbon assimilation.

A transcriptomic analysis of sugarcane response to Leifsonia xyli subsp. xyli infection

Sugarcane ratoon stunting disease (RSD) caused by Leifsonia xyli subsp. xyli (Lxx) is a common destructive disease that occurs around the world. Lxx is an obligate pathogen of sugarcane, and previous studies have reported some physiological responses of RSD-affected sugarcane. However, the molecular understanding of sugarcane response to Lxx infection remains unclear. In the present study, transcriptomes of healthy and Lxx-infected sugarcane stalks and leaves were studied to gain more insights into the gene activity in sugarcane in response to Lxx infection. RNA-Seq analysis of healthy and diseased plants transcriptomes identified 107,750 unigenes. Analysis of these unigenes showed a large number of differentially expressed genes (DEGs) occurring mostly in leaves of infected plants. Sugarcane responds to Lxx infection mainly via alteration of metabolic pathways such as photosynthesis, phytohormone biosynthesis, phytohormone action-mediated regulation, and plant-pathogen interactions. It was also found that cell wall defense pathways and protein phosphorylation/dephosphorylation pathways may play important roles in Lxx pathogeneis. In Lxx-infected plants, significant inhibition in photosynthetic processes through large number of differentially expressed genes involved in energy capture, energy metabolism and chloroplast structure. Also, Lxx infection caused down-regulation of gibberellin response through an increased activity of DELLA and down-regulation of GID1 proteins. This alteration in gibberellic acid response combined with the inhibition of photosynthetic processes may account for the majority of growth retardation occurring in RSD-affected plants. A number of genes associated with plant-pathogen interactions were also differentially expressed in Lxx-infected plants. These include those involved in secondary metabolite biosynthesis, protein phosphorylation/dephosphorylation, cell wall biosynthesis, and phagosomes, implicating an active defense response to Lxx infection. Considering the fact that RSD occurs worldwide and a significant cause of sugarcane productivity, a better understanding of Lxx resistance-related processes may help develop tools and technologies for producing RSD-resistant sugarcane varieties through conventional and/or molecular breeding.

The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns

The protein kinase (PK) superfamily is one of the largest superfamilies in plants and the core regulator of cellular signaling. Despite this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here, we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, and these were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between the species, this study offers insights into Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq and identified significant similarities between Sbi and Ssp. Moreover, coexpression networks allowed inference of a core structure of kinase interactions with specific key elements. This study provides the first categorization of the allelic specificity of a kinome and offers a wide reservoir of molecular and genetic information, thereby enhancing the understanding of Sbi and Ssp PK evolutionary history.

Developing mathematical model for diurnal dynamics of photosynthesis in Saccharum officinarum responsive to different irrigation and silicon application

In the dynamic era of climate change, agricultural farming systems are facing various unprecedented problems worldwide. Drought stress is one of the serious abiotic stresses that hinder the growth potential and crop productivity. Silicon (Si) can improve crop yield by enhancing the efficiency of inputs and reducing relevant losses. As a quasi-essential element and the 2nd most abundant element in the Earth's crust, Si is utilized by plants and applied exogenously to combat drought stress and improve plant performance by increasing physiological, cellular and molecular responses. However, the physiological mechanisms that respond to water stress are still not well defined in Saccharum officinarum plants. To the best of our knowledge, the dynamics of photosynthesis responsive to different exogenous Si levels in Saccharum officinarum has not been reported to date. The current experiment was carried out to assess the protective role of Si in plant growth and photosynthetic responses in Saccharum officinarum under water stress conditions. Saccharum officinarum cv. 'GT 42' plants were subjected to drought stress conditions (80-75%, 55-50% and 35-30% of soil moisture) after ten weeks of normal growth, followed by the soil irrigation of Si (0, 100, 300 and 500 mg L-1) for 8 weeks. The results indicated that Si addition mitigated the inhibition in Saccharum officinarum growth and photosynthesis, and improved biomass accumulation during water stress. The photosynthetic responses (photosynthesis, transpiration and stomatal conductance) were found down-regulated under water stress, and it was significantly enhanced by Si application. No phytotoxic effects were monitored even at excess (500 mg L-1). Soil irrigation of 300 mg L-1 of Si was more effective as 100 and 500 mg L-1 under water stress condition. It is concluded that the stress in Saccharum officinarum plants applied with Si was alleviated by improving plant fitness, photosynthetic capacity and biomass accumulation as compared with the control. Thus, this study offers new information towards the assessment of growth, biomass accumulation and physiological changes related to water stress with Si application in plants.

Silicon Supply Improves Leaf Gas Exchange, Antioxidant Defense System and Growth in Saccharum officinarum Responsive to Water Limitation

Silicon (Si) is not categorized as a biologically essential element for plants, yet a great number of scientific reports have shown its significant effects in various crop plants and environmental variables. Plant Si plays biologically active role in plant life cycle, and the significant impact depends on its bioaccumulation in plant tissues or parts. In particular, it has been investigated for its involvement in limited irrigation management. Therefore, this experiment was conducted to examine the effect of Si application in eco-physiological, enzymatic and non-enzymatic activities of sugarcane plants against water stress. Four irrigation levels, i.e., normal (100-95% of soil moisture), 80-75, 55-50, and 35-30% of soil moisture were treated for the sugarcane cultivar GT 42 plants supplied with 0, 100, 200, 300, 400 and 500 mg Si L-1 and exposed for 60 days after Si application. Under stress, reduction in plant length (~26-67%), leaf area-expansion (~7-51%), relative water content (~18-57%), leaf greenness (~12-35%), photosynthetic pigments (~12-67%), physiological responses such as photosynthesis (22-63%), stomatal conductance (~25-61%), and transpiration rate (~32-63%), and biomass production were observed in the plants without Si application. The drought condition also inhibited the activities of antioxidant enzymes like catalase (~10-52%), peroxidase (ca. 4-35), superoxide dismutase (10-44%) and enhanced proline (~73-410%), and malondialdehyde content (ca. 15-158%), respectively. However, addition of Si ameliorated drought induced damage in sugarcane plants. The findings suggest that the active involvement of Si in sugarcane responsive to water stress ranges from plant performance and physiological processes, to antioxidant defense systems.

Comparative analysis of drought-responsive transcriptomes of sugarcane genotypes with differential tolerance to drought

Water stress causes considerable yield losses in sugarcane. To investigate differentially expressed genes under water stress, two sugarcane genotypes were subjected to three water-deficit levels (mild, moderate, and severe) and subsequent recovery and leaf transcriptome was generated using Illumina NextSeq sequencing. Among the differentially expressed genes, the tolerant genotype Co 06022 generated 2970 unigenes (p ≤ 0.05, functionally known, non-redundant DEGs) at 2-day stress, and there was a progressive decrease in the expressed genes as the stress period increased with 2109 unigenes at 6-day stress and 2307 unigenes at 10-day stress. There was considerable reduction at recovery with 1334 unigenes expressed at 10 days after recovery. However, in the susceptible genotype Co 8021, the number of unigenes expressed at 2 days was lower (2025) than the tolerant genotype and a further reduction was seen at 6-day stress (1552). During recovery, more differentially expressed genes were observed in the susceptible cultivar indicating that the cultivar has to activate more functions/processes to recover from the damage caused by stress. Comparison of DEGs between all stages of stress and recovery in both genotypes revealed that, the commonly up- and down-regulated genes across different stages were approximately double in the tolerant genotype. The most enriched gene ontology classes were heme binding, peroxidase activity and metal ion binding in the biological process and response to oxidative stress, hydrogen peroxide catabolic process and response to stress in the molecular function category. The cellular component was enriched with DEGs involved in extracellular region followed by integral component of membrane. The KEGG pathway analysis revealed important metabolic activities and functionally important genes involved in mitigating water-deficit stress in both the varieties. In addition, several unannotated genes in important pathways were detected and together may provide novel insights into water-deficit tolerance mechanisms in sugarcane. The reliability of the observed expression patterns was confirmed by qRT-PCR. The results of this study will help to identify useful genes for improving drought tolerance in sugarcane.

Rhythms of Transcription in Field-Grown Sugarcane Are Highly Organ Specific

Circadian clocks improve plant fitness in a rhythmic environment. As each cell has its own circadian clock, we hypothesized that sets of cells with different functions would have distinct rhythmic behaviour. To test this, we investigated whether different organs in field-grown sugarcane follow the same rhythms in transcription. We assayed the transcriptomes of three organs during a day: leaf, a source organ; internodes 1 and 2, sink organs focused on cell division and elongation; and internode 5, a sink organ focused on sucrose storage. The leaf had twice as many rhythmic transcripts (>68%) as internodes, and the rhythmic transcriptomes of the internodes were more like each other than to those of the leaves. Among the transcripts expressed in all organs, only 7.4% showed the same rhythmic pattern. Surprisingly, the central oscillators of these organs - the networks that generate circadian rhythms - had similar dynamics, albeit with different amplitudes. The differences in rhythmic transcriptomes probably arise from amplitude differences in tissue-specific circadian clocks and different sensitivities to environmental cues, highlighted by the sampling under field conditions. The vast differences suggest that we must study tissue-specific circadian clocks in order to understand how the circadian clock increases the fitness of the whole plant.

Label-Free Quantitative Proteomics of Enriched Nuclei from Sugarcane (Saccharum ssp) Stems in Response to Drought Stress

Drought is considered the major abiotic stress limiting crop productivity. This study seeks to identify proteins involved in the drought response in sugarcane stems submitted to drought stress. The integration of nuclei enrichment sample preparation with the shotgun proteomic approach results in great coverage of the sugarcane stem proteome with 5381 protein groups identified. A total of 1204 differentially accumulated proteins are detected in response to drought, among which 586 and 618 are increased and reduced in abundance, respectively. A total of 115 exclusive proteins are detected, being 41 exclusives of drought-stressed plants and 74 exclusives of control plants. In the control plants, most of these proteins are related to cell wall metabolism, indicating that drought affects negatively the cell wall metabolism. Also, 37 transcription factors (TFs) are identified, which are low abundant nuclear proteins and are differentially accumulated in response to drought stress. These TFs are associated to protein domains such as leucine-rich (bZIP), C2H2, NAC, C3H, LIM, Myb-related, heat shock factor (HSF) and auxin response factor (ARF). Increased abundance of chromatin remodeling and RNA processing proteins are also observed. It is suggested that these variations result from an imbalance of protein synthesis and degradation processes induced by drought.

Draft Genome Analysis Offers Insights Into the Mechanism by Which Streptomyces chartreusis WZS021 Increases Drought Tolerance in Sugarcane

Drought directly affects sugarcane production. Plant growth-promoting bacteria have gained attention as growth promoters of plants under abiotic stresses. The present study focused on genome assessment of the plant-beneficial endophyte Streptomyces chartreusis WZS021 and its vital role in sugarcane plants under drought stress. Based on in vitro plant growth-promoting trait analyses, WZS021 had multiple abilities, including tolerance to drought and production of 1-aminocyclopropane-1-carboxylic deaminase, siderophores, and indole acetic acid. We confirmed root colonization of sugarcane transplants by WZS021 by a sterile sand assay and scanning electron microscopy. Plants inoculated with strain WZS021 had a positive influence on the root parameters such as length and biomass when compared to the control plants. A comparative study of the responses of two sugarcane varieties (ROC22 and B8) to different levels of drought stress in the presence or absence of WZS021 was conducted by assessing the plant chemistry. The expression of antioxidants in sugarcane leaves varied with water stress level. WZS021 inoculation improved the contents of chlorophyll, proline, and phytohormones, revealing some potential for the mechanisms by which this strain improves drought tolerance in sugarcane plants. We identified several genes that might be involved in the plant growth- and drought tolerance-promoting effects of this strain.

Network Analyses and Data Integration of Proteomics and Metabolomics From Leaves of Two Contrasting Varieties of Sugarcane in Response to Drought

Uncovering the molecular mechanisms involved in the responses of crops to drought is crucial to understand and enhance drought tolerance mechanisms. Sugarcane (Saccharum spp.) is an important commercial crop cultivated mainly in tropical and subtropical areas for sucrose and ethanol production. Usually, drought tolerance has been investigated by single omics analysis (e.g. global transcripts identification). Here we combine label-free quantitative proteomics and metabolomics data (GC-TOF-MS), using a network-based approach, to understand how two contrasting commercial varieties of sugarcane, CTC15 (tolerant) and SP90-3414 (susceptible), adjust their leaf metabolism in response to drought. To this aim, we propose the utilization of regularized canonical correlation analysis (rCCA), which is a modification of classical CCA, and explores the linear relationships between two datasets of quantitative variables from the same experimental units, with a threshold set to 0.99. Light curves revealed that after 4 days of drought, the susceptible variety had its photosynthetic capacity already significantly reduced, while the tolerant variety did not show major reduction. Upon 12 days of drought, photosynthesis in the susceptible plants was completely reduced, while the tolerant variety was at a third of its rate under control conditions. Network analysis of proteins and metabolites revealed that different biological process had a stronger impact in each variety (e.g. translation in CTC15, generation of precursor metabolites, response to stress and energy in SP90-3414). Our results provide a reference data set and demonstrate that rCCA can be a powerful tool to infer experimentally metabolite-protein or protein-metabolite associations to understand plant biology.

Physio-biochemical assessment and expression analysis of genes associated with drought tolerance in sugarcane (Saccharum spp. hybrids) exposed to GA3 at grand growth stage

Drought is one of the most serious environmental factors limiting production of sugarcane worldwide. In order to assess the influence of gibberellins (GA₃ ) on drought and plant growth, along with associated physio-biochemical attributes, expression of eight drought-responsive genes were quantified and analysed. At grand growth stage (120 DAP) two sugarcane varieties (CoLk94184, CoPK05191) were exposed to drought by withholding irrigation. GA₃ (35 ppm) was applied using battery-operated uniform controlled dispensing sprayer twice at 1-week intervals on 2-week drought-stressed plants. Physio-biochemical attributes including antioxidant enzyme activities were estimated following standard protocols. RT-PCR was performed to visualise the drought-associated gene expression patterns. Drought triggered a reduction in RWC and chlorophyll content but these recovered when droughted plants were exposed to GA₃ . Proline content increased many fold in both varieties under stress, but decreased under the influence of GA₃ . There was a mixed response of antioxidant enzyme activity, which distinctly declined after GA₃ exposure, together with a lesser reduction in dry matter content over that of control plants. With increasing stress, expression of pyrroline-5-carboxylase synthetase (P5CS) and betaine-aldehyde dehydrogenase genes was observed, selectively up-regulated in CoPK05191. Expression of proline oxidase/transporter was high in CoPK05191 but diminished along with proline content after exposure to GA_3. CoLk94184 showed no significant difference in P5CS gene expression under stress condition, whereas expression of betaine-aldehyde dehydrogenase gene was unchanged in response to stress. Results demonstrated that exposure of droughted plants to GA₃ not only led to recovery of activity of drought-associated physio-biochemical attributes, but also minimised impact on cane dry weight and quality. Further, GA₃ application caused differential gene expression that possibly triggers increased responsiveness towards drought tolerance in sugarcane.

ScGAI is a key regulator of culm development in sugarcane

Sugarcane contributes more than 70% of sugar production and is the second largest feedstock for ethanol production globally. Since sugar accumulates in sugarcane culms, culm biomass and sucrose content are the most commercially important traits. Despite extensive breeding, progress in both cane yield and sugar content remains very slow in most countries. We hypothesize that manipulating the genetic elements controlling culm growth will alter source-sink regulation and help break down the yield barriers. In this study, we investigate the role of sugarcane ScGAI, an ortholog of SLR1/D8/RHT1/GAI, on culm development and source-sink regulation through a combination of molecular techniques and transgenic strategies. We show that ScGAI is a key molecular regulator of culm growth and development. Changing ScGAI activity created substantial culm growth and carbon allocation changes for structural molecules and storage. ScGAI regulates spatio-temporal growth of sugarcane culm and leaf by interacting with ScPIF3/PIF4 and ethylene signaling elements ScEIN3/ScEIL1, and its action appears to be regulated by SUMOylation in leaf but not in the culm. Collectively, the remarkable culm growth variation observed suggests that ScGAI could be used as an effective molecular breeding target for breaking the slow yield gain in sugarcane.

Characterization of promoter of EgPAL1, a novel PAL gene from the oil palm Elaeis guineensis Jacq

The oil palm EgPAL1 gene promoter and its regulatory region were functional as a promoter in the heterologous system of Arabidopsis according to the cis-acting elements present in that region. The promoter was developmentally regulated, vascular tissue specific and responsive to water stress agents. Phenylalanine ammonia lyase (PAL, EC 4.3.1.24) is the key enzyme of the phenylpropanoid pathway which plays important roles in plant development and adaptation. To date, there is no report on the study of PAL from oil palm (Elaeis guineensis), an economically important oil crop. In this study, the 5' regulatory sequence of a highly divergent oil palm PAL gene (EgPAL1) was isolated and fused with GUS in Arabidopsis to create two transgenic plants carrying the minimal promoter with (2302 bp) and without its regulatory elements (139 bp). The regulatory sequence contained cis-acting elements known to be important for plant development and stress response including the AC-II element for lignin biosynthesis and several stress responsive elements. The promoter and its regulatory region were fully functional in Arabidopsis. Its activities were characterised by two common fundamental features of PAL which are responsive to plant internal developmental programme and external factors. The promoter was developmentally regulated in certain organs; highly active in young organs but less active or inactive in mature organs. The presence of the AC elements and global activity of the EgPAL1 promoter in all organs resembled the property of lignin-related genes. The existence of the MBS element and enhancement of the promoter activity by PEG reflected the behaviour of drought-responsive genes. Our findings provide a platform for evaluating oil palm gene promoters in the heterologous system of Arabidopsis and give insights into the activities of EgPAL1 promoter in oil palm.

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.

Molecular Characterization and Co-expression Analysis of the SnRK2 Gene Family in Sugarcane (Saccharum officinarum L.)

In plants, both abscisic acid (ABA) dependent and independent pathways form the basis for the response to environmental stresses. Sucrose non-fermenting 1-related protein kinase 2 (SnRK2) plays a central role in plant stress signal transduction. However, complete annotation and specific expression patterns of SnRK2s in sugarcane remain unclear. For the present study, we performed a full-length cDNA library survey of sugarcane, thus identifying ten SoSnRK2 genes via phylogenetic, local BLAST methods, and various bioinformatics analyses. Phylogenetic analysis indicated division of SoSnRK2 genes into three subgroups, similar to other plant species. Gene structure comparison with Arabidopsis suggested a unique evolutionary imprint of the SnRK2 gene family in sugarcane. Both sequence alignment and structural annotation provided an overview of the conserved N-terminal and variations of the C-terminal, suggesting functional divergence. Transcript and transient expression assays revealed SoSnRK2s to be involved in the responses to diverse stress signals, and strong ABA induction of SoSnRK2s in subgroup III. Co-expression network analyses indicated the existence of both conserved and variable biological functions among different SoSnRK2s members. In summary, this comprehensive analysis will facilitate further studies of the SoSnRK2 family and provide useful information for the functional validation of SoSnRK2s.

Improved Drought Stress Response in Alfalfa Plants Nodulated by an IAA Over-producing Rhizobium Strain

The drought-stress response in plant involves the cross-talk between abscisic acid (ABA) and other phytohormones, such as jasmonates and ethylene. The auxin indole-3-acetic acid (IAA) plays an integral part in plant adaptation to drought stress. Investigation was made to see how the main auxin IAA interacted with other plant hormones under water stress, applied through two different growth conditions (solid and hydroponic). Medicago sativa plants nodulated by the Ensifer meliloti wild type 1021 (Ms-1021) and its IAA-overproducing RD64 derivative strains (Ms-RD64) were subjected to drought stress, comparing their response. When the expression of nifH gene and the activity of the nitrogenase enzyme were measured after stress treatments, Ms-RD64 plants recorded a significantly weaker damage. These results were correlated with a lower biomass reduction, and a higher Rubisco protein level measured for the Ms-RD64-stressed plants as compared to the Ms-1021-stressed ones. It has been verified that the stress response observed for Ms-RD64-stressed plants was related to the production of greater amount of low-molecular-weight osmolytes, such as proline and pinitol, measured in these plants. For the Ms-RD64 plants the immunoblotting analysis of thylakoid membrane proteins showed that some of the photosystem proteins increased after the stress. An increased non-photochemical quenching after the stress was also observed for these plants. The reduced wilting signs observed for these plants were also connected to the significant down-regulation of the MtAA03 gene involved in the ABA biosynthesis, and with the unchanged expression of the two genes (Mt-2g006330 and Mt-8g095330) of ABA signaling. When the expression level of the ethylene-signaling genes was evaluated by qPCR analysis no significant alteration of the key positive regulators was recorded for Ms-RD64-stressed plants. Coherently, these plants accumulated 40% less ethylene as compared to Ms-1021-stressed ones. The results presented herein indicate that the variations in endogenous IAA levels, triggered by the overproduction of rhizobial IAA inside root nodules, positively affected drought stress response in nodulated alfalfa plants.

Transcriptional profiling of sugarcane leaves and roots under progressive osmotic stress reveals a regulated coordination of gene expression in a spatiotemporal manner

Sugarcane is one of the most important crops worldwide and is a key plant for the global production of sucrose. Sugarcane cultivation is severely affected by drought stress and it is considered as the major limiting factor for their productivity. In recent years, this plant has been subjected to intensive research focused on improving its resilience against water scarcity; particularly the molecular mechanisms in response to drought stress have become an underlying issue for its improvement. To better understand water stress and the molecular mechanisms we performed a de novo transcriptomic assembly of sugarcane (var. Mex 69-290). A total of 16 libraries were sequenced in a 2x100 bp configuration on a HiSeq-Illumina platform. A total of 536 and 750 genes were differentially up-regulated along with the stress treatments for leave and root tissues respectively, while 1093 and 531 genes were differentially down-regulated in leaves and roots respectively. Gene Ontology functional analysis showed that genes related to response of water deprivation, heat, abscisic acid, and flavonoid biosynthesis were enriched during stress treatment in our study. The reliability of the observed expression patterns was confirmed by RT-qPCR. Additionally, several physiological parameters of sugarcane were significantly affected due to stress imposition. The results of this study may help identify useful target genes and provide tissue-specific data set of genes that are differentially expressed in response to osmotic stress, as well as a complete analysis of the main groups is significantly enriched under this condition. This study provides a useful benchmark for improving drought tolerance in sugarcane and other economically important grass species.

Transcriptome and Metabolome Analyses Provide Insights into the Occurrence of Peel Roughing Disorder on Satsuma Mandarin (Citrus unshiu Marc.) Fruit

Roughing disorder (RD) is a significant quality barrier in citrus fruit, prevalent on easy-peeling mandarins. As RD is not yet well-understood, this study aimed to examine the changes and synergic molecular processes involved in peel RD. Peel with RD was induced by severely defruiting Satsuma mandarin trees. Morphology observations, RNA-sequencing, and targeted and untargeted metabolic analyses were conducted. The results showed that the primary metabolites of sugars, organic acids and amino acids are dramatically changed in RD peel. The RD peel was always characterized by higher magnesium content during development. Comparative transcriptome profiling was performed for CK and RD peels at 30, 80, and 170 days after full bloom (DAFB) which represented fruit at cell division stage, cell enlargement stage and fruit maturity stage, respectively. Physiological and molecular biological evidence suggested that the month after full bloom is a crucial stage for RD initiation. A total of 4,855 differentially expressed genes (DEGs) in RD peel, relative to CK peel were detected at cell division stage, about 2 to 4-fold more than other stages had. Among the differentially expressed transcription factors, the bHLH family were affected most by RD, and six bHLH transcription factors functionally involved in GA metabolism were assessed to associate with RD occurrence. Gene set enrichment analysis suggested that RD significantly altered starch and GA metabolism in peel. Higher starch content and hydrolysed chain status were found in RD peel at cell division stage. RD occurrence on the peel was influenced significantly by GA, especially abundant GA before July. These changes may mean a significant alteration in sink strength of RD peel. The findings of this study provide insights into the emergence, development and molecular mechanisms of RD.

Genotype-dependent regulation of drought-responsive genes in tolerant and sensitive sugarcane cultivars

Drought is the most damaging among the major abiotic stresses. Transcriptomic studies allow a global overview of expressed genes, providing the basis for molecular markers development. Here, the HT-SuperSAGE technique allowed the evaluation of four drought-tolerant cultivars and four-sensitive cultivars, after 24h of irrigation suppression. We identified 9831 induced unitags from roots of the tolerant cultivars with different regulations by the -sensitive cultivars after the applied stress. These unitags allowed a proposal of 15 genes, whose expressed profiles were validated by RT-qPCR, evaluating each cultivar independently. These genes covered broad metabolic processes: ethylene stress attenuation (ACCD); root growth (β-EXP8); protein degradation [ubiquitination pathway (E2, 20SPβ4); plant proteases (AP, C13)]; oxidative detoxification (TRX); fatty acid synthesis (ACC); amino acid transport (AAT), and carbohydrate metabolism [glycolysis (PFK, TPI, FBA); TCA cycle (LDP, MDH); pentose phosphate pathway (TKT)]. The expressed profiles showed a genotype-dependent regulation of the target genes. Two drought-tolerant cultivars (SP83-2847; CTC6) presented each one, nine of the induced genes. Among the -sensitive cultivars, CTC13 induced only one, while SP90-1636 induced two genes. These genes should help breeders to identify accessions managing drought stress tolerance responses, showing better ethylene stress attenuation, energy allocation, amino acid transport, and protein homeostasis.

Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions

Sugarcane is a unique crop with the ability to accumulate high levels of sugar and is a commercially viable source of biomass for bioelectricity and second-generation bioethanol. Water deficit is the single largest abiotic stress affecting sugarcane productivity and the development of water use efficient and drought tolerant cultivars is an imperative for all major sugarcane producing countries. This review summarizes the physiological and molecular studies on water deficit stress in sugarcane, with the aim to help formulate more effective research strategies for advancing our knowledge on genes and mechanisms underpinning plant response to water stress. We also overview transgenic studies in sugarcane, with an emphasis on the potential strategies to develop superior sugarcane varieties that improve crop productivity in drought-prone environments.

Integrated analysis of the potential roles of miRNA‑mRNA networks in triple negative breast cancer

Triple negative breast cancer (TNBC) is a type of breast cancer where the tumor cells are negative for the estrogen, progesterone and human epidermal growth factor 2 receptors. To date, expression profiling of microRNA (miRNA/miR) and mRNA sequences have been widely applied for the diagnosis of TNBC. In the present study, an integrated analysis of miRNA‑mRNA profiling arrays was performed. A total of five dysregulated miRNAs in patients with TNBC were identified, including upregulated miR‑558 expression and downregulated miR‑320d‑1, miR‑548v, miR‑99a and miR‑21 expression. In addition, 49 potential target mRNA sequences were identified. Bioinformatics analyses were performed on the identified miRNAs and mRNAs, including gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes pathway and miRNA‑mRNA network analyses. A total of 31 GO terms and three signaling pathways were identified. The results indicated that the differentially expressed miRNAs and their potential target mRNAs may affect the pathogenesis of TNBC, and may therefore be considered as promising biomarkers for the early diagnosis and targeted therapy of patients with TNBC.

Temporal and spatial changes in gene expression, metabolite accumulation and phytohormone content in rice seedlings grown under drought stress conditions

In order to analyze the molecular mechanisms underlying the responses of plants to different levels of drought stress, we developed a soil matric potential (SMP)-based irrigation system that precisely controls soil moisture. Using this system, rice seedlings were grown under three different drought levels, denoted Md1, Md2 and Md3, with SMP values set to -9.8, -31.0 and -309.9 kPa, respectively. Although the Md1 treatment did not alter the visible phenotype, the Md2 treatment caused stomatal closure and shoot growth retardation (SGR). The Md3 treatment markedly induced SGR, without inhibition of photosynthesis. More severe drought (Sds) treatment, under which irrigation was terminated, resulted in the wilting of leaves and inhibition of photosynthesis. Metabolome analysis revealed the accumulation of primary sugars under Md3 and Sds and of most amino acids under Sds. The starch content was increased under Md3 and decreased under Sds. Transcriptome data showed that the expression profiles of associated genes supported the observed changes in photosynthesis and metabolites, suggesting that the time lag from SGR to inhibition of photosynthesis might lead to the accumulation of photosynthates under Md3, which can be used as osmolytes under Sds. To gain further insight into the observed SGR, transcriptome and hormonome analyses were performed in specific tissues. The results showed specific decreases in indole-3-acetic acid (IAA) and cytokinin levels in Md2-, Md3- and Sds-treated shoot bases, though the expression levels of hormone metabolism-related genes were not reflected in IAA and cytokinin contents. These observations suggest that drought stress affects the distribution or degradation of cytokinin and IAA molecules.

Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions

Sugarcane is a unique crop with the ability to accumulate high levels of sugar and is a commercially viable source of biomass for bioelectricity and second-generation bioethanol. Water deficit is the single largest abiotic stress affecting sugarcane productivity and the development of water use efficient and drought tolerant cultivars is an imperative for all major sugarcane producing countries. This review summarizes the physiological and molecular studies on water deficit stress in sugarcane, with the aim to help formulate more effective research strategies for advancing our knowledge on genes and mechanisms underpinning plant response to water stress. We also overview transgenic studies in sugarcane, with an emphasis on the potential strategies to develop superior sugarcane varieties that improve crop productivity in drought-prone environments.

Distinct gene networks drive differential response to abrupt or gradual water deficit in potato

Water-limiting conditions affect dramatically plant growth and development and, ultimately, yield of potato plants (Solanum tuberosum L.). Therefore, understanding the mechanisms underlying the response to water deficit is of paramount interest to obtain drought tolerant potato varieties. Herein, potato 10K cDNA array slides were used to profile transcriptomic changes of two potato cell populations under abrupt (shocked cells) or gradual exposure (adapted cells) to polyethylene glycol (PEG)-mediated water stress. Data analysis identified >1000 differentially expressed genes (DEGs) in our experimental conditions. Noteworthy, our microarray study also suggests that distinct gene networks underlie the cellular response to shock or gradual water stress. On the basis of our experimental findings, it is possible to speculate that DEGs identified in shocked cells participate in early protective and sensing mechanisms to environmental insults, while the genes whose expression was modulated in adapted cells are directly involved in the acquisition of a new cellular homeostasis to cope with water stress conditions. To validate microarray data obtained for potato cells, the expression analysis of 21 selected genes of interest was performed by Real-Time Quantitative Reverse Transcription PCR (qRT-PCR). Intriguingly, the expression levels of these transcripts in 4-week old potato plants exposed to long-term water-deficit. qRT-PCR analysis showed that several genes were regulated similarly in potato cells cultures and tissues exposed to drought, thus confirming the efficacy of our simple experimental system to capture important genes involved in osmotic stress response. Highlighting the differences in gene expression between shock-like and adaptive response, our findings could contribute to the discussion on the biological function of distinct gene networks involved in the response to abrupt and gradual adaptation to water deficit.