Effects of water-deficit stress on the transcriptomes of developing immature ear and tassel in maize

The battle of crops against drought: Genetic dissection and improvement

With ongoing global climate change, water scarcity-induced drought stress remains a major threat to agricultural productivity. Plants undergo a series of physiological and morphological changes to cope with drought stress, including stomatal closure to reduce transpiration and changes in root architecture to optimize water uptake. Combined phenotypic and multi-omics studies have recently identified a number of drought-related genetic resources in different crop species. The functional dissection of these genes using molecular techniques has enriched our understanding of drought responses in crops and has provided genetic targets for enhancing resistance to drought. Here, we review recent advances in the cloning and functional analysis of drought resistance genes and the development of technologies to mitigate the threat of drought to crop production.

Trehalose: a promising osmo-protectant against salinity stress-physiological and molecular mechanisms and future prospective

Salt stress is one of the leading threats to crop growth and productivity across the globe. Salt stress induces serious alterations in plant physiological, metabolic, biochemical functioning and it also disturbs antioxidant activities, cellular membranes, photosynthetic performance, nutrient uptake and plant water uptake and resulting in a significant reduction in growth and production. The application of osmoprotectants is considered as an important strategy to induce salt tolerance in plants. Trehalose (Tre) has emerged an excellent osmolyte to induce salinity tolerance and it got considerable attention in recent times. Under salinity stress, Tre helps to maintain the membrane integrity, and improves plant water relations, nutrient uptake and reduces the electrolyte leakage and lipid per-oxidation. Tre also improves gas exchange characteristics, protects the photosynthetic apparatus from salinity induced oxidative damages and brings ultra-structure changes in the plant body to induce salinity tolerance. Moreover, Tre also improves antioxidant activities and expression of stress responsive proteins and genes and confers salt tolerance in plants. Additionally, Tre is also involved in signaling association with signaling molecules and phytohormones and resultantly improved the plant performance under salt stress. Thus, it is interesting to understand the role of Tre in mediating the salinity tolerance in plants. Therefore, in this review we have summarized the different physiological and molecular roles of Tre to induce salt tolerance in plants. Moreover, we have also provided the information on Tre cross-talk with various osmolytes and hormones, and its role in stress responsive genes and antioxidant activities. Lastly, we also shed light on research gaps that need to be addressed in future studies. Therefore, this review will help the scientists to learn more about the Tre in changing climate conditions and it will also provide new insights to insights that could be used to develop salinity tolerance in plants.

A transcriptomic analysis reveals the adaptability of the growth and physiology of immature tassel to long-term soil water deficit in Zea mays L

Drought is a key threat to maize growth and yield. Understanding the mechanism of immature tassel (IT) response to long term drought is of paramount importance. Here, the maize inbred line PH6WC was tested under well-watered (CK) and two water deficit treatments (WD1 and WD2). The final IT length in the WD1 and WD2 treatments decreased by nearly 6.2% and 21.2% compared to the CK, respectively, and the average accumulation rate IT dry matter was 1.5-fold and 1.8-fold slower, respectively. Furthermore, RNA sequencing analysis was conducted on the IT sampled at 30 days after the WD treatments. In total, the cellular component in gene ontology (GO) analysis suggested that the differentially expressed genes were significantly enriched in three common terms (apoplast, plant-type cell wall, and anchored component of membrane) among the CK vs WD1, CK vs WD2, and WD1 vs WD2 comparisons. Next, a co-expression network analysis identified 44 modules that contained global expression genes. Finally, by combining the GO analysis with modules, nine genes involved in carbohydrate metabolism and the antioxidant system were screened out, and the six corresponding physiological parameters were all significantly increased under the WD treatments. These results showed that, although the IT length and dry matter decreased, the IT enhanced the adaptation to drought by regulating their own genetic and physiological changes.

PhePEBP family genes regulated by plant hormones and drought are associated with the activation of lateral buds and seedling growth in Phyllostachys edulis

Development of lateral buds on the underground rhizome in moso bamboo is essentially the early stage of the development of aboveground branching, which is regulated by Phosphatidyl-Ethanolamine Binding Protein (PEBP) family genes, but it is unknown whether the PEBP family genes are involved in the activation and development of lateral buds underground. By scanning the whole-genome sequence of moso bamboo, we identified 25 PhePEBP family genes and amplified their full-length open reading frames (ORFs). A sequence analysis revealed that they are composed of four exons and three introns, except for PheFT10, which contains six exons and five introns. PheFT10 underwent alternative splicing, resulting in at least four transcripts (PheFT10α, PheFT10β, PheFT10γ and PheFT10δ). Although PhePEBP genes are generally expressed at low levels and show dramatically organ-specific expressions, the transcription levels of most PhePEBP genes, including the transcripts of PheFT10, change with plant age. Together with the observation that the expression of PhePEBP family genes can be regulated by plant hormones and drought, our data suggest that PhePEBP family genes might be involved in the activation of lateral buds and seedling growth. Particularly, PheFT9, PheTFL2 and PheTFL8 may play vital roles during the activation of dormant buds based on the analysis of amino acid substitution and expression profile. These findings provide insights for in-depth exploration of the biological functions of the PhePEBP family genes in regulating the activation of dormant bud and the development of seedling in moso bamboo.

Effects of maize organ-specific drought stress response on yields from transcriptome analysis

BACKGROUND

Drought is a serious causal factor of reduced crop yields than any other abiotic stresses. As one of the most widely distributed crops, maize plants frequently suffer from drought stress, which causes great losses in the final kernel yield. Drought stress response in plants showed tissue- and developmental stage-specific characteristics.

RESULTS

In this study, the ears at the V9 stage, kernels and ear leaf at the 5DAP (days after pollination) stage of maize were used for morphological, physiological and comparative transcriptomics analysis to understand the different features of "sink" or "source" organs and the effects on kernel yield under drought stress conditions. The ABA-, NAC-mediate signaling pathway, osmotic protective substance synthesis and protein folding response were identified as common drought stress response in the three organs. Tissue-specific drought stress responses and the regulators were identified, they were highly correlated with growth, physiological adaptation and yield loss under drought stress. For ears, drought stress inhibited ear elongation, led to the abnormal differentiation of the paired spikelet, and auxin signaling involved in the regulation of cell division and growth and primordium development changes. In the kernels, reduced kernel size caused by drought stress was observed, and the obvious differences of auxin, BR and cytokine signaling transduction appeared, which indicated the modification in carbohydrate metabolism, cell differentiation and growth retardation. For the ear leaf, dramatically and synergistically reduced the expression of photosynthesis genes were observed when suffered from drought stress, the ABA- and NAC- mediate signaling pathway played important roles in the regulation of photosynthesis.

CONCLUSIONS

Transcriptomic changes caused by drought were highly correlated with developmental and physiological adaptation, which was closely related to the final yield of maize, and a sketch of tissue- and developmental stage-specific responses to drought stress in maize was drafted.

Developmental and transcriptional responses of maize to drought stress under field conditions

Drought is a common abiotic stress which significantly limits global crop productivity. Maize is an important staple crop and its yield is determined by successful development of the female inflorescence, the ear. We investigated drought stress responses across several developmental stages of the maize B73 inbred line under field conditions. Drought suppressed plant growth, but had little impact on progression through developmental stages. While ear growth was suppressed by drought, the process of spikelet initiation was not significantly affected. Tassel growth was reduced to a lesser extent compared to the observed reduction in ear growth under stress. Parallel RNA-seq profiling of leaves, ears, and tassels at several developmental stages revealed tissue-specific differences in response to drought stress. High temperature fluctuation was an additional environmental factor that also likely influenced gene expression patterns in the field. Drought induced significant transcriptional changes in leaves and ears but only minor changes in the tassel. Additionally, more genes were drought responsive in ears compared to leaves over the course of drought treatment. Genes that control DNA replication, cell cycle, and cell division were significantly down-regulated in stressed ears, which was consistent with inhibition of ear growth under drought. Inflorescence meristem genes were affected by drought to a lesser degree which was consistent with the minimal impact of drought on spikelet initiation. In contrast, genes that are involved in floret and ovule development were sensitive to stress, which is consistent with the detrimental effect of drought on gynoecium development and kernel set.

Effect of water-deficit on tassel development in maize

Maize often exhibits asynchronous pollination under abiotic and biotic stress conditions; however, the molecular basis of this developmental deficiency has not been elucidated. Tassel development is a key process affecting the anthesis-silking interval (ASI) in maize. In this study, we showed that pollen shedding was delayed and ASI was significantly increased in B73 and Chang7-2 inbred lines under water deficit conditions, which resulted in longer barren tip length and decreased yields under both controlled and field conditions. Comparative transcriptome analysis performed on immature tassels derived from plants grown under well-watered and water deficit conditions identified 1931 and 1713 differentially expressed genes (DEGs) in B73 and Chang7-2, respectively. Further, 28 differentially co-expressed transcription factors were identified across both lines. Collectively, we demonstrated that the molecular regulation of tassel development is associated with water deficit stress at early vegetative stage in maize. This finding extends our understanding of the molecular basis of maize tassel development during abiotic stress.

Transcriptome Analysis of Two Species of Jute in Response to Polyethylene Glycol (PEG)- induced Drought Stress

Drought stress results in significant crop yield losses. Comparative transcriptome analysis between tolerant and sensitive species can provide insights into drought tolerance mechanisms in jute. We present a comprehensive study on drought tolerance in two jute species-a drought tolerant species (Corchorus olitorius L., GF) and a drought sensitive species (Corchorus capsularis L., YY). In total, 45,831 non-redundant unigenes with average sequence length of 1421 bp were identified. Higher numbers of differentially expressed genes (DEGs) were discovered in YY (794) than in GF (39), implying that YY was relatively more vulnerable or hyper-responsive to drought stress at the molecular level; the two main pathways, phenylpropanoid biosynthesis and peroxisome pathway, significantly involved in scavenging of reactive oxygen species (ROS) and 14 unigenes in the two pathways presented a significant differential expression in response to increase of superoxide. Our classification analysis showed that 1769 transcription factors can be grouped into 81 families and 948 protein kinases (PKs) into 122 families. In YY, we identified 34 TF DEGs from and 23 PK DEGs, including 19 receptor-like kinases (RLKs). Most of these RLKs were downregulated during drought stress, implying their role as negative regulators of the drought tolerance mechanism in jute.

Genome-wide identification of gene expression in contrasting maize inbred lines under field drought conditions reveals the significance of transcription factors in drought tolerance

Drought is a major threat to maize growth and production. Understanding the molecular regulation network of drought tolerance in maize is of great importance. In this study, two maize inbred lines with contrasting drought tolerance were tested in the field under natural soil drought and well-watered conditions. In addition, the transcriptomes of their leaves was analyzed by RNA-Seq. In total, 555 and 2,558 genes were detected to specifically respond to drought in the tolerant and the sensitive line, respectively, with a more positive regulation tendency in the tolerant genotype. Furthermore, 4,700, 4,748, 4,403 and 4,288 genes showed differential expression between the two lines under moderate drought, severe drought and their well-watered controls, respectively. Transcription factors were enriched in both genotypic differentially expressed genes and specifically responsive genes of the tolerant line. It was speculated that the genotype-specific response of 20 transcription factors in the tolerance line and the sustained genotypically differential expression of 22 transcription factors might enhance tolerance to drought in maize. Our results provide new insight into maize drought tolerance-related regulation systems and provide gene resources for subsequent studies and drought tolerance improvement.

Aberrant Meiotic Modulation Partially Contributes to the Lower Germination Rate of Pollen Grains in Maize (Zea mays L.) Under Low Nitrogen Supply

Pollen germination is an essential step towards successful pollination during maize reproduction. How low niutrogen (N) affects pollen germination remains an interesting biological question to be addressed. We found that only low N resulted in a significantly lower germination rate of pollen grains after 4 weeks of low N, phosphorus or potassium treatment in maize production. Importantly, cytological analysis showed 7-fold more micronuclei in male meiocytes under the low N treatment than in the control, indicating that the lower germination rate of pollen grains was partially due to numerous chromosome loss events resulting from preceding meiosis. The appearance of 10 bivalents in the control and low N cells at diakinesis suggested that chromosome pairing and recombination in meiosis I was not affected by low N. Further gene expression analysis revealed dramatic down-regulation of Nuclear Division Cycle 80 (Ndc80) and Regulator of Chromosome Condensation 1 (Rcc1-1) expression and up-regulation of Cell Division Cycle 20 (Cdc20-1) expression, although no significant difference in the expression level of kinetochore foundation proteins Centromeric Histone H3 (Cenh3) and Centromere Protein C (Cenpc) and cohesion regulators Recombination 8 (Rec8) and Shugoshin (Sgo1) was observed. Aberrant modulation of three key meiotic regulators presumably resulted in a high likelihood of erroneous chromosome segregation, as testified by pronounced lagging chromosomes at anaphase I or cell cycle disruption at meiosis II. Thus, we proposed a cytogenetic mechanism whereby low N affects male meiosis and causes a higher chromosome loss frequency and eventually a lower germination rate of pollen grains in a staple crop plant.

Transcriptome Analysis of Flowering Time Genes under Drought Stress in Maize Leaves

Flowering time is an important factor determining yield and seed quality in maize. A change in flowering time is a strategy used to survive abiotic stresses. Among abiotic stresses, drought can increase anthesis-silking intervals (ASI), resulting in negative effects on maize yield. We have analyzed the correlation between flowering time and drought stress using RNA-seq and bioinformatics tools. Our results identified a total of 619 genes and 126 transcripts whose expression was altered by drought stress in the maize B73 leaves under short-day condition. Among drought responsive genes, we also identified 20 genes involved in flowering times. Gene Ontology (GO) enrichment analysis was used to predict the functions of the drought-responsive genes and transcripts. GO categories related to flowering time included reproduction, flower development, pollen-pistil interaction, and post-embryonic development. Transcript levels of several genes that have previously been shown to affect flowering time, such as PRR37, transcription factor HY5, and CONSTANS, were significantly altered by drought conditions. Furthermore, we also identified several drought-responsive transcripts containing C₂H₂ zinc finger, CCCH, and NAC domains, which are frequently involved in transcriptional regulation and may thus have potential to alter gene expression programs to change maize flowering time. Overall, our results provide a genome-wide analysis of differentially expressed genes (DEGs), novel transcripts, and isoform variants expressed during the reproductive stage of maize plants subjected to drought stress and short-day condition. Further characterization of the drought-responsive transcripts identified in this study has the potential to advance our understanding of the mechanisms that regulate flowering time under drought stress.

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

Water stress causes considerable yield losses in sugarcane. To investigate differentially expressed genes under water stress, a pot experiment was performed with the sugarcane variety GT21 at three water-deficit levels (mild, moderate, and severe) during the elongation stage and gene expression was analyzed using microarray technology. Physiological parameters of sugarcane showed significant alterations in response to drought stress. Based on the expression profile of 15,593 sugarcane genes, 1,501 (9.6%) genes were differentially expressed under different water-level treatments; 821 genes were upregulated and 680 genes were downregulated. A gene similarity analysis showed that approximately 62.6% of the differentially expressed genes shared homology with functional proteins. In a Gene Ontology (GO) analysis, 901 differentially expressed genes were assigned to 36 GO categories. Moreover, 325 differentially expressed genes were classified into 101 pathway categories involved in various processes, such as the biosynthesis of secondary metabolites, ribosomes, carbon metabolism, etc. In addition, some unannotated genes were detected; these may provide a basis for studies of water-deficit tolerance. The reliability of the observed expression patterns was confirmed by RT-PCR. The results of this study may help identify useful genes for improving drought tolerance in sugarcane.

Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit

Water deficit is the most important environmental constraint severely limiting global crop growth and productivity. This study investigated early transcriptome changes in maize (Zea mays L.) primary root tissues in response to moderate water deficit conditions by RNA-Sequencing. Differential gene expression analyses revealed a high degree of plasticity of the water deficit response. The activity status of genes (active/inactive) was determined by a Bayesian hierarchical model. In total, 70% of expressed genes were constitutively active in all tissues. In contrast, <3% (50 genes) of water deficit-responsive genes (1915) were consistently regulated in all tissues, while >75% (1501 genes) were specifically regulated in a single root tissue. Water deficit-responsive genes were most numerous in the cortex of the mature root zone and in the elongation zone. The most prominent functional categories among differentially expressed genes in all tissues were 'transcriptional regulation' and 'hormone metabolism', indicating global reprogramming of cellular metabolism as an adaptation to water deficit. Additionally, the most significant transcriptomic changes in the root tip were associated with cell wall reorganization, leading to continued root growth despite water deficit conditions. This study provides insight into tissue-specific water deficit responses and will be a resource for future genetic analyses and breeding strategies to develop more drought-tolerant maize cultivars.

Identification of Drought Tolerant Mechanisms in Maize Seedlings Based on Transcriptome Analysis of Recombination Inbred Lines

Zea mays is an important crop that is sensitive to drought stress, but survival rates and growth status remain strong in some drought-tolerant lines under stress conditions. Under drought conditions, many biological processes, such as photosynthesis, carbohydrate metabolism and energy metabolism, are suppressed, while little is known about how the transcripts of genes respond to drought stress in the genome-wide rang in the seedling stage. In our study, the transcriptome profiles of two maize recombination inbred lines (drought-tolerant RIL70 and drought-sensitive RIL93) were analyzed at different drought stages to elucidate the dynamic mechanisms underlying drought tolerance in maize seedlings during drought conditions. Different numbers of differentially expressed genes presented in the different stages of drought stress in the two RILs, for the numbers of RIL93 vs. RIL70 were: 9 vs. 358, 477 vs. 103, and 5207 vs. 152 respectively in DT1, DT2, and DT5. Gene Ontology enrichment analysis revealed that in the initial drought-stressed stage, the primary differentially expressed genes involved in cell wall biosynthesis and transmembrane transport biological processes were overrepresented in RIL70 compared to RIL93. On the contrary, differentially expressed genes profiles presented at 2 and 5 day-treatments, the primary differentially expressed genes involved in response to stress, protein folding, oxidation-reduction, photosynthesis and carbohydrate metabolism, were overrepresented in RIL93 compared to RIL70. In addition, the transcription of genes encoding key members of the cell cycle and cell division processes were blocked, but ABA- and programmed cell death-related processes responded positively in RIL93. In contrast, the expression of cell cycle genes, ABA- and programmed cell death-related genes was relatively stable in RIL70. The results we obtained supported the working hypothesis that signaling events associated with turgor homeostasis, as established by cell wall biosynthesis regulation- and aquaporin-related genes, responded early in RIL70, which led to more efficient detoxification signaling (response to stress, protein folding, oxidation-reduction) during drought stress. This energy saving response at the early stages of drought should facilitate more cell activity under stress conditions and result in drought tolerance in RIL70.

Genome-wide comparative analysis of digital gene expression tag profiles during maize ear development

The present study profiled and analyzed gene expression of the maize ear at four key developmental stages. Based on genome-wide profile analysis, we detected differential mRNA of maize genes. Some of the differentially expressed genes (DEGs) were predicted to be potential candidates of maize ear development. Several well-known genes were found with reported mutant analyses, such as, compact plant2 (ct2), zea AGAMOUS homolog1 (zag1), bearded ear (bde), and silky1 (si1). MicroRNAs such as microRNA156 were predicted to target genes involved in maize ear development. Antisense transcripts were widespread throughout all the four stages, and are suspected to play important roles in maize ear development. Thus, identification and characterization of important genes and regulators at all the four developmental stages will contribute to an improved understanding of the molecular mechanisms responsible for maize ear development.

Effects of drought after pollination on grain yield and quality of fresh waxy maize

BACKGROUND

Waxy maize is consumed as a vegetable when harvested at fresh stage (23-26 days after pollination) in China. Fresh waxy maize is normally grown under rain-fed conditions and suffers drought frequently during plant growth. The effect of drought on grain development of fresh waxy maize is not known.

RESULTS

Two years of pot trials showed that drought decreased fresh grain number and weight, which consequently reduced fresh ear and grain yields, especially in Yunuo7. Moisture and starch contents in grains were not affected but protein content was increased under drought treatment in both varieties. Grain soluble sugar content response to drought was not affected in Suyunuo5 but was decreased in Yunuo7. Pasting and gelatinization temperatures, trough viscosity, final viscosity, setback viscosity, gelatinization enthalpy and springiness of grain were little affected by drought. Drought decreased peak viscosity, breakdown viscosity and adhesiveness (absolute value), whereas it increased hardness. The retrogradation percentage was increased in both varieties in both years.

CONCLUSION

Drought after pollination decreased the fresh waxy maize yield. Grain quality was reduced through decreased peak viscosity and adhesiveness (absolute value), while its hardness and retrogradation percentage were increased, which might be due to the increased protein content.

Identification of candidate genes for drought tolerance by whole-genome resequencing in maize

BACKGROUND

Drought stress is one of the major limiting factors for maize production. With the availability of maize B73 reference genome and whole-genome resequencing of 15 maize inbreds, common variants (CV) and clustering analyses were applied to identify non-synonymous SNPs (nsSNPs) and corresponding candidate genes for drought tolerance.

RESULTS

A total of 524 nsSNPs that were associated with 271 candidate genes involved in plant hormone regulation, carbohydrate and sugar metabolism, signaling molecules regulation, redox reaction and acclimation of photosynthesis to environment were detected by CV and cluster analyses. Most of the nsSNPs identified were clustered in bin 1.07 region that harbored six previously reported QTL with relatively high phenotypic variation explained for drought tolerance. Genes Ontology (GO) analysis of candidate genes revealed that there were 35 GO terms related to biotic stimulus and membrane-bounded organelle, showing significant differences between the candidate genes and the reference B73 background. Changes of expression level in these candidate genes for drought tolerance were detected using RNA sequencing for fertilized ovary, basal leaf meristem tissue and roots collected under drought stressed and well-watered conditions. The results indicated that 70% of candidate genes showed significantly expression changes under two water treatments and our strategies for mining candidate genes are feasible and relatively efficient.

CONCLUSIONS

Our results successfully revealed candidate nsSNPs and associated genes for drought tolerance by comparative sequence analysis of 16 maize inbred lines. Both methods we applied were proved to be efficient for identifying candidate genes for complex traits through the next-generation sequencing technologies (NGS). These selected genes will not only facilitate understanding of genetic basis of drought stress response, but also accelerate genetic improvement through marker-assisted selection in maize.

Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq

Drought stress affects cereals especially during the reproductive stage. The maize (Zea mays) drought transcriptome was studied using RNA-Seq analysis to compare drought-treated and well-watered fertilized ovary and basal leaf meristem tissue. More drought-responsive genes responded in the ovary compared with the leaf meristem. Gene Ontology enrichment analysis revealed a massive decrease in transcript abundance of cell division and cell cycle genes in the drought-stressed ovary only. Among Gene Ontology categories related to carbohydrate metabolism, changes in starch and Suc metabolism-related genes occurred in the ovary, consistent with a decrease in starch levels, and in Suc transporter function, with no comparable changes occurring in the leaf meristem. Abscisic acid (ABA)-related processes responded positively, but only in the ovaries. Related responses suggested the operation of low glucose sensing in drought-stressed ovaries. The data are discussed in the context of the susceptibility of maize kernel to drought stress leading to embryo abortion and the relative robustness of dividing vegetative tissue taken at the same time from the same plant subjected to the same conditions. Our working hypothesis involves signaling events associated with increased ABA levels, decreased glucose levels, disruption of ABA/sugar signaling, activation of programmed cell death/senescence through repression of a phospholipase C-mediated signaling pathway, and arrest of the cell cycle in the stressed ovary at 1 d after pollination. Increased invertase levels in the stressed leaf meristem, on the other hand, resulted in that tissue maintaining hexose levels at an "unstressed" level, and at lower ABA levels, which was correlated with successful resistance to drought stress.

Trehalose metabolism is activated upon chilling in grapevine and might participate in Burkholderia phytofirmans induced chilling tolerance

During the last decade, there has been growing interest in the role of trehalose metabolism in tolerance to abiotic stress in higher plants, especially cold stress. So far, this metabolism has not yet been studied in Vitis vinifera L., despite the economic importance of this crop. The goal of this paper was to investigate the involvement of trehalose metabolism in the response of grapevine to chilling stress, and to compare the response in plants bacterised with Burkholderia phytofirmans strain PsJN, a plant growth-promoting rhizobacterium that confers grapevine chilling tolerance, with mock-inoculated plants. In silico analysis revealed that the V. vinifera L. genome contains genes encoding the enzymes responsible for trehalose synthesis and degradation. Transcript analysis showed that these genes were differentially expressed in various plant organs, and we also characterised their response to chilling. Both trehalose and trehalose 6-phosphate (T6P) were present in grapevine tissues and showed a distinct pattern of accumulation upon chilling. Our results suggest a role for T6P as the main active molecule in the metabolism upon chilling, with a possible link with sucrose metabolism. Furthermore, plants colonised by B. phytofirmans and cultivated at 26°C accumulated T6P and trehalose in stems and leaves at concentrations similar to non-bacterised plants exposed to chilling temperatures for 1 day. Overall, our data suggest that T6P and trehalose accumulate upon chilling stress in grapevine and might participate in the resistance to chilling stress conferred by B. phytofirmans.

Genome-wide transcriptomic analysis of cotton under drought stress reveal significant down-regulation of genes and pathways involved in fibre elongation and up-regulation of defense responsive genes

Cotton is an important source of natural fibre used in the textile industry and the productivity of the crop is adversely affected by drought stress. High throughput transcriptomic analyses were used to identify genes involved in fibre development. However, not much information is available on cotton genome response in developing fibres under drought stress. In the present study a genome wide transcriptome analysis was carried out to identify differentially expressed genes at various stages of fibre growth under drought stress. Our study identified a number of genes differentially expressed during fibre elongation as compared to other stages. High level up-regulation of genes encoding for enzymes involved in pectin modification and cytoskeleton proteins was observed at fibre initiation stage. While a large number of genes encoding transcription factors (AP2-EREBP, WRKY, NAC and C2H2), osmoprotectants, ion transporters and heat shock proteins and pathways involved in hormone (ABA, ethylene and JA) biosynthesis and signal transduction were up-regulated and genes involved in phenylpropanoid and flavonoid biosynthesis, pentose and glucuronate interconversions and starch and sucrose metabolism pathways were down-regulated during fibre elongation. This study showed that drought has relatively less impact on fibre initiation but has profound effect on fibre elongation by down-regulating important genes involved in cell wall loosening and expansion process. The comprehensive transcriptome analysis under drought stress has provided valuable information on differentially expressed genes and pathways during fibre development that will be useful in developing drought tolerant cotton cultivars without compromising fibre quality.

The panorama of physiological responses and gene expression of whole plant of maize inbred line YQ7-96 at the three-leaf stage under water deficit and re-watering

Changes in water potential, growth elongation, photosynthesis of three-leaf-old seedlings of maize inbred line YQ7-96 under water deficit (WD) for 0.5, 1 and 2 h and re-watering (RW) for 24 h were characterized. Gene expression was analyzed using cDNA microarray covering 11,855 maize unigenes. As for whole maize plant, the expression of WD-regulated genes was characterized by up-regulation. The expression of WD-regulated genes was categorized into eight different patterns, respectively, in leaves and roots. Newly found and WD-affected cellular processes were metabolic process, amino acid and derivative metabolic process and cell death. A great number of the analyzed genes were found to be regulated specifically by RW and commonly by both WD and RW, respectively, in leaves. It is therefore concluded that (1) whole maize plant tolerance to WD, as well as growth recovery from WD, depends at least in part on transcriptional coordination between leaves and roots; (2) WD exerts effects on the maize, especially on basal metabolism; (3) WD could probably affect CO(2) uptake and partitioning, and transport of fixed carbons; (4) WD could likely influence nuclear activity and genome stability; and (5) maize growth recovery from WD is likely involved in some specific signaling pathways related to RW-specific responsive genes.

Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

BACKGROUND

Global transcriptional analysis of loblolly pine (Pinus taeda L.) is challenging due to limited molecular tools. PtGen2, a 26,496 feature cDNA microarray, was fabricated and used to assess drought-induced gene expression in loblolly pine propagule roots. Statistical analysis of differential expression and weighted gene correlation network analysis were used to identify drought-responsive genes and further characterize the molecular basis of drought tolerance in loblolly pine.

RESULTS

Microarrays were used to interrogate root cDNA populations obtained from 12 genotype × treatment combinations (four genotypes, three watering regimes). Comparison of drought-stressed roots with roots from the control treatment identified 2445 genes displaying at least a 1.5-fold expression difference (false discovery rate = 0.01). Genes commonly associated with drought response in pine and other plant species, as well as a number of abiotic and biotic stress-related genes, were up-regulated in drought-stressed roots. Only 76 genes were identified as differentially expressed in drought-recovered roots, indicating that the transcript population can return to the pre-drought state within 48 hours. Gene correlation analysis predicts a scale-free network topology and identifies eleven co-expression modules that ranged in size from 34 to 938 members. Network topological parameters identified a number of central nodes (hubs) including those with significant homology (E-values ≤ 2 × 10-30) to 9-cis-epoxycarotenoid dioxygenase, zeatin O-glucosyltransferase, and ABA-responsive protein. Identified hubs also include genes that have been associated previously with osmotic stress, phytohormones, enzymes that detoxify reactive oxygen species, and several genes of unknown function.

CONCLUSION

PtGen2 was used to evaluate transcriptome responses in loblolly pine and was leveraged to identify 2445 differentially expressed genes responding to severe drought stress in roots. Many of the genes identified are known to be up-regulated in response to osmotic stress in pine and other plant species and encode proteins involved in both signal transduction and stress tolerance. Gene expression levels returned to control values within a 48-hour recovery period in all but 76 transcripts. Correlation network analysis indicates a scale-free network topology for the pine root transcriptome and identifies central nodes that may serve as drivers of drought-responsive transcriptome dynamics in the roots of loblolly pine.

Trehalose and plant stress responses: friend or foe?

The disaccharide trehalose is involved in stress response in many organisms. However, in plants, its precise role remains unclear, although some data indicate that trehalose has a protective role during abiotic stresses. By contrast, some trehalose metabolism mutants exhibit growth aberrations, revealing potential negative effects on plant physiology. Contradictory effects also appear under biotic stress conditions. Specifically, trehalose is essential for the infectivity of several pathogens but at the same time elicits plant defense. Here, we argue that trehalose should not be regarded only as a protective sugar but rather like a double-faced molecule and that further investigation is required to elucidate its exact role in stress tolerance in plants.

Differential gene expression analysis of maize leaf at heading stage in response to water-deficit stress

The whole-genomic gene-expression changes of maize (Zea mays L.) plants in response to water-deficit stress at the heading stage have not been previously studied. The present work utilized a maize oligonucleotide array ('57K', approximately 57000 sequences; http://www.maizearray.org/) representing more than 30000 unique genes, to profile transcriptome changes in maize leaves subjected to 1d (day) and 7d water-deficit stress. After 1d and 7d water-stress treatment, 195 and 1008 differential genes were identified respectively. One-third of 1d-water-stress-induced genes had known or putative functions in various cellular signalling pathways, indicating that signal-transduction-related genes play important roles in the early responses of maize leaves to water stress. The 7d-stress-regulated genes were involved in a broad range of cellular and biochemical activities. The most notable genes may function in compatible osmolyte metabolism, particularly in proline, sucrose, trehalose and raffinose metabolism in the leaves. The present study provided a valuable starting point for further elucidation of molecular mechanisms in the drought tolerance of maize plants.