Examining the drought stress transcriptome in cotton leaf and root tissue

Terpene synthase TgHPTPS2 from Torreya grandis modulates terpenoid profiles to balance ROS and confer drought tolerance in plants

Drought stress is a significant environmental constraint that hampers plant growth and productivity, largely due to oxidative damage caused by excessive reactive oxygen species (ROS) accumulation. Terpenoids, a class of essential secondary metabolites, are essential in alleviating oxidative stress by regulating ROS homeostasis. However, the molecular mechanisms by which terpenoid metabolism enhances drought tolerance remain unclear. Herein, we characterized TgHPTPS2, a hypothetical terpene synthase gene from Torreya grandis, which is transcriptionally upregulated in response to drought stress. The ectopic expression of TgHPTPS2 in Arabidopsis thaliana resulted in enhanced drought tolerance, characterized by improved ROS scavenging capacity and greater root system development. Targeted metabolomics revealed that TgHPTPS2 alters terpenoid metabolism, resulting in reduced ROS levels in transgenic lines. Furthermore, dual-luciferase reporter and yeast one-hybrid assays revealed that TgMYB12, a drought-inducible transcription factor, directly binds to the TgHPTPS2 promoter and inhibits its expression. These findings designate TgHPTPS2 as a crucial regulatory component in terpenoid-mediated drought tolerance and offer a new perspective on the transcriptional regulation of terpenoid biosynthesis in response to abiotic stress.

Crop Root Responses to Drought Stress: Molecular Mechanisms, Nutrient Regulations, and Interactions with Microorganisms in the Rhizosphere

Roots play important roles in determining crop development under drought. Under such conditions, the molecular mechanisms underlying key responses and interactions with the rhizosphere in crop roots remain limited compared with model species such as Arabidopsis. This article reviews the molecular mechanisms of the morphological, physiological, and metabolic responses to drought stress in typical crop roots, along with the regulation of soil nutrients and microorganisms to these responses. Firstly, we summarize how root growth and architecture are regulated by essential genes and metabolic processes under water-deficit conditions. Secondly, the functions of the fundamental plant hormone, abscisic acid, on regulating crop root growth under drought are highlighted. Moreover, we discuss how the responses of crop roots to altered water status are impacted by nutrients, and vice versa. Finally, this article explores current knowledge of the feedback between plant and soil microbial responses to drought and the manipulation of rhizosphere microbes for improving the resilience of crop production to water stress. Through these insights, we conclude that to gain a more comprehensive understanding of drought adaption mechanisms in crop roots, future studies should have a network view, linking key responses of roots with environmental factors.

Transcriptome and DNA methylome provide insights into the molecular regulation of drought stress in sea buckthorn

Sea buckthorn is a typical drought-resistant tree species. However, there is a general lack of understanding of the pattern of DNA methylation linked with sea buckthorn responses to drought, and its relationship with drought tolerance mechanisms. In this study, we performed whole-transcriptome RNA sequencing and methylome sequencing in response to drought stress to explore differentially expressed mRNAs, miRNAs, lncRNAs and circRNAs in sea buckthorn leaves. Based on predicted DE pairs, we constructed a competitive endogenous RNA network, which revealed potential transcriptional regulatory roles in response to drought stress. The results of methylome sequencing revealed that the DNA methylation level was increased in sea buckthorn leaves under drought stress. We identified 13,405 differentially methylated regions between CK and TR. We found one DMR-associated DEG (Vacuolar-sorting receptor 6) involved in the ABA accumulation pathway. In addition, two DNA methyltransferases (HrMET1 and HrDRM1) were closely associated with drought-induced hypermethylation in sea buckthorn. Together, we firstly conducted a comprehensive transcriptomic and epigenetic analysis of sea buckthorn under drought stress, providing a resource for further study of the potential functions of genes, miRNAs, lncRNAs, circRNAs and DNA methyltransferases.

Transcriptomic Analysis Reveals Regulatory Networks for Osmotic Water Stress and Rewatering Response in the Leaves of Ginkgo biloba

To elucidate the transcriptomic regulation mechanisms that underlie the response of Ginkgo biloba to dehydration and rehydration, we used ginkgo saplings exposed to osmotically driven water stress and subsequent rewatering. When compared with a control group, 137, 1453, 1148, and 679 genes were differentially expressed in ginkgo leaves responding to 2, 6, 12, and 24 h of water deficit, and 796 and 1530 genes were differentially expressed responding to 24 and 48 h of rewatering. Upregulated genes participated in the biosynthesis of abscisic acid, eliminating reactive oxygen species (ROS), and biosynthesis of flavonoids and bilobalide, and downregulated genes were involved in water transport and cell wall enlargement in water stress-treated ginkgo leaves. Under rehydration conditions, the genes associated with water transport and cell wall enlargement were upregulated, and the genes that participated in eliminating ROS and the biosynthesis of flavonoids and bilobalide were downregulated in the leaves of G. biloba. Furthermore, the weighted gene coexpression networks were established and correlated with distinct water stress and rewatering time-point samples. Hub genes that act as key players in the networks were identified. Overall, these results indicate that the gene coexpression networks play essential roles in the transcriptional reconfiguration of ginkgo leaves in response to water stress and rewatering.

Crosstalk between phytohormones and secondary metabolites in the drought stress tolerance of crop plants: A review

Drought stress negatively affects crop performance and weakens global food security. It triggers the activation of downstream pathways, mainly through phytohormones homeostasis and their signaling networks, which further initiate the biosynthesis of secondary metabolites (SMs). Roots sense drought stress, the signal travels to the above-ground tissues to induce systemic phytohormones signaling. The systemic signals further trigger the biosynthesis of SMs and stomatal closure to prevent water loss. SMs primarily scavenge reactive oxygen species (ROS) to protect plants from lipid peroxidation and also perform additional defense-related functions. Moreover, drought-induced volatile SMs can alert the plant tissues to perform drought stress mitigating functions in plants. Other phytohormone-induced stress responses include cell wall and cuticle thickening, root and leaf morphology alteration, and anatomical changes of roots, stems, and leaves, which in turn minimize the oxidative stress, water loss, and other adverse effects of drought. Exogenous applications of phytohormones and genetic engineering of phytohormones signaling and biosynthesis pathways mitigate the drought stress effects. Direct modulation of the SMs biosynthetic pathway genes or indirect via phytohormones' regulation provides drought tolerance. Thus, phytohormones and SMs play key roles in plant development under the drought stress environment in crop plants.

Coordinated mechanisms of leaves and roots in response to drought stress underlying full-length transcriptome profiling in Vicia sativa L

BACKGROUND

Common vetch (Vicia sativa L.) is an important self-pollinating annual forage legume and is of interest for drought prone regions as a protein source to feed livestock and human consumption. However, the development and production of common vetch are negatively affected by drought stress. Plants have evolved common or distinct metabolic pathways between the aboveground and underground in response to drought stress. Little is known regarding the coordinated response of aboveground and underground tissues of common vetch to drought stress.

RESULTS

Our results showed that a total of 30,427 full-length transcripts were identified in 12 samples, with an average length of 2278.89 bp. Global transcriptional profiles of the above 12 samples were then analysed via Illumina-Seq. A total of 3464 and 3062 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. Gene Ontology (GO) enrichment analyses identified that the dehydrin genes and Δ¹-pyrroline-5-carboxylate synthase were induced for the biosynthesis of proline and water conservation. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results indicated that the DEGs were significantly enriched in hormone signal transduction, starch and sucrose metabolism, and arginine and proline metabolism, and various drought response candidate genes were also identified. Abscisic acid (ABA; the AREB/ABF-SnRK2 pathway) regulates the activity of AMY3 and BAM1 to induce starch degradation in leaves and increase carbon export to roots, which may be associated with the drought stress responses in common vetch. Among the co-induced transcription factors (TFs), AREB/ABF, bHLH, MYB, WRKY, and AP2/ERF had divergent expression patterns and may be key in the crosstalk between leaves and roots during adaption to drought stress. In transgenic yeast, the overexpression of four TFs increased yeast tolerance to osmotic stresses.

CONCLUSION

The multipronged approach identified in the leaves and roots broadens our understanding of the coordinated mechanisms of drought response in common vetch, and further provides targets to improve drought resistance through genetic engineering.

Physiological and transcriptomic responses of reproductive stage soybean to drought stress

KEY MESSAGE

The dynamic alterations of the physiological and molecular processes in reproductive stage soybean indicated the dramatic impact caused by drought. Drought is a major abiotic stress that limits soybean (Glycine max) production. Most prior studies were focused on either model species or crops that are at their vegetative stages. It is known that the reproductive stage of soybean is more susceptible to drought. Therefore, an understanding on the responsive mechanisms during this stage will not only be important for basic plant physiology, but the knowledge can also be used for crop improvement via either genetic engineering or molecular breeding. In this study, physiological measurements and RNA-Seq analysis were used to dissect the metabolic alterations and molecular responses in the leaves of soybean grown at drought condition. Photosynthesis rate, stomata conductance, transpiration, and water potential were reduced. The activities of SOD and CAT were increased, while the activity of POD stayed unchanged. A total of 2771 annotated genes with at least twofold changes were found to be differentially expressed in the drought-stressed plants in which 1798 genes were upregulated and 973 were downregulated. Via KEGG analysis, these genes were assigned to multiple molecular pathways, including ABA biogenesis, compatible compound accumulation, secondary metabolite synthesis, fatty acid desaturation, plant transcription factors, etc. The large number of differentially expressed genes and the diverse pathways indicated that soybean employs complicated mechanisms to cope with drought. Some of the identified genes and pathways can be used as targets for genetic engineering or molecular breeding to improve drought resistance in soybean.

Single-base resolution methylomes of upland cotton (Gossypium hirsutum L.) reveal epigenome modifications in response to drought stress

BACKGROUND

DNA methylation, with a cryptic role in genome stability, gene transcription and expression, is involved in the drought response process in plants, but the complex regulatory mechanism is still largely unknown.

RESULTS

Here, we performed whole-genome bisulfite sequencing (WGBS) and identified long non-coding RNAs on cotton leaves under drought stress and re-watering treatments. We obtained 31,223 and 30,997 differentially methylated regions (representing 2.48% of the genome) after drought stress and re-watering treatments, respectively. Our data also showed that three sequence contexts, including ^mCpG, ^mCHG, ^mCHH, all presented a hyper-methylation pattern under drought stress and were nearly restored to normal levels after the re-watering treatment. Among all the methylation variations, asymmetric CHH methylation was the most consistent with external environments, suggesting that methylation/demethylation in a CHH context may constitute a novel epigenetic modification in response to drought stress. Combined with the targets of long non-coding RNAs, we found that long non-coding RNAs may mediate variations in methylation patterns by splicing into microRNAs. Furthermore, the many hormone-related genes with methylation variations suggested that plant hormones might be a potential mechanism in the drought response.

CONCLUSIONS

Future crop-improvement strategies may benefit by taking into account not only the DNA genetic variations in cotton varieties but also the epigenetic modifications of the genome.

Proteomic responses of drought-tolerant and drought-sensitive cotton varieties to drought stress

Drought, one of the most widespread factors reducing agricultural crop productivity, affects biological processes such as development, architecture, flowering and senescence. Although protein analysis techniques and genome sequencing have made facilitated the proteomic study of cotton, information on genetic differences associated with proteomic changes in response to drought between different cotton genotypes is lacking. To determine the effects of drought stress on cotton seedlings, we used two-dimensional polyacrylamide gel electrophoresis (2-DE) and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry to comparatively analyze proteome of drought-responsive proteins during the seedling stage in two cotton (Gossypium hirsutum L.) cultivars, drought-tolerant KK1543 and drought-sensitive Xinluzao26. A total of 110 protein spots were detected on 2-DE maps, of which 56 were identified by MALDI-TOF and MALDI-TOF/TOF mass spectrometry. The identified proteins were mainly associated with metabolism (46.4 %), antioxidants (14.2 %), and transport and cellular structure (23.2 %). Some key proteins had significantly different expression patterns between the two genotypes. In particular, 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase, UDP-D-glucose pyrophosphorylase and ascorbate peroxidase were up-regulated in KK1543 compared with Xinluzao26. Under drought stress conditions, the vacuolar H(+)-ATPase catalytic subunit, a 14-3-3g protein, translation initiation factor 5A and pathogenesis-related protein 10 were up-regulated in KK1543, whereas ribosomal protein S12, actin, cytosolic copper/zinc superoxide dismutase, protein disulfide isomerase, S-adenosylmethionine synthase and cysteine synthase were down-regulated in Xinluzao26. This work represents the first characterization of proteomic changes that occur in response to drought in roots of cotton plants. These differentially expressed proteins may be related to biochemical pathways responsible for drought tolerance in KK1543. Although further studies are needed, this proteomic analysis underlines the role of post-translational events. The differentially expressed proteins and their corresponding genes may be used as markers for the breeding of drought tolerance in cotton.

Genome-wide transcriptomic comparison of cotton (Gossypium herbaceum) leaf and root under drought stress

In this study, the 454 pyrosequencing platform was used for analyzing the comparative transcriptomic profiles of leaf and root tissues of 1-month-old cotton (Gossypium herbaceum) plants under drought stress. A total of 56,354 and 49,308 reads were generated from leaf and root tissues, respectively, and clustered into 6,313 and 5,858 unigenes. The differentially expressed unigenes that showed up-regulation (≥2-fold) or down-regulation (2≤-fold) were considered for further analysis. A total of 3,517 unigenes were differentially expressed in both tissues. The 1,528 genes specific to leaves and 1,128 specific to roots were obtained. The 28 biological pathways in two tissues were found to respond significantly to drought stress. A total of 289 in leaf and 277 in root unknown (novel) unigenes were found to be remarkably regulated by drought stress. Some key regulatory genes involved in abiotic stress such as WRKY, ERF, AP2 EREBP, MYB, and LEA were highly expressed in leaves. The genes RHD3, LBD, and transcription factor WRKY75, known for root development under various stress conditions, were expressed specifically in root. The genes related to chlorophyll a/b binding protein and photosystem-related proteins showed significant higher expression in roots and as compared to leaves. It can be concluded that cotton leaves are distinct from roots in terms of molecular mechanisms for responses to drought stress.

Toward Coalescing Gene Expression and Function with QTLs of Water-Deficit Stress in Cotton

Cotton exhibits moderately high vegetative tolerance to water-deficit stress but lint production is restricted by the available rainfed and irrigation capacity. We have described the impact of water-deficit stress on the genetic and metabolic control of fiber quality and production. Here we examine the association of tentative consensus sequences (TCs) derived from various cotton tissues under irrigated and water-limited conditions with stress-responsive QTLs. Three thousand sixteen mapped sequence-tagged-sites were used as anchored targets to examine sequence homology with 15,784 TCs to test the hypothesis that putative stress-responsive genes will map within QTLs associated with stress-related phenotypic variation more frequently than with other genomic regions not associated with these QTLs. Approximately 1,906 of 15,784 TCs were mapped to the consensus map. About 35% of the annotated TCs that mapped within QTL regions were genes involved in an abiotic stress response. By comparison, only 14.5% of the annotated TCs mapped outside these QTLs were classified as abiotic stress genes. A simple binomial probability calculation of this degree of bias being observed if QTL and non-QTL regions are equally likely to contain stress genes was P (x ≥ 85) = 7.99  × 10(-15). These results suggest that the QTL regions have a higher propensity to contain stress genes.

Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

Next-generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required to make these data amenable to functional genomics analyses. The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences. It uses the MapMan 'BIN' ontology, which is tailored for functional annotation of plant 'omics' data. The classification procedure performs parallel sequence searches against reference databases, compiles the results and computes the most likely MapMan BINs for each query. In the current version, the pipeline relies on manually curated reference classifications originating from the three reference organisms (Arabidopsis, Chlamydomonas, rice), various other plant species that have a reviewed SwissProt annotation, and more than 2000 protein domain and family profiles at InterPro, CDD and KOG. Functional annotations predicted by Mercator achieve accuracies above 90% when benchmarked against manual annotation. In addition to mapping files for direct use in the visualization software MapMan, Mercator provides graphical overview charts, detailed annotation information in a convenient web browser interface and a MapMan-to-GO translation table to export results as GO terms. Mercator is available free of charge via http://mapman.gabipd.org/web/guest/app/Mercator.

RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress

An RNA-Seq experiment was performed using field grown well-watered and naturally rain fed cotton plants to identify differentially expressed transcripts under water-deficit stress. Our work constitutes the first application of the newly published diploid D5 Gossypium raimondii sequence in the study of tetraploid AD1 upland cotton RNA-seq transcriptome analysis. A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed root tissues, in patterns that confirm the accuracy of this technique for future studies in cotton genomics. Additionally, putative sequence based genome localization of differentially expressed transcripts detected A2 genome specific gene expression under water-deficit stress. These data will facilitate efforts to understand the complex responses governing transcriptomic regulatory mechanisms and to identify candidate genes that may benefit applied plant breeding programs.

Transcriptome characterization and sequencing-based identification of drought-responsive genes in potato

Potato (Solanum tubersosum L.) is relatively vulnerable to abiotic stress conditions such as drought, but the tolerance mechanisms to such stress in potato are largely unknown. To gain insight into the transcriptome dynamics that are associated with drought stress, genome-wide gene expression profile was conducted by Solexa sequencing to generate a large dataset and a comprehensive transcriptome profile for potato. Here, we report a reference for the potato transcriptome using leaf tissues under drought-stressed condition from a local potato cultivar 'Longshu 3'. Analysis of 86,965,482 RNA-Seq reads permitted the detection and quantification of expression levels of 7,284 genes at transcriptional levels, among them, 6,754 genes were enriched in draught-treated leaves while 6,419 in control. We identified 842 drought-responsive up-regulated and 494 down-regulated candidate genes with significantly differentially expression under continued drought stress treatments. Those differently expressed genes were mostly enriched in 89 gene categories and 21 KEGG pathways. Drought-stressed leaves had increased expression of genes involved in stress response compared with control leaves. A subset of differentially expressed genes associated with drought response was examined using quantitative real-time PCR. These results provide a broad spectrum of candidate genes that are essential for understanding the molecular regulation of potato in response to abiotic stresses.

A receptor-like kinase gene (GbRLK) from Gossypium barbadense enhances salinity and drought-stress tolerance in Arabidopsis

BACKGROUND

Cotton (Gossypium spp.) is widely cultivated due to the important economic value of its fiber. However, extreme environmental degradation impedes cotton growth and production. Receptor-like kinase (RLK) proteins play important roles in signal transduction and participate in a diverse range of processes in response to plant hormones and environmental cues. Here, we introduced an RLK gene (GbRLK) from cotton into Arabidopsis and investigated its role in imparting abiotic stress tolerance.

RESULTS

GbRLK transcription was induced by exogenously supplied abscisic acid (ABA), salicylic acid, methyl jasmonate, mock drought conditions and high salinity. We cloned the promoter sequence of this gene via self-formed adaptor PCR. Sequence analysis revealed that the promoter region contains many cis-acting stress-responsive elements such as ABRE, W-Box, MYB-core, W-Box core, TCA-element and others. We constructed a vector containing a 1,890-bp sequence in the 5' region upstream of the initiation codon of this promoter and transformed it into Arabidopsis thaliana. GUS histochemical staining analysis showed that GbRLK was expressed mainly in leaf veins, petioles and roots of transgenic Arabidopsis, but not in the cotyledons or root hairs. GbRLK promoter activity was induced by ABA, PEG, NaCl and Verticillium dahliae. Transgenic Arabidopsis with constitutive overexpression of GbRLK exhibited a reduced rate of water loss in leaves in vitro, along with improved salinity and drought tolerance and increased sensitivity to ABA compared with non-transgenic Col-0 Arabidopsis. Expression analysis of stress-responsive genes in GbRLK Arabidopsis revealed that there was increased expression of genes involved in the ABA-dependent signaling pathway (AtRD20, AtRD22 and AtRD26) and antioxidant genes (AtCAT1, AtCCS, AtCSD2 and AtCSD1) but not ion transporter genes (AtNHX1, AtSOS1).

CONCLUSIONS

GbRLK is involved in the drought and high salinity stresses pathway by activating or participating in the ABA signaling pathway. Overexpression of GbRLK may improve stress tolerance by regulating stress-responsive genes to reduce water loss. GbRLK may be employed in the genetic engineering of novel cotton cultivars in the future. Further studying of GbRLK will help elucidate abiotic stress signaling pathways.

Understanding the molecular events underpinning cultivar differences in the physiological performance and heat tolerance of cotton (Gossypium hirsutum)

Diurnal or prolonged exposure to air temperatures above the thermal optimum for a plant can impair physiological performance and reduce crop yields. This study investigated the molecular response to heat stress of two high-yielding cotton (Gossypium hirsutum L.) cultivars with contrasting heat tolerance. Using global gene profiling, 575 of 21854 genes assayed were affected by heat stress, ~60% of which were induced. Genes encoding heat shock proteins, transcription factors and protein cleavage enzymes were induced, whereas genes encoding proteins associated with electron flow, photosynthesis, glycolysis, cell wall synthesis and secondary metabolism were generally repressed under heat stress. Cultivar differences for the expression profiles of a subset of heat-responsive genes analysed using quantitative PCR over a 7-h heat stress period were associated with expression level changes rather than the presence or absence of transcripts. Expression differences reflected previously determined differences for yield, photosynthesis, electron transport rate, quenching, membrane integrity and enzyme viability under growth cabinet and field-generated heat stress, and may explain cultivar differences in leaf-level heat tolerance. This study provides a platform for understanding the molecular changes associated with the physiological performance and heat tolerance of cotton cultivars that may aid breeding for improved performance in warm and hot field environments.

Dimensionality reduction for microarray data using local mean based discriminant analysis

A new method is proposed for finding a low dimensional subspace of high dimensional microarray data. We developed a new criterion for constructing the weight matrix by using local neighborhood information to discover the intrinsic discriminant structure in the data. Also this approach applies regularized least square technique to extract relevant features. We assess the performance of the proposed methodology by applying it to four publicly available tumor datasets. In a low dimensional subspace, the proposed method classified these tumors accurately and reliably. Also, through a comparison study, we verify the reliability of the dimensionality reduction and discrimination results.

Genome-wide identification of differentially expressed genes under water deficit stress in upland cotton (Gossypium hirsutum L.)

BACKGROUND

Cotton is the world's primary fiber crop and is a major agricultural commodity in over 30 countries. Like many other global commodities, sustainable cotton production is challenged by restricted natural resources. In response to the anticipated increase of agricultural water demand, a major research direction involves developing crops that use less water or that use water more efficiently. In this study, our objective was to identify differentially expressed genes in response to water deficit stress in cotton. A global expression analysis using cDNA-Amplified Fragment Length Polymorphism was conducted to compare root and leaf gene expression profiles from a putative drought resistant cotton cultivar grown under water deficit stressed and well watered field conditions.

RESULTS

We identified a total of 519 differentially expressed transcript derived fragments. Of these, 147 transcript derived fragment sequences were functionally annotated according to their gene ontology. Nearly 70 percent of transcript derived fragments belonged to four major categories: 1) unclassified, 2) stress/defense, 3) metabolism, and 4) gene regulation. We found heat shock protein-related and reactive oxygen species-related transcript derived fragments to be among the major parts of functional pathways induced by water deficit stress. Also, twelve novel transcripts were identified as both water deficit responsive and cotton specific. A subset of differentially expressed transcript derived fragments was verified using reverse transcription-polymerase chain reaction. Differential expression analysis also identified five pairs of duplicated transcript derived fragments in which four pairs responded differentially between each of their two homologues under water deficit stress.

CONCLUSIONS

In this study, we detected differentially expressed transcript derived fragments from water deficit stressed root and leaf tissues in tetraploid cotton and provided their gene ontology, functional/biological distribution, and possible roles of gene duplication. This discovery demonstrates complex mechanisms involved with polyploid cotton's transcriptome response to naturally occurring field water deficit stress. The genes identified in this study will provide candidate targets to manipulate the water use characteristics of cotton at the molecular level.

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.