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      Transcriptomic analysis reveals the differentially expressed genes and pathways involved in drought tolerance in pearl millet [ Pennisetum glaucum (L.) R. Br]

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          Abstract

          Pearl millet is a cereal crop known for its high tolerance to drought, heat and salinity stresses as well as for its nutritional quality. The molecular mechanism of drought tolerance in pearl millet is unknown. Here we attempted to unravel the molecular basis of drought tolerance in two pearl millet inbred lines, ICMB 843 and ICMB 863 using RNA sequencing. Under greenhouse condition, ICMB 843 was found to be more tolerant to drought than ICMB 863. We sequenced the root transcriptome from both lines under control and drought conditions using an Illumina Hi-Seq platform, generating 139.1 million reads. Mapping of sequenced reads against the foxtail millet genome, which has been relatively well-annotated, led to the identification of several differentially expressed genes under drought stress. Total of 6799 and 1253 differentially expressed genes were found in ICMB 843 and ICMB 863, respectively. Pathway and gene function analysis by KEGG online tool revealed that the drought response in pearl millet is mainly regulated by pathways related to photosynthesis, plant hormone signal transduction and mitogen-activated protein kinase signaling. The changes in expression of drought-responsive genes determined by RNA sequencing were confirmed by reverse-transcription PCR for 7 genes. These results are a first step to understanding the molecular mechanisms of drought tolerance in pearl millet and lay a foundation for its genetic improvement.

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          Drought and Salt Tolerance in Plants

          Ramanjulu Sunkar, Dorothea Bartels (2005)
          Article 0 comments Cited 576 times – based on 0 reviews     Review now
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            Photosynthesis and drought: can we make metabolic connections from available data?

            C Pinheiro, M M Chaves (2011)
            Photosynthesis is one of the key processes to be affected by water deficits, via decreased CO2 diffusion to the chloroplast and metabolic constraints. The relative impact of those limitations varies with the intensity of the stress, the occurrence (or not) of superimposed stresses, and the species we are dealing with. Total plant carbon uptake is further reduced due to the concomitant or even earlier inhibition of growth. Leaf carbohydrate status, altered directly by water deficits or indirectly (via decreased growth), acts as a metabolic signal although its role is not totally clear. Other relevant signals acting under water deficits comprise: abscisic acid (ABA), with an impact on stomatal aperture and the regulation at the transcription level of a large number of genes related to plant stress response; other hormones that act either concurrently (brassinosteroids, jasmonates, and salycilic acid) or antagonistically (auxin, cytokinin, or ethylene) with ABA; and redox control of the energy balance of photosynthetic cells deprived of CO2 by stomatal closure. In an attempt to systematize current knowledge on the complex network of interactions and regulation of photosynthesis in plants subjected to water deficits, a meta-analysis has been performed covering >450 papers published in the last 15 years. This analysis shows the interplay of sugars, reactive oxygen species (ROS), and hormones with photosynthetic responses to drought, involving many metabolic events. However, more significantly it highlights (i) how fragmented and often non-comparable the results are and (ii) how hard it is to relate molecular events to plant physiological status, namely photosynthetic activity, and to stress intensity. Indeed, the same data set usually does not integrate these different levels of analysis. Considering these limitations, it was hard to find a general trend, particularly concerning molecular responses to drought, with the exception of the genes ABI1 and ABI3. These genes, irrespective of the stress type (acute versus chronic) and intensity, show a similar response to water shortage in the two plant systems analysed (Arabidopsis and barley). Both are associated with ABA-mediated metabolic responses to stress and the regulation of stomatal aperture. Under drought, ABI1 transcription is up-regulated while ABI3 is usually down-regulated. Recently ABI3 has been hypothesized to be essential for successful drought recovery.
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              Abscisic Acid and abiotic stress signaling.

              Narendra Tuteja (2007)
              Abiotic stress is severe environmental stress, which impairs crop production on irrigated land worldwide. Overall, the susceptibility or tolerance to the stress in plants is a coordinated action of multiple stress responsive genes, which also cross-talk with other components of stress signal transduction pathways. Plant responses to abiotic stress can be determined by the severity of the stress and by the metabolic status of the plant. Abscisic acid (ABA) is a phytohormone critical for plant growth and development and plays an important role in integrating various stress signals and controlling downstream stress responses. Plants have to adjust ABA levels constantly in responce to changing physiological and environmental conditions. To date, the mechanisms for fine-tuning of ABA levels remain elusive. The mechanisms by which plants respond to stress include both ABA-dependent and ABA-independent processes. Various transcription factors such as DREB2A/2B, AREB1, RD22BP1 and MYC/MYB are known to regulate the ABA-responsive gene expression through interacting with their corrosponding cis-acting elements such as DRE/CRT, ABRE and MYCRS/MYBRS, respectively. Understanding these mechanisms is important to improve stress tolerance in crops plants. This article first describes the general pathway for plant stress response followed by roles of ABA and transcription factors in stress tolerance including the regulation of ABA biosynthesis.
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                Author and article information

                Contributors
                Ambika Dudhate: Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Harshraj Shinde: Role: Data curationRole: Formal analysisRole: MethodologyRole: SoftwareRole: Validation
                Daisuke Tsugama: Role: ValidationRole: Writing – review & editing
                Shenkui Liu: Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: ResourcesRole: Writing – review & editing
                Tetsuo Takano:
                ORCID: http://orcid.org/0000-0003-0811-8006
                Role: ConceptualizationRole: Funding acquisitionRole: Supervision
                Rattan Singh Yadav: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, CA USA )
                ISSN (Electronic): 1932-6203
                Publication date (Electronic): 13 April 2018
                Publication date Collection: 2018
                Volume: 13
                Issue: 4
                Electronic Location Identifier: e0195908
                Affiliations
                [1 ] Asian Natural Environmental Science Center (ANESC), the University of Tokyo, Nishitokyo-shi, Tokyo, Japan
                [2 ] Hokkaido University, Hokkaido, Japan
                [3 ] State Key Laboratory of Subtropical Silviculture, Zhejiang A and F University, Lin’an, Hangzhou, China
                Aberystwyth University, UNITED KINGDOM
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0003-0811-8006
                Article
                Publisher ID: PONE-D-18-00307
                DOI: 10.1371/journal.pone.0195908
                PMC ID: 5898751
                PubMed ID: 29652907
                SO-VID: 81219657-c00c-44d2-ac1a-5aad7f48d6b1
                Copyright © © 2018 Dudhate et al
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 4 January 2018
                Date accepted : 2 April 2018
                Page count
                Figures: 7, Tables: 2, Pages: 14
                Funding
                The authors received no specific funding for this work.
                Categories
                Subject: Research Article
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Eukaryota
                Subject: Plants
                Subject: Grasses
                Subject: Millet
                Subject: Biology and Life Sciences
                Subject: Agriculture
                Subject: Crop Science
                Subject: Crops
                Subject: Cereal Crops
                Subject: Biology and Life Sciences
                Subject: Plant Science
                Subject: Plant Physiology
                Subject: Plant Defenses
                Subject: Plant Resistance to Abiotic Stress
                Subject: Drought Adaptation
                Subject: Biology and Life Sciences
                Subject: Plant Science
                Subject: Plant Pathology
                Subject: Plant Resistance to Abiotic Stress
                Subject: Drought Adaptation
                Subject: Biology and Life Sciences
                Subject: Ecology
                Subject: Plant Ecology
                Subject: Plant-Environment Interactions
                Subject: Plant Resistance to Abiotic Stress
                Subject: Drought Adaptation
                Subject: Ecology and Environmental Sciences
                Subject: Ecology
                Subject: Plant Ecology
                Subject: Plant-Environment Interactions
                Subject: Plant Resistance to Abiotic Stress
                Subject: Drought Adaptation
                Subject: Biology and Life Sciences
                Subject: Plant Science
                Subject: Plant Ecology
                Subject: Plant-Environment Interactions
                Subject: Plant Resistance to Abiotic Stress
                Subject: Drought Adaptation
                Subject: Biology and Life Sciences
                Subject: Plant Science
                Subject: Plant Physiology
                Subject: Plant Defenses
                Subject: Plant Resistance to Abiotic Stress
                Subject: Biology and Life Sciences
                Subject: Plant Science
                Subject: Plant Pathology
                Subject: Plant Resistance to Abiotic Stress
                Subject: Biology and Life Sciences
                Subject: Ecology
                Subject: Plant Ecology
                Subject: Plant-Environment Interactions
                Subject: Plant Resistance to Abiotic Stress
                Subject: Ecology and Environmental Sciences
                Subject: Ecology
                Subject: Plant Ecology
                Subject: Plant-Environment Interactions
                Subject: Plant Resistance to Abiotic Stress
                Subject: Biology and Life Sciences
                Subject: Plant Science
                Subject: Plant Ecology
                Subject: Plant-Environment Interactions
                Subject: Plant Resistance to Abiotic Stress
                Subject: Biology and life sciences
                Subject: Cell biology
                Subject: Signal transduction
                Subject: Cell signaling
                Subject: Signaling cascades
                Subject: MAPK signaling cascades
                Subject: Ecology and Environmental Sciences
                Subject: Drought
                Subject: Biology and Life Sciences
                Subject: Cell Biology
                Subject: Signal Transduction
                Subject: Cell Signaling
                Subject: Signaling Cascades
                Subject: Stress Signaling Cascade
                Subject: Biology and life sciences
                Subject: Molecular biology
                Subject: Molecular biology techniques
                Subject: Sequencing techniques
                Subject: RNA sequencing
                Subject: Research and analysis methods
                Subject: Molecular biology techniques
                Subject: Sequencing techniques
                Subject: RNA sequencing
                Custom metadata
                Data Availability DATA in FASTQ format were submitted to SRA (Sequence read archive), NCBI (Bio project Id: PRJNA419859). The raw reads can be accessed with accession number SRR6327851 to SRR6327856 for control samples and SRR6327857 to SRR6327862 for drought-stressed samples.

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                ScienceOpen disciplines: Uncategorized

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