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Transcriptomic Signature Of Drought Response In Pearl Millet (Pennisetum Glaucum (L.) And Development Of Web-genomic Resources

Sarika Jaiswal, Tushar J. Antala, M. K. Mandavia, Meenu Chopra, Rahul Singh Jasrotia, Rukam Singh Tomar, Jashminkumar Kheni, U. B. Angadi, Mir Asif Iquebal, B. A. Golakia, Anil Rai, Dinesh Kumar
Published 2018 · Medicine, Biology
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Pearl millet, (Pennisetum glaucum L.), an efficient (C4) crop of arid/semi-arid regions is known for hardiness. Crop is valuable for bio-fortification combating malnutrition and diabetes, higher caloric value and wider climatic resilience. Limited studies are done in pot-based experiments for drought response at gene-expression level, but field-based experiment mimicking drought by withdrawal of irrigation is still warranted. We report de novo assembly-based transcriptomic signature of drought response induced by irrigation withdrawal in pearl millet. We found 19983 differentially expressed genes, 7595 transcription factors, gene regulatory network having 45 hub genes controlling drought response. We report 34652 putative markers (4192 simple sequence repeats, 12111 SNPs and 6249 InDels). Study reveals role of purine and tryptophan metabolism in ABA accumulation mediating abiotic response in which MAPK acts as major intracellular signal sensing drought. Results were validated by qPCR of 13 randomly selected genes. We report the first web-based genomic resource ( which can be used for candidate genes-based SNP discovery programs and trait-based association studies. Looking at climatic change, nutritional and pharmaceutical importance of this crop, present investigation has immense value in understanding drought response in field condition. This is important in germplasm management and improvement in endeavour of pearl millet productivity.
This paper references
ABA-Mediated ROS in Mitochondria Regulate Root Meristem Activity by Controlling PLETHORA Expression in Arabidopsis
Li Yang (2014)
Living with water stress: evolution of osmolyte systems.
Paul H Yancey (1982)
Seedling root responses to soil moisture and the identification of a belowground trait spectrum across three growth forms.
Julie E. Larson (2016)
Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.
Kenneth J Livak (2001)
Identification of a microsatellite marker associated with stem rust resistance gene Sr35 in wheat
Ebrahiem M Babiker (2009)
Plant MicroRNAs
Blake C. Meyers (2010)
SNP-Seek II: A resource for allele mining and analysis of big genomic data in Oryza sativa ☆
Locedie Mansueto (2016)
Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants
Changying Zeng (2010)
Gene expression regulation in roots under drought.
Agnieszka Janiak (2016)
Analysis of Drought-Induced Proteomic and Metabolomic Changes in Barley (Hordeum vulgare L.) Leaves and Roots Unravels Some Aspects of Biochemical Mechanisms Involved in Drought Tolerance
Klaudia Chmielewska (2016)
Quantifying pearl millet response to high temperature stress: thresholds, sensitive stages, genetic variability and relative sensitivity of pollen and pistil.
Maduraimuthu Djanaguiraman (2018)
Contribution of the drought tolerance‐related Stress‐responsive NAC1 transcription factor to resistance of barley to Ramularia leaf spot
Graham R. D. Mcgrann (2015)
Deep sequencing reveals important roles of microRNAs in response to drought and salinity stress in cotton
Fuliang Xie (2015)
psRNATarget: a plant small RNA target analysis server
Xinbin Dai (2011)
A view of plant dehydrins using antibodies specific to the carboxy terminal peptide
Timothy J. Close (2004)
Circos: an information aesthetic for comparative genomics.
Martin Krzywinski (2009)
Comparative Advantages of Genetic - SSRs Over Genomic SSRs for Crop Improvement
S. N. Shingane (2014)
SNP discovery by transcriptome pyrosequencing.
William Brad Barbazuk (2011)
Drought Adaptation in Millets
Zerihun Tadele (2016)
SNP Discovery Using Next Generation Transcriptomic Sequencing in Atlantic Herring (Clupea harengus)
Sarah J Helyar (2012)
Prunus transcription factors: breeding perspectives
Valmor João Bianchi (2015)
De Novo Assembly of the Common Bean Transcriptome Using Short Reads for the Discovery of Drought-Responsive Genes
Jeremy Wu (2014)
Multiple roles of MAP kinases in plant signal transduction
Heribert Hirt (1997)
Marker-assisted selection: an approach for precision plant breeding in the twenty-first century
Bertrand C. Y. Collard (2007)
Development of SCAR marker associated with downy mildew disease resistance in pearl millet (Pennisetum glaucum L.)
Sudisha Jogaiah (2014)
Development of simple sequence repeat markers from bacterial artificial chromosomes without subcloning.
Xiao-kun Qi (2001)
PlnTFDB: updated content and new features of the plant transcription factor database
Paulino Pérez-Rodríguez (2010)
Transcriptomic changes due to water deficit define a general soybean response and accession-specific pathways for drought avoidance
Jin Hee Shin (2015)
Identification and functional characterization of the sulfate transporter gene GmSULTR1;2b in soybean
Yiqiong Ding (2016)
Bulked sample analysis in genetics, genomics and crop improvement
Cheng Zou (2016)
Positive eating and problem treating : Nutraceuticals and cereal-based foods in the 21st century
A. Elizabeth Sloan (1999)
Physiological Investigation and Transcriptome Analysis of Polyethylene Glycol (PEG)-Induced Dehydration Stress in Cassava
Lili Fu (2016)
Functional characterization of the late embryogenesis abundant (LEA) protein gene family from Pinus tabuliformis (Pinaceae) in Escherichia coli
Jie Ying Gao (2016)
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul T. Shannon (2003)
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Brian J. Haas (2013)
Molecular characterization of Sclerospora graminicola, the incitant of pearl millet downy mildew revealed by ISSR markers
S. Jogaiah (2009)
FmTFDb: a foxtail millet transcription factors database for expediting functional genomics in millets
Venkata Suresh Bonthala (2014)
The Sequence Alignment/Map format and SAMtools
Heng Li (2009)
The contrasting microRNA content of a drought tolerant and a drought susceptible wheat cultivar.
Behnam Bakhshi (2017)
Regulation of proline biosynthesis, degradation, uptake and transport in higher plants : Its implications in plant growth and abiotic stress tolerance
Puneet Kishor (2005)
Development of a molecular linkage map of pearl millet integrating DArT and SSR markers
A. Supriya (2011)
Proso Millet (Panicum miliaceum L.) and Its Potential for Cultivation in the Pacific Northwest, U.S.: A Review
Cedric Habiyaremye (2017)
Identification of SSR markers associated with height using pool-based genome-wide association mapping in sorghum
Yi-hong Wang (2011)
GBF3 transcription factor imparts drought tolerance in Arabidopsis thaliana
Venkategowda Ramegowda (2017)
Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL
Jose M Barrero (2015)
MISA—Microsatellite identification tool
T. Thiel (2003)
Plant MicroRNAs, Methods in Molecular Biology
M Accerbi (2010)
Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis
Desalegn D. Serba (2015)
Proso Millet (Panicum miliaceum L.) and Its Potential for Cultivation in the Pacific Northwest, US: A Review. Frontiers in plant science
C Habiyaremye (2016)
Exploration of Genetic and Genomic Resources for Abiotic and Biotic Stress Tolerance in Pearl Millet
Radha Shivhare (2017)
Development and Characterization of Genic SSR Markers from Indian Mulberry Transcriptome and Their Transferability to Related Species of Moraceae
B. Mathi Thumilan (2016)
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Mark D. Robinson (2010)
Using genetic mapping and genomics approaches in understanding and improving drought tolerance in pearl millet.
Rattan S Yadav (2011)
Transcriptional profiling in pearl millet (Pennisetum glaucum L.R. Br.) for identification of differentially expressed drought responsive genes
Minakshi Choudhary (2015)
Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells
Valentina Boeva (2016)
Biofortification in Millets: A Sustainable Approach for Nutritional Security
Agilandeswari Vinoth (2017)
Prunus transcription factors: breeding perspectives. Front
V J Bianchi (2015)
Potential functional implications of Pearl millet(Pennisetum glaucum) in health and disease
Vanisha S. Nambiar (2011)
Genome and Transcriptome sequence of Finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties
Shailaja Hittalmani (2017)
Identification of novel drought-responsive microRNAs and trans-acting siRNAs from Sorghum bicolor (L.) Moench by high-throughput sequencing analysis
Amit Katiyar (2015)
Characterizing the Saltol Quantitative Trait Locus for Salinity Tolerance in Rice
Michael J Thomson (2010)
Development of new simple sequence repeat markers for pearl millet
Om Parkash Yadav (2007)
Development of Capsicum EST–SSR markers for species identification and in silico mapping onto the tomato genome sequence
Kenta Shirasawa (2012)
KvLEA, a New Isolated Late Embryogenesis Abundant Protein Gene from Kosteletzkya virginica Responding to Multiabiotic Stresses
Xiaoli Tang (2016)
FmMDb: A Versatile Database of Foxtail Millet Markers for Millets and Bioenergy Grasses Research
Venkata Suresh B. (2013)
Microsatellite marker development, mapping and applications in rice genetics and breeding
Susan R McCouch (2004)
Development and Utilization of SSRs to Estimate the Degree of Genetic Relationships in a Collection of Pearl Millet Germplasm
Hikmet Budak (2003)
Gene-based microsatellite development for mapping and phylogeny studies in eggplant
Anikó Stágel (2008)
Rapid Up-regulation of HKT1, a high-affinity potassium transporter gene, in roots of barley and wheat following withdrawal of potassium
Wang (1998)
Microsatellite markers in hybridity tests to identify true hybrids of sugarcane.
Norvie L. Manigbas (2004)
Transcriptome sequencing and SNP detection in Phoebe chekiangensis
Bing He (2017)
Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage
Peiguo Guo (2009)
Role of Amino Acids in Plant Responses to Stresses
Vinay Kumar Rai (2004)
Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics
Ana Conesa (2008)
De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
Brian J. Haas (2013)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger (2014)
A Small GTPase of the Rab Family Is Required for Root Hair Formation and Preinfection Stages of the Common Bean–Rhizobium Symbiotic Association[W]
Flavio Antonio Blanco (2009)
Western white pine SNP discovery and high-throughput genotyping for breeding and conservation applications
Jun-Jun Liu (2014)
Development and characterization of a high temperature stress responsive subtractive cDNA library in Pearl Millet Pennisetum glaucum (L
D James (2015)
FAOSTAT: Production, Crops, Millet, data". Food and Agriculture Organization
Development and mapping of Simple Sequence Repeat markers for pearl millet from data mining of Expressed Sequence Tags
Senapathy Senthilvel (2008)
Genome-wide gene expression analysis supports a developmental model of low temperature tolerance gene regulation in wheat (Triticum aestivum L.)
Debbie Laudencia-Chingcuanco (2011)
Glycemic index and quality evaluation of little millet (Panicum miliare) flakes with enhanced shelf life
K. Patil (2014)
Development of a set of SNP markers present in expressed genes of the apple.
David Chagné (2008)
Polymorphism Identification and Improved Genome Annotation of Brassica rapa Through Deep RNA Sequencing
Upendra Kumar Devisetty (2014)
MicroRNAs preferentially target the genes with high transcriptional regulation complexity.
Qinghua Cui (2007)
Identification of microRNAs in Response to Drought in Common Wild Rice (Oryza rufipogon Griff.) Shoots and Roots
Jing-wen Zhang (2017)
Microsatellites for cultivar identification in Pelargonium
Stefan Becher (2000)
How tree roots respond to drought
Ivano Brunner (2015)
Transcriptomic Analysis of Tea Plant Responding to Drought Stress and Recovery
Sheng-chuan Liu (2016)
Potential of SSR markers for plant breeding and variety identification in Australian barley germplasm
Angelo Karakousis (2003)
Antioxidant defences in olive trees during drought stress: changes in activity of some antioxidant enzymes.
Adriano Sofo (2005)
Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata)
Prabin Bajgain (2010)
Genomic Tools in Pearl Millet Breeding for Drought Tolerance: Status and Prospects
Desalegn D. Serba (2016)
An mRNA Putatively Coding for an O-Methyltransferase Accumulates Preferentially in Maize Roots and Is Located Predominantly in the Region of the Endodermis
Bruce M. Held (1993)
Alternative uses of sorghum and pearl millet in Asia: proceedings of the Expert Meeting, ICRISAT, Patancheru, Andhra Pradesh, India, 1-4 July 2003
Cfc (2004)
Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes
Andreas Wagner (1999)
Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea
Alice Kujur (2015)
Transcriptome landscape of perennial wild Cicer microphyllum uncovers functionally relevant molecular tags regulating agronomic traits in chickpea
Rishi Srivastava (2016)
The purine metabolite allantoin enhances abiotic stress tolerance through synergistic activation of abscisic acid metabolism.
Shunsuke Watanabe (2014)
Increasing drought under global warming in observations and models
Aiguo Dai (2013)
Inference of SNP-Gene Regulatory Networks by Integrating Gene Expressions and Genetic Perturbations
Dong-Chul Kim (2014)
Water Deficit Enhances C Export to the Roots in Arabidopsis thaliana Plants with Contribution of Sucrose Transporters in Both Shoot and Roots1[OPEN]
Mickaël Durand (2016)
Analysis of relative gene expression data using rea l—time quantitative PCR a nd the 2 一 ct method
J. Brand Kenneth (2001)
Water deficit enhances C export to the roots in Arabidopsis thaliana plants with contribution of sucrose transporters in both shoot and roots. Plant physiology
M Durand (2016)
Pearl millet [Pennisetum glaucum (L.) R. Br.] consensus linkage map constructed using four RIL mapping populations and newly developed EST-SSRs
Vengaldas Rajaram (2012)
Proteomic analysis indicates massive changes in metabolism prior to the inhibition of growth and photosynthesis of grapevine (Vitis vinifera L.) in response to water deficit
Grant R. Cramer (2013)
Plant responses to stresses: Role of ascorbate peroxidase in the antioxidant protection
Andréia Caverzan (2012)
Comparative Advantages of Genetic-SSRs Over Genomic SSRs for Crop Improvement. http://www.biotecharticles
S. N. Shingane (2014)
New Insights on Drought Stress Response by Global Investigation of Gene Expression Changes in Sheepgrass (Leymus chinensis)
Pincang Zhao (2016)
The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression
Lawrence S. Hon (2007)
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Bo Li (2011)
Analysis of gene expression in response to water deficit of chickpea (Cicer arietinum L.) varieties differing in drought tolerance
Deepti Jain (2009)
Primer3—new capabilities and interfaces
Andreas Untergasser (2012)
Roles of dehydrin genes in wheat tolerance to drought stress
Nemat M. Hassan (2015)
Characterization and Expression Analysis of a Serine Acetyltransferase Gene Family Involved in a Key Step of the Sulfur Assimilation Pathway in Arabidopsis1
Cintia Goulart Kawashima (2005)
Identification and functional characterization of the sulfate transporter gene GmSULTR1
Y Ding (2016)
Transcriptomic Changes Drive Physiological Responses to Progressive Drought Stress and Rehydration in Tomato
Paolo Iovieno (2016)
Wheat WRKY genes TaWRKY2 and TaWRKY19 regulate abiotic stress tolerance in transgenic Arabidopsis plants.
Can-Fang Niu (2012)
Drought Tolerance in Wheat
Arash Nezhadahmadi (2013)
The bench scientist's guide to statistical analysis of RNA-Seq data
Craig R. Yendrek (2012)
A DNA-based method for studying root responses to drought in field-grown wheat genotypes
Chun Y Huang (2013)
Functional Roles of microRNAs in Agronomically Important Plants—Potential as Targets for Crop Improvement and Protection
Arnaud T. Djami-Tchatchou (2017)
SRK2C, a SNF1-related protein kinase 2, improves drought tolerance by controlling stress-responsive gene expression in Arabidopsis thaliana.
Taishi Umezawa (2004)
High-throughput multiplex microsatellite marker assay for detection and quantification of adulteration in Basmati rice (Oryza sativa).
Sunil Archak (2007)
Differentially Expressed Genes Associated with Improved Drought Tolerance in Creeping Bentgrass Overexpressing a Gene for Cytokinin Biosynthesis
Emily B. Merewitz (2016)
Structural basis for recognition of Gibberellin by its receptor GID1 (GA-INSENSITIVE DWARF1) in Oil Palm
S. Rahman (2015)
Transcriptome profiling and validation of gene based single nucleotide polymorphisms (SNPs) in sorghum genotypes with contrasting responses to cold stress
Ratan Chopra (2015)
Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments
Rajeev Kumar Varshney (2017)
Millets and Sorghum: Biology and Genetic Improvement
Jaywant Vilasrao Patil (2017)
Development and characterization of a high temperature stress responsive subtractive cDNA library in Pearl Millet Pennisetum glaucum (L.) R.Br.
Donald James (2015)
Resistance in transgenic potato expressing the potato leafroll virus coat protein gene.
Lawrence Michael Kawchuk (1990)
Millet Grains: Nutritional Quality, Processing, and Potential Health Benefits
Ahmed S. M. Saleh (2013)
The Forkhead Transcription Factor FOXK2 Promotes AP-1-Mediated Transcriptional Regulation
Zongling Ji (2011)
MicroRNAs play critical roles during plant development and in response to abiotic stresses
Júlio César de Lima (2012)
Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci
Deepmala Sehgal (2011)
Molecular Characterization of Sclerospora graminicola, the Incitant of Pearl Millet Downy Mildew Using ISSR Markers
J. Sudisha (2009)

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