Analysis of drought-responsive signalling network in two contrasting rice cultivars using transcriptome-based approach

Traditional cultivars of rice in India exhibit tolerance to drought stress due to their inherent genetic variations. Here we present comparative physiological and transcriptome analyses of two contrasting cultivars, drought tolerant Dhagaddeshi (DD) and susceptible IR20. Microarray analysis revealed several differentially expressed genes (DEGs) exclusively in DD as compared to IR20 seedlings exposed to 3 h drought stress. Physiologically, DD seedlings showed higher cell membrane stability and differential ABA accumulation in response to dehydration, coupled with rapid changes in gene expression. Detailed analyses of metabolic pathways enriched in expression data suggest interplay of ABA dependent along with secondary and redox metabolic networks that activate osmotic and detoxification signalling in DD. By co-localization of DEGs with QTLs from databases or published literature for physiological traits of DD and IR20, candidate genes were identified including those underlying major QTL qDTY1.1 in DD. Further, we identified previously uncharacterized genes from both DD and IR20 under drought conditions including OsWRKY51, OsVP1 and confirmed their expression by qPCR in multiple rice cultivars. OsFBK1 was also functionally validated in susceptible PB1 rice cultivar and Arabidopsis for providing drought tolerance. Some of the DEGs mapped to the known QTLs could thus, be of potential significance for marker-assisted breeding.

[1]  S. Komatsu,et al.  Characterization of fructose-bisphosphate aldolase regulated by gibberellin in roots of rice seedling , 2004, Plant Molecular Biology.

[2]  H. Kato‐Noguchi,et al.  Contribution of momilactone A and B to rice allelopathy. , 2010, Journal of plant physiology.

[3]  Lizhong Xiong,et al.  Over-expression of a LEA gene in rice improves drought resistance under the field conditions , 2007, Theoretical and Applied Genetics.

[4]  Mukesh Jain,et al.  Genomic Survey and Gene Expression Analysis of the Basic Leucine Zipper Transcription Factor Family in Rice1[W][OA] , 2007, Plant Physiology.

[5]  S. Clough,et al.  Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. , 1998, The Plant journal : for cell and molecular biology.

[6]  K. Shimamoto,et al.  Simple RNAi vectors for stable and transient suppression of gene function in rice. , 2004, Plant & cell physiology.

[7]  D. Latowski,et al.  Xanthophyll cycle – a mechanism protecting plants against oxidative stress , 2011, Redox report : communications in free radical research.

[8]  Jitendra P Khurana,et al.  Transcript profiling reveals diverse roles of auxin‐responsive genes during reproductive development and abiotic stress in rice , 2009, The FEBS journal.

[9]  K. Shinozaki,et al.  Gene networks involved in drought stress response and tolerance. , 2006, Journal of experimental botany.

[10]  Huy Q. Dinh,et al.  Epigenetic Regulation of Repetitive Elements Is Attenuated by Prolonged Heat Stress in Arabidopsis[W][OA] , 2010, Plant Cell.

[11]  L. Stein,et al.  Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). , 2002, DNA research : an international journal for rapid publication of reports on genes and genomes.

[12]  Hideyuki Suzuki,et al.  Integrated Analysis of the Effects of Cold and Dehydration on Rice Metabolites, Phytohormones, and Gene Transcripts1[W][OPEN] , 2014, Plant Physiology.

[13]  N. Hayashi,et al.  Blast resistance of CC-NB-LRR protein Pb1 is mediated by WRKY45 through protein–protein interaction , 2013, Proceedings of the National Academy of Sciences.

[14]  Ashutosh Kumar Singh,et al.  MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress , 2007, BMC Genomics.

[15]  S. Goff,et al.  A network of rice genes associated with stress response and seed development , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[16]  A. Mohanty,et al.  Agrobacterium-mediated high frequency transformation of an elite indica rice variety Pusa Basmati 1 and transmission of the transgenes to R2 progeny , 1999 .

[17]  C. Claudel-Renard,et al.  MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters , 2008, BMC Genomics.

[18]  R. Yoshida,et al.  WRKY45-dependent priming of diterpenoid phytoalexin biosynthesis in rice and the role of cytokinin in triggering the reaction , 2014, Plant Molecular Biology.

[19]  R. Wu,et al.  Induced over-expression of the transcription factor OsDREB2A improves drought tolerance in rice. , 2011, Plant physiology and biochemistry : PPB.

[20]  L. Xiong,et al.  Identification of quantitative trait loci for ABA sensitivity at seed germination and seedling stages in rice. , 2006, Yi chuan xue bao = Acta genetica Sinica.

[21]  Jinguang Huang,et al.  Identification and characterization of fructose 1,6-bisphosphate aldolase genes in Arabidopsis reveal a gene family with diverse responses to abiotic stresses. , 2012, Gene.

[22]  S. Mafu,et al.  To gibberellins and beyond! Surveying the evolution of (di)terpenoid metabolism. , 2014, Annual review of plant biology.

[23]  Mukesh Jain,et al.  Modified expression of an auxin-responsive rice CC-type glutaredoxin gene affects multiple abiotic stress responses , 2013, Planta.

[24]  Olga Popova,et al.  Transgenerational Inheritance and Resetting of Stress-Induced Loss of Epigenetic Gene Silencing in Arabidopsis , 2010, Molecular plant.

[25]  A. Henry,et al.  Drought susceptibility of modern rice varieties: an effect of linkage of drought tolerance with undesirable traits , 2015, Scientific Reports.

[26]  H. Mock,et al.  Sugars as hydroxyl radical scavengers: proof-of-concept by studying the fate of sucralose in Arabidopsis. , 2015, The Plant journal : for cell and molecular biology.

[27]  A. Kumar,et al.  Identification and characterization of large-effect quantitative trait loci for grain yield under lowland drought stress in rice using bulk-segregant analysis , 2009, Theoretical and Applied Genetics.

[28]  Q. Zeng,et al.  Functional Divergence of the Glutathione S-Transferase Supergene Family in Physcomitrella patens Reveals Complex Patterns of Large Gene Family Evolution in Land Plants1[W][OA] , 2012, Plant Physiology.

[29]  Kazuo Shinozaki,et al.  Recent advances in the dissection of drought-stress regulatory networks and strategies for development of drought-tolerant transgenic rice plants , 2015, Front. Plant Sci..

[30]  Arvind Kumar,et al.  Identification and mapping of a QTL (qDTY1.1) with a consistent effect on grain yield under drought , 2012 .

[31]  Gary Atlin,et al.  A large-effect QTL for grain yield under reproductive-stage drought stress in upland rice. , 2007 .

[32]  Hui Chen,et al.  Drought-responsive mechanisms in rice genotypes with contrasting drought tolerance during reproductive stage. , 2012, Journal of plant physiology.

[33]  S. Sopory,et al.  Glyoxalase and Methylglyoxal as Biomarkers for Plant Stress Tolerance , 2014 .

[34]  P. Duque,et al.  The Plant-Specific SR45 Protein Negatively Regulates Glucose and ABA Signaling during Early Seedling Development in Arabidopsis1[W] , 2010, Plant Physiology.

[35]  Jian-Kang Zhu,et al.  Salt and drought stress signal transduction in plants. , 2002, Annual review of plant biology.

[36]  Gokare A. Ravishankar,et al.  Influence of abiotic stress signals on secondary metabolites in plants , 2011, Plant signaling & behavior.

[37]  Nobuhiro Suzuki,et al.  Reactive oxygen species homeostasis and signalling during drought and salinity stresses. , 2010, Plant, cell & environment.

[38]  M. Yano,et al.  Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions , 2013, Nature Genetics.

[39]  Jing-xia Zhang,et al.  QTLs for cell-membrane stability mapped in rice (Oryza sativa L.) under drought stress , 2000, Theoretical and Applied Genetics.

[40]  M. Jansen,et al.  Complementary interactions between oxidative stress and auxins control plant growth responses at plant, organ, and cellular level. , 2005, Journal of experimental botany.

[41]  Hur-Song Chang,et al.  Expression profiling of rice segregating for drought tolerance QTLs using a rice genome array , 2005, Functional & Integrative Genomics.

[42]  Mukesh Jain,et al.  F-Box Proteins in Rice. Genome-Wide Analysis, Classification, Temporal and Spatial Gene Expression during Panicle and Seed Development, and Regulation by Light and Abiotic Stress1[W][OA] , 2007, Plant Physiology.

[43]  Alok K. Singh,et al.  qDTY1.1, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds , 2011, BMC Genetics.

[44]  A. Bharti,et al.  Mutants of Arabidopsis as Tools to Understand the Regulation of Phenylpropanoid Pathway and UVB Protection Mechanisms , 1997, Photochemistry and photobiology.

[45]  H. Barrs,et al.  A Re-Examination of the Relative Turgidity Technique for Estimating Water Deficits in Leaves , 1962 .

[46]  S. Yadav,et al.  AN OVERVIEW ON THE ROLE OF METHYLGLYOXAL AND GLYOXALASES IN PLANTS , 2008, Drug metabolism and drug interactions.

[47]  A. R. Walker,et al.  The Arabidopsis TDS4 gene encodes leucoanthocyanidin dioxygenase (LDOX) and is essential for proanthocyanidin synthesis and vacuole development. , 2003, The Plant journal : for cell and molecular biology.

[48]  Edward S. Buckler,et al.  Gramene database in 2010: updates and extensions , 2010, Nucleic Acids Res..

[49]  A. Fernie,et al.  Highway or byway: the metabolic role of the GABA shunt in plants. , 2008, Trends in plant science.

[50]  B. Demmig‐Adams,et al.  The role of xanthophyll cycle carotenoids in the protection of photosynthesis , 1996 .

[51]  B. Courtois,et al.  Genetic Analysis of Water Use Efficiency in Rice (Oryza sativa L.) at the Leaf Level , 2010, Rice.

[52]  G. Prelich.  Gene Overexpression: Uses, Mechanisms, and Interpretation , 2012, Genetics.

[53]  C. Foyer,et al.  The Roles of Reactive Oxygen Metabolism in Drought: Not So Cut and Dried[1][C][W] , 2014, Plant Physiology.

[54]  Mukesh Jain,et al.  Emerging Roles of Auxin in Abiotic Stress Responses , 2015 .

[55]  Jianhua Zhang,et al.  Glucose-induced delay of seed germination in rice is mediated by the suppression of ABA catabolism rather than an enhancement of ABA biosynthesis. , 2009, Plant and Cell Physiology.

[56]  Takuji Sasaki,et al.  The map-based sequence of the rice genome , 2005, Nature.

[57]  M. Van Montagu,et al.  A group 3 LEA cDNA of rice, responsive to abscisic acid, but not to jasmonic acid, shows variety-specific differences in salt stress response. , 1997, Gene.

[58]  I. D. Teare,et al.  Rapid determination of free proline for water-stress studies , 1973, Plant and Soil.

[59]  M. Ray,et al.  Methylglyoxal levels in plants under salinity stress are dependent on glyoxalase I and glutathione. , 2005, Biochemical and biophysical research communications.

[60]  S. Bunnag,et al.  Selection of Rice (Oryza sativa L.) Cultivars Tolerant to Drought Stress at the Vegetative Stage under Field Conditions , 2013 .

[61]  Z. Pei,et al.  NADPH oxidase AtrbohD and AtrbohF genes function in ROS‐dependent ABA signaling in Arabidopsis , 2003, The EMBO journal.

[62]  Mukesh Jain,et al.  Comprehensive expression analysis suggests overlapping and specific roles of rice glutathione S-transferase genes during development and stress responses , 2010, BMC Genomics.

[63]  O. Mittelsten Scheid,et al.  Stress-Induced Chromatin Changes: A Critical View on Their Heritability , 2012, Plant & cell physiology.

[64]  L. K. Bose,et al.  Breeding resilient and productive genotypes adapted to drought-prone rainfed ecosystem of India , 2010 .

[65]  M. Fujita,et al.  Stress-induced changes of methylglyoxal level and glyoxalase I activity in pumpkin seedlings and cDNA cloning of glyoxalase I gene. , 2009 .

[66]  A. Stead,et al.  HAWAIIAN SKIRT: An F-Box Gene That Regulates Organ Fusion and Growth in Arabidopsis1[C][W][OA] , 2007, Plant Physiology.

[67]  O. Mathieu,et al.  Stress-Induced Activation of Heterochromatic Transcription , 2010, PLoS genetics.

[68]  Guanghui Yu,et al.  The dominant glutamic acid metabolic flux to produce γ-amino butyric acid over proline in Nicotiana tabacum leaves under water stress relates to its significant role in antioxidant activity. , 2011, Journal of integrative plant biology.

[69]  R. Stracke,et al.  Leucoanthocyanidin Dioxygenase in Arabidopsis thaliana: characterization of mutant alleles and regulation by MYB-BHLH-TTG1 transcription factor complexes. , 2011, Gene.

[70]  A. Wellburn.  The Spectral Determination of Chlorophylls a and b, as well as Total Carotenoids, Using Various Solvents with Spectrophotometers of Different Resolution* , 1994 .

[71]  Mukesh Jain,et al.  Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. , 2006, Biochemical and biophysical research communications.

[72]  Bin Han,et al.  Microarray Analysis Reveals Similarities and Variations in Genetic Programs Controlling Pollination/Fertilization and Stress Responses in Rice (Oryza sativa L.) , 2005, Plant Molecular Biology.

[73]  Akhilesh K. Tyagi,et al.  Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice , 2011, Functional & Integrative Genomics.

[74]  A. Pandey,et al.  Upregulation of jasmonate biosynthesis and jasmonate-responsive genes in rice leaves in response to a bacterial pathogen mimic , 2014, Functional & Integrative Genomics.

[75]  K. Jung,et al.  The Submergence Tolerance Regulator Sub1A Mediates Stress-Responsive Expression of AP2/ERF Transcription Factors1[C][W][OA] , 2010, Plant Physiology.

[76]  R. Last,et al.  Induction of Arabidopsis Tryptophan Pathway Enzymes and Camalexin by Amino Acid Starvation, Oxidative Stress, and an Abiotic Elicitor , 1998, Plant Cell.

[77]  Arvind Kumar,et al.  Linkages and Interactions Analysis of Major Effect Drought Grain Yield QTLs in Rice , 2016, PloS one.

[78]  P. Beyer,et al.  A Third Phytoene Synthase Is Devoted to Abiotic Stress-Induced Abscisic Acid Formation in Rice and Defines Functional Diversification of Phytoene Synthase Genes1[W] , 2008, Plant Physiology.

[79]  Wei Zhao,et al.  Gramene: a bird's eye view of cereal genomes , 2005, Nucleic Acids Res..

[80]  Mukesh Jain,et al.  Transcriptome analysis in different rice cultivars provides novel insights into desiccation and salinity stress responses , 2016, Scientific Reports.

[81]  Zichao Li,et al.  Comparison of gene expression between upland and lowland rice cultivars under water stress using cDNA microarray , 2007, Theoretical and Applied Genetics.

[82]  Yun Zhang,et al.  Over-expression of OsDREB genes lead to enhanced drought tolerance in rice , 2008, Biotechnology Letters.

[83]  R. Sunkar,et al.  Drought and Salt Tolerance in Plants , 2005 .

[84]  K. Shinozaki,et al.  Monitoring Expression Profiles of Rice Genes under Cold, Drought, and High-Salinity Stresses and Abscisic Acid Application Using cDNA Microarray and RNA Gel-Blot Analyses1[w] , 2003, Plant Physiology.