Skip to main content
SpringerLink
Log in

Molecular Approaches in Deciphering Abiotic Stress Signaling Mechanisms in Plants

  • Chapter
Elucidation of Abiotic Stress Signaling in Plants

Abstract

There has been considerable interest in the area of abiotic stress research, especially in the direction of producing improved crop varieties that can encounter adversities of abiotic stresses such as heat, cold, drought, osmotic, and salinity effectively. These stresses can act alone or in combination cause greater damage to plants. Thus, in order to combat and survive in these extreme environmental conditions, plants have evolved tolerance mechanisms. These mechanisms include interconnected networks of signaling cascade, which involves role of a large number of genes and their products in tolerance mechanism. The clear-cut understanding of these stress tolerance/resistance mechanisms is critical in order to improve the performance of the plant. Deciphering such complex signaling cascades using traditional genomic approach has been difficult, and therefore, high-throughput functional genomics approaches need to be employed using tools like expression profiling, transcriptomics, proteomics, and metabolomics during tolerance response.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell 15(1):63–78

    PubMed Central  CAS  PubMed  Google Scholar 

  • Akpınar BA, Lucas SJ, Budak H (2013) Genomics approaches for crop improvement against abiotic stress. Scientific World Journal 2013

    Google Scholar 

  • Bae MS, Cho EJ, Choi EY, Park OK (2003) Analysis of the Arabidopsis nuclear proteome and its response to cold stress. Plant J 36(5):652–663

    CAS  PubMed  Google Scholar 

  • Baxter A, Mittler R, Suzuki N (2014) ROS as key players in plant stress signalling. J Exp Bot 65(5):1229–1240

    CAS  PubMed  Google Scholar 

  • Benschop JJ, Mohammed S, O’Flaherty M, Heck AJ, Slijper M, Menke FL (2007) Quantitative phosphoproteomics of early elicitor signaling in Arabidopsis. Mol Cell Proteomics 6(7):1198–1214

    CAS  PubMed  Google Scholar 

  • Bienert GP, Møller AL, Kristiansen KA, Schulz A, Møller IM, Schjoerring JK, Jahn TP (2007) Specific aquaporins facilitate the diffusion of hydrogen peroxide across membranes. J Biol Chem 282(2):1183–1192

    CAS  PubMed  Google Scholar 

  • Bindschedler LV, Dewdney J, Blee KA, Stone JM, Asai T, Plotnikov J, Denoux C, Hayes T, Gerrish C, Davies DR (2006) Peroxidase-dependent apoplastic oxidative burst in Arabidopsis required for pathogen resistance. Plant J 47(6):851–863

    PubMed Central  CAS  PubMed  Google Scholar 

  • Bohnert HJ, Ayoubi P, Borchert C, Bressan RA, Burnap RL, Cushman JC, Cushman MA, Deyholos M, Fischer R, Galbraith DW (2001) A genomics approach towards salt stress tolerance. Plant Physiol Biochem 39(3):295–311

    CAS  Google Scholar 

  • Bouchez D, Höfte H (1998) Functional genomics in plants. Plant Physiol 118(3):725–732

    PubMed Central  CAS  PubMed  Google Scholar 

  • Brandt B, Brodsky DE, Xue S, Negi J, Iba K, Kangasjärvi J, Ghassemian M, Stephan AB, Hu H, Schroeder JI (2012) Reconstitution of abscisic acid activation of SLAC1 anion channel by CPK6 and OST1 kinases and branched ABI1 PP2C phosphatase action. Proc Natl Acad Sci 109(26):10593–10598

    PubMed Central  CAS  PubMed  Google Scholar 

  • Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18(6):630–634

    CAS  PubMed  Google Scholar 

  • Bressan RA, Hasegawa PM, Pardo JM (1998) Plants use calcium to resolve salt stress. Trends Plant Sci 3(11):411–412

    Google Scholar 

  • Burke E (2003) High-throughput TAIL-PCR as a tool to identify DNA flanking insertions. Plant Functional Genomics. Springer, In, pp 241–271

    Google Scholar 

  • Caldwell DG, McCallum N, Shaw P, Muehlbauer GJ, Marshall DF, Waugh R (2004) A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.). Plant J 40(1):143–150

    CAS  PubMed  Google Scholar 

  • Chater C, Kamisugi Y, Movahedi M, Fleming A, Cuming AC, Gray JE, Beerling DJ (2011) Regulatory mechanism controlling stomatal behavior conserved across 400 million years of land plant evolution. Curr Biol 21(12):1025–1029

    CAS  PubMed  Google Scholar 

  • Chen L, Huang L, Min D, Phillips A, Wang S, Madgwick PJ, Parry MA, Hu Y-G (2012) Development and characterization of a new TILLING population of common bread wheat (Triticum aestivum L.). PLoS One 7(7):e41570

    PubMed Central  CAS  PubMed  Google Scholar 

  • Chinnusamy V, Ohta M, Kanrar S, Lee BH, Hong X, Agarwal M, Zhu JK (2003) ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev 17(8):1043–1054. doi:10.1101/gad.1077503

    PubMed Central  CAS  PubMed  Google Scholar 

  • Close TJ, Wanamaker SI, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP (2004) A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiol 134(3):960–968

    PubMed Central  CAS  PubMed  Google Scholar 

  • Comai L, Young K, Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR (2004) Efficient discovery of DNA polymorphisms in natural populations by ecotilling. Plant J 37(5):778–786

    CAS  PubMed  Google Scholar 

  • Cook D, Fowler S, Fiehn O, Thomashow MF (2004) A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis. Proc Natl Acad Sci U S A 101(42):15243–15248

    PubMed Central  CAS  PubMed  Google Scholar 

  • Cooper J, Till B, Laport R, Darlow M, Kleffner J, Jamai A, El-Mellouki T, Liu S, Ritchie R, Nielsen N (2008) TILLING to detect induced mutations in soybean. BMC Plant Biol 8(1):9

    PubMed Central  PubMed  Google Scholar 

  • Cooper JL, Henikoff S, Comai L, Till BJ (2013) TILLING and ecotilling for rice. In: Rice protocols. Springer, pp 39–56

    Google Scholar 

  • Cui S, Huang F, Wang J, Ma X, Cheng Y, Liu J (2005) A proteomic analysis of cold stress responses in rice seedlings. Proteomics 5(12):3162–3172

    CAS  PubMed  Google Scholar 

  • Cushman JC, Bohnert HJ (2000) Genomic approaches to plant stress tolerance. Curr Opin Plant Biol 3(2):117–124

    CAS  PubMed  Google Scholar 

  • Dani V, Simon WJ, Duranti M, Croy RR (2005) Changes in the tobacco leaf apoplast proteome in response to salt stress. Proteomics 5(3):737–745

    CAS  PubMed  Google Scholar 

  • de Lorenzo L, Merchan F, Laporte P, Thompson R, Clarke J, Sousa C, Crespi M (2009) A novel plant leucine-rich repeat receptor kinase regulates the response of Medicago truncatula roots to salt stress. Plant Cell 21(2):668–680

    PubMed Central  PubMed  Google Scholar 

  • Delauney AJ, Verma DPS (1993) Proline biosynthesis and osmoregulation in plants. Plant J 4(2):215–223

    CAS  Google Scholar 

  • Du J, Huang YP, Xi J, Cao MJ, Ni WS, Chen X, Zhu JK, Oliver DJ, Xiang CB (2008) Functional gene-mining for salt-tolerance genes with the power of Arabidopsis. Plant J 56(4):653–664

    PubMed Central  CAS  PubMed  Google Scholar 

  • Ergen NZ, Thimmapuram J, Bohnert HJ, Budak H (2009) Transcriptome pathways unique to dehydration tolerant relatives of modern wheat. Funct Integr Genomics 9(3):377–396

    CAS  PubMed  Google Scholar 

  • Flowers T, Yeo A (1995) Breeding for salinity resistance in crop plants: where next? Funct Plant Biol 22(6):875–884

    Google Scholar 

  • Ford CW (1984) Accumulation of low molecular weight solutes in water-stressed tropical legumes. Phytochemistry 23(5):1007–1015

    CAS  Google Scholar 

  • Foyer CH, Parry M, Noctor G (2003) Markers and signals associated with nitrogen assimilation in higher plants. J Exp Bot 54(382):585–593

    CAS  PubMed  Google Scholar 

  • Frova C, Krajewski P, Di Fonzo N, Villa M, Sari-Gorla M (1999) Genetic analysis of drought tolerance in maize by molecular markers I. Yield components. Theor Appl Genet 99(1–2):280–288

    Google Scholar 

  • Fujii H, Chinnusamy V, Rodrigues A, Rubio S, Antoni R, Park S-Y, Cutler SR, Sheen J, Rodriguez PL, Zhu J-K (2009) In vitro reconstitution of an abscisic acid signalling pathway. Nature 462(7273):660–664

    PubMed Central  CAS  PubMed  Google Scholar 

  • Fujita Y, Yoshida T, Yamaguchi-Shinozaki K (2013) Pivotal role of the AREB/ABF-SnRK2 pathway in ABRE-mediated transcription in response to osmotic stress in plants. Physiol Plant 147(1):15–27

    CAS  PubMed  Google Scholar 

  • Gong Q, Li P, Ma S, Indu Rupassara S, Bohnert HJ (2005) Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana. Plant J 44(5):826–839

    CAS  PubMed  Google Scholar 

  • Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G, Mello CC (2001) Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106(1):23–34

    CAS  PubMed  Google Scholar 

  • Gronlund M, Olsen A, Johansen E, Jakobsen I (2010) Protocol: using virus-induced gene silencing to study the arbuscular mycorrhizal symbiosis in Pisum sativum. Plant Methods 6(1):28

    PubMed Central  PubMed  Google Scholar 

  • Gupta B, Saha J, Sengupta A, Gupta K (2013) Plant abiotic stress: ‘omics’ approach. J Plant Biochem Physiol 1:e108

    Google Scholar 

  • Halfter U, Ishitani M, Zhu JK (2000) The Arabidopsis SOS2 protein kinase physically interacts with and is activated by the calcium-binding protein SOS3. Proc Natl Acad Sci U S A 97(7):3735–3740. doi:10.1073/pnas.040577697

    PubMed Central  CAS  PubMed  Google Scholar 

  • Hamilton AJ, Baulcombe DC (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286(5441):950–952

    CAS  PubMed  Google Scholar 

  • Hanin M, Paszkowski J (2003) Plant genome modification by homologous recombination. Curr Opin Plant Biol 6(2):157–162

    CAS  PubMed  Google Scholar 

  • Hayashi H, Czaja I, Lubenow H, Schell J, Walden R (1992) Activation of a plant gene by T-DNA tagging: auxin-independent growth in vitro. Science 258(5086):1350–1353

    CAS  PubMed  Google Scholar 

  • Hoth S, Morgante M, Sanchez J-P, Hanafey MK, Tingey SV, Chua N-H (2002) Genome-wide gene expression profiling in Arabidopsis thaliana reveals new targets of abscisic acid and largely impaired gene regulation in the abi1-1 mutant. J Cell Sci 115(24):4891–4900

    CAS  PubMed  Google Scholar 

  • Huo X, Schnabel E, Hughes K, Frugoli J (2006) RNAi phenotypes and the localization of a protein: GUS fusion imply a role for Medicago truncatula PIN genes in nodulation. J Plant Growth Regul 25(2):156–165

    PubMed Central  CAS  PubMed  Google Scholar 

  • Ichikawa T, Nakazawa M, Kawashima M, Muto S, Gohda K, Suzuki K, Ishikawa A, Kobayashi H, Yoshizumi T, Tsumoto Y (2003) Sequence database of 1172 T-DNA insertion sites in Arabidopsis activation-tagging lines that showed phenotypes in T1 generation. Plant J 36(3):421–429

    CAS  PubMed  Google Scholar 

  • Ichikawa T, Nakazawa M, Kawashima M, Iizumi H, Kuroda H, Kondou Y, Tsuhara Y, Suzuki K, Ishikawa A, Seki M (2006) The FOX hunting system: an alternative gain-of-function gene hunting technique. Plant J 48(6):974–985

    CAS  PubMed  Google Scholar 

  • Imin N, Kerim T, Rolfe BG, Weinman JJ (2004) Effect of early cold stress on the maturation of rice anthers. Proteomics 4(7):1873–1882

    CAS  PubMed  Google Scholar 

  • Initiative AG (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408(6814):796

    Google Scholar 

  • Ishitani M, Liu J, Halfter U, Kim C-S, Shi W, Zhu J-K (2000) SOS3 function in plant salt tolerance requires N-myristoylation and calcium binding. Sci Signal 12(9):1667

    CAS  Google Scholar 

  • Iuchi S, Kobayashi M, Yamaguchi-Shinozaki K, Shinozaki K (2000) A stress-inducible gene for 9-cis-epoxycarotenoid dioxygenase involved in abscisic acid biosynthesis under water stress in drought-tolerant cowpea. Plant Physiol 123(2):553–562

    PubMed Central  CAS  PubMed  Google Scholar 

  • Jammes F, Song C, Shin D, Munemasa S, Takeda K, Gu D, Cho D, Lee S, Giordo R, Sritubtim S (2009) MAP kinases MPK9 and MPK12 are preferentially expressed in guard cells and positively regulate ROS-mediated ABA signaling. Proc Natl Acad Sci 106(48):20520–20525

    PubMed Central  CAS  PubMed  Google Scholar 

  • Jung S-H, Lee J-Y, Lee D-H (2003) Use of SAGE technology to reveal changes in gene expression in Arabidopsis leaves undergoing cold stress. Plant Mol Biol 52(3):553–567

    CAS  PubMed  Google Scholar 

  • Kachroo A, Ghabrial S (2012) Virus-Induced Gene Silencing in Soybean. Antiviral Resistance in Plants. Springer, In, pp 287–297

    Google Scholar 

  • Kamei A, Seki M, Umezawa T, Ishida J, Satou M, Akiyama K, ZHU JK, Shinozaki K (2005) Analysis of gene expression profiles in Arabidopsis salt overly sensitive mutants sos2–1 and sos3–1. Plant Cell Environ 28(10):1267–1275

    CAS  Google Scholar 

  • Kaplan F, Kopka J, Haskell DW, Zhao W, Schiller KC, Gatzke N, Sung DY, Guy CL (2004) Exploring the temperature-stress metabolome of Arabidopsis. Plant Physiol 136(4):4159–4168

    PubMed Central  CAS  PubMed  Google Scholar 

  • Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, Kawai K, Galbraith D, Bohnert HJ (2001) Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13(4):889–905

    PubMed Central  CAS  PubMed  Google Scholar 

  • Kim T-H, Böhmer M, Hu H, Nishimura N, Schroeder JI (2010) Guard cell signal transduction network: advances in understanding abscisic acid, CO2, and Ca2+ signaling. Annu Rev Plant Biol 61:561

    PubMed Central  CAS  PubMed  Google Scholar 

  • Knight H, Trewavas AJ, Knight MR (1997) Calcium signalling in Arabidopsis thaliana responding to drought and salinity. Plant J 12(5):1067–1078

    CAS  PubMed  Google Scholar 

  • Koch M, Vorwerk S, Masur C, Sharifi-Sirchi G, Olivieri N, Schlaich NL (2006) A role for a flavin-containing mono-oxygenase in resistance against microbial pathogens in Arabidopsis. Plant J 47(4):629–639

    CAS  PubMed  Google Scholar 

  • Koiwa H, Bressan RA, Hasegawa PM (2006) Identification of plant stress-responsive determinants in Arabidopsis by large-scale forward genetic screens. J Exp Bot 57(5):1119–1128

    CAS  PubMed  Google Scholar 

  • Komatsu K, Nishikawa Y, Ohtsuka T, Taji T, Quatrano RS, Tanaka S, Sakata Y (2009) Functional analyses of the ABI1-related protein phosphatase type 2C reveal evolutionarily conserved regulation of abscisic acid signaling between Arabidopsis and the moss Physcomitrella patens. Plant Mol Biol 70(3):327–340

    CAS  PubMed  Google Scholar 

  • Kudapa H, Ramalingam A, Nayakoti S, Chen X, Zhuang W-J, Liang X, Kahl G, Edwards D, Varshney RK (2013) Functional genomics to study stress responses in crop legumes: progress and prospects. Funct Plant Biol 40(12):1221–1233

    CAS  Google Scholar 

  • Kurowska M, Daszkowska-Golec A, Gruszka D, Marzec M, Szurman M, Szarejko I, Maluszynski M (2011) TILLING-a shortcut in functional genomics. J Appl Genet 52(4):371–390

    PubMed Central  PubMed  Google Scholar 

  • Larkindale J, Vierling E (2008) Core genome responses involved in acclimation to high temperature. Plant Physiol 146(2):748–761

    PubMed Central  CAS  PubMed  Google Scholar 

  • Lee J-Y, Lee D-H (2003) Use of serial analysis of gene expression technology to reveal changes in gene expression in Arabidopsis pollen undergoing cold stress. Plant Physiol 132(2):517–529

    PubMed Central  CAS  PubMed  Google Scholar 

  • Lee S-C, Kim J-Y, Kim S-H, Kim S-J, Lee K, Han S-K, Choi H-S, Jeong D-H, An G, Kim S-R (2004) Trapping and characterization of cold-responsive genes from T-DNA tagging lines in rice. Plant Science 166(1):69–79

    Google Scholar 

  • Li S, Zhou X, Chen L, Huang W, Yu D (2010) Functional characterization of Arabidopsis thaliana WRKY39 in heat stress. Mol Cells 29(5):475–483

    CAS  PubMed  Google Scholar 

  • Liu J, Zhu J-K (1998) A calcium sensor homolog required for plant salt tolerance. Science 280(5371):1943–1945

    CAS  PubMed  Google Scholar 

  • Liu J, Ishitani M, Halfter U, Kim C-S, Zhu J-K (2000) The Arabidopsis thaliana SOS2 gene encodes a protein kinase that is required for salt tolerance. Proc Natl Acad Sci 97(7):3730–3734

    PubMed Central  CAS  PubMed  Google Scholar 

  • Liu HT, Gao F, Li GL, Han JL, Liu DL, Sun DY, Zhou RG (2008) The calmodulin‐binding protein kinase 3 is part of heat‐shock signal transduction in Arabidopsis thaliana. Plant J 55(5):760–773

    CAS  PubMed  Google Scholar 

  • LIU HC, LIAO HT, CHARNG YY (2011) The role of class A1 heat shock factors (HSFA1s) in response to heat and other stresses in Arabidopsis. Plant Cell Environ 34(5):738–751

    CAS  PubMed  Google Scholar 

  • Lobell DB, Schlenker W, Costa-Roberts J (2011) Climate trends and global crop production since 1980. Science 333(6042):616–620

    CAS  PubMed  Google Scholar 

  • Lopez-Molina L, Mongrand S, Chua N-H (2001) A postgermination developmental arrest checkpoint is mediated by abscisic acid and requires the ABI5 transcription factor in Arabidopsis. Proc Natl Acad Sci 98(8):4782–4787

    PubMed Central  CAS  PubMed  Google Scholar 

  • Louis P, Galinski EA (1997) Characterization of genes for the biosynthesis of the compatible solute ectoine from Marinococcus halophilus and osmoregulated expression in Escherichia coli. Microbiology 143(4):1141–1149

    CAS  PubMed  Google Scholar 

  • Loukehaich R, Wang T, Ouyang B, Ziaf K, Li H, Zhang J, Lu Y, Ye Z (2012) SpUSP, an annexin-interacting universal stress protein, enhances drought tolerance in tomato. J Exp Bot 63(15):5593–5606

    PubMed Central  CAS  PubMed  Google Scholar 

  • Luo M, Liu J, Lee RD, Scully BT, Guo B (2010) Monitoring the expression of maize genes in developing kernels under drought stress using oligo-microarray. J Integr Plant Biol 52(12):1059–1074

    CAS  PubMed  Google Scholar 

  • Ma Y, Szostkiewicz I, Korte A, Moes D, Yang Y, Christmann A, Grill E (2009) Regulators of PP2C phosphatase activity function as abscisic acid sensors. Science 324(5930):1064–1068

    CAS  PubMed  Google Scholar 

  • Macas J, Lambert GM, Dolezel D, Galbraith DW (1998) Nuclear expressed sequence tag(NEST) analysis: A novel means to study transcription through amplification of nuclear RNA. Cytometry 33(4):460–468

    CAS  PubMed  Google Scholar 

  • Mahajan S, Tuteja N (2005) Cold, salinity and drought stresses: an overview. Arch Biochem Biophys 444(2):139–158

    CAS  PubMed  Google Scholar 

  • Manickavelu A, Kawaura K, Oishi K, Shin T, Kohara Y, Yahiaoui N, Keller B, Abe R, Suzuki A, Nagayama T (2012) Comprehensive functional analyses of expressed sequence tags in common wheat (Triticum aestivum). DNA Res 19(2):165–177

    PubMed Central  CAS  PubMed  Google Scholar 

  • Mantri NL, Ford R, Coram TE, Pang EC (2010) Evidence of unique and shared responses to major biotic and abiotic stresses in chickpea. Environ Exp Bot 69(3):286–292

    Google Scholar 

  • Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18(9):1509–1517

    PubMed Central  CAS  PubMed  Google Scholar 

  • Maruyama K, Takeda M, Kidokoro S, Yamada K, Sakuma Y, Urano K, Fujita M, Yoshiwara K, Matsukura S, Morishita Y (2009) Metabolic pathways involved in cold acclimation identified by integrated analysis of metabolites and transcripts regulated by DREB1A and DREB2A. Plant Physiol 150(4):1972–1980

    PubMed Central  CAS  PubMed  Google Scholar 

  • Matsumura H, Nirasawa S, Terauchi R (1999) Transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression (SAGE). Plant J 20(6):719–726

    CAS  PubMed  Google Scholar 

  • Matsumura H, Reich S, Ito A, Saitoh H, Kamoun S, Winter P, Kahl G, Reuter M, Krüger DH, Terauchi R (2003) Gene expression analysis of plant host–pathogen interactions by SuperSAGE. Proc Natl Acad Sci 100(26):15718–15723

    PubMed Central  CAS  PubMed  Google Scholar 

  • Matsumura H, Ito A, Saitoh H, Winter P, Kahl G, Reuter M, Krüger DH, Terauchi R (2005) SuperSAGE. Cell Microbiol 7(1):11–18

    CAS  PubMed  Google Scholar 

  • Matsumura H, Yoshida K, Luo S, Kimura E, Fujibe T, Albertyn Z, Barrero RA, Krüger DH, Kahl G, Schroth GP (2010) High-throughput SuperSAGE for digital gene expression analysis of multiple samples using next generation sequencing. PLoS One 5(8):e12010

    PubMed Central  PubMed  Google Scholar 

  • McCallum CM, Comai L, Greene EA, Henikoff S (2000) Targeting induced local lesions in genomes (TILLING) for plant functional genomics. Plant Physiol 123(2):439–442

    PubMed Central  CAS  PubMed  Google Scholar 

  • McClung CR, Davis SJ (2010) Ambient thermometers in plants: from physiological outputs towards mechanisms of thermal sensing. Curr Biol 20(24):R1086–R1092

    CAS  PubMed  Google Scholar 

  • McCue KF, Hanson AD (1990) Drought and salt tolerance: towards understanding and application. Trends Biotechnol 8:358–362

    CAS  Google Scholar 

  • McGinnis KM (2010) RNAi for functional genomics in plants. Brief Funct Genomics 9(2):111–117

    CAS  PubMed  Google Scholar 

  • McInnis SM, Desikan R, Hancock JT, Hiscock SJ (2006) Production of reactive oxygen species and reactive nitrogen species by angiosperm stigmas and pollen: potential signalling crosstalk? New Phytol 172(2):221–228

    CAS  PubMed  Google Scholar 

  • McKersie BD, Bowley SR (1997) Active oxygen and freezing tolerance in transgenic plants. In: Li PH, Chen THH (eds) Plant cold hardiness. Plenum, New York, pp 203–214

    Google Scholar 

  • Melcher K, Ng L-M, Zhou XE, Soon F-F, Xu Y, Suino-Powell KM, Park S-Y, Weiner JJ, Fujii H, Chinnusamy V (2009) A gate–latch–lock mechanism for hormone signalling by abscisic acid receptors. Nature 462(7273):602–608

    PubMed Central  CAS  PubMed  Google Scholar 

  • Mette M, Aufsatz W, Van der Winden J, Matzke M, Matzke A (2000) Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J 19(19):5194–5201

    PubMed Central  CAS  PubMed  Google Scholar 

  • Miki D, Shimamoto K (2004) Simple RNAi vectors for stable and transient suppression of gene function in rice. Plant Cell Physiol 45(4):490–495

    CAS  PubMed  Google Scholar 

  • Miller G, Schlauch K, Tam R, Cortes D, Torres MA, Shulaev V, Dangl JL, Mittler R (2009) The plant NADPH oxidase RBOHD mediates rapid systemic signaling in response to diverse stimuli. Sci Signal 2(84):ra45

    PubMed  Google Scholar 

  • Mishkind M, Vermeer JE, Darwish E, Munnik T (2009) Heat stress activates phospholipase D and triggers PIP2 accumulation at the plasma membrane and nucleus. Plant J 60(1):10–21

    CAS  PubMed  Google Scholar 

  • Mittler R, Blumwald E (2010) Genetic engineering for modern agriculture: challenges and perspectives. Annu Rev Plant Biol 61:443–462

    CAS  PubMed  Google Scholar 

  • Mittler R, Vanderauwera S, Gollery M, Van Breusegem F (2004) Reactive oxygen gene network of plants. Trends Plant Sci 9(10):490–498

    CAS  PubMed  Google Scholar 

  • Mittler R, Vanderauwera S, Suzuki N, Miller G, Tognetti VB, Vandepoele K, Gollery M, Shulaev V, Van Breusegem F (2011) ROS signaling: the new wave? Trends Plant Sci 16(6):300–309

    CAS  PubMed  Google Scholar 

  • Mittler R, Finka A, Goloubinoff P (2012) How do plants feel the heat? Trends Biochem Sci 37(3):118–125

    CAS  PubMed  Google Scholar 

  • Molina C, Rotter B, Horres R, Udupa S, Besser B, Bellarmino L, Baum M, Matsumura H, Terauchi R, Kahl G, Winter P (2008) SuperSAGE: the drought stress-responsive transcriptome of chickpea roots. BMC Genomics 9(1):553

    PubMed Central  PubMed  Google Scholar 

  • Molina C, Zaman-Allah M, Khan F, Fatnassi N, Horres R, Rotter B, Steinhauer D, Amenc L, Drevon J-J, Winter P, Kahl G (2011) The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE. BMC Plant Biol 11(1):31

    PubMed Central  CAS  PubMed  Google Scholar 

  • Møller IM, Sweetlove LJ (2010) ROS signalling–specificity is required. Trends Plant Sci 15(7):370–374

    PubMed  Google Scholar 

  • Monshausen G, Bibikova T, Messerli M, Shi C, Gilroy S (2007) Oscillations in extracellular pH and reactive oxygen species modulate tip growth of Arabidopsis root hairs. Proc Natl Acad Sci 104(52):20996–21001

    PubMed Central  CAS  PubMed  Google Scholar 

  • Mustilli A-C, Merlot S, Vavasseur A, Fenzi F, Giraudat J (2002) Arabidopsis OST1 protein kinase mediates the regulation of stomatal aperture by abscisic acid and acts upstream of reactive oxygen species production. Plant Cell 14(12):3089–3099

    PubMed Central  CAS  PubMed  Google Scholar 

  • Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320(5881):1344–1349

    PubMed Central  CAS  PubMed  Google Scholar 

  • Nakano M, Nobuta K, Vemaraju K, Tej SS, Skogen JW, Meyers BC (2006) Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res 34(suppl 1):D731–D735

    PubMed Central  CAS  PubMed  Google Scholar 

  • Negrão S, Cecília Almadanim M, Pires IS, Abreu IA, Maroco J, Courtois B, Gregorio GB, McNally KL, Margarida Oliveira M (2013) New allelic variants found in key rice salt-tolerance genes: an association study. Plant Biotechnol J 11(1):87–100

    PubMed  Google Scholar 

  • Nielsen KL, Høgh AL, Emmersen J (2006) DeepSAGE—digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples. Nucleic Acids Res 34(19):e133

    PubMed Central  PubMed  Google Scholar 

  • Nishimura N, Hitomi K, Arvai AS, Rambo RP, Hitomi C, Cutler SR, Schroeder JI, Getzoff ED (2009) Structural mechanism of abscisic acid binding and signaling by dimeric PYR1. Science 326(5958):1373–1379

    PubMed Central  CAS  PubMed  Google Scholar 

  • Nishimura N, Sarkeshik A, Nito K, Park SY, Wang A, Carvalho PC, Lee S, Caddell DF, Cutler SR, Chory J (2010) PYR/PYL/RCAR family members are major in vivo ABI1 protein phosphatase 2C-interacting proteins in Arabidopsis. Plant J 61(2):290–299

    PubMed Central  CAS  PubMed  Google Scholar 

  • Niu X, Bressan RA, Hasegawa PM, Pardo JM (1995) Ion homeostasis in NaCl stress environments. Plant Physiol 109(3):735

    PubMed Central  CAS  PubMed  Google Scholar 

  • Novillo F, Alonso JM, Ecker JR, Salinas J (2004) CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in stress tolerance in Arabidopsis. Proc Natl Acad Sci U S A 101(11):3985–3990

    PubMed Central  CAS  PubMed  Google Scholar 

  • Nunes AS, Vianna G, Cuneo F, Amaya-Farfán J, Capdeville G, Rech E, Aragão FL (2006) RNAi-mediated silencing of the myo-inositol-1-phosphate synthase gene (GmMIPS1) in transgenic soybean inhibited seed development and reduced phytate content. Planta 224(1):125–132. doi:10.1007/s00425-005-0201-0

    CAS  PubMed  Google Scholar 

  • O’Brien JA, Daudi A, Finch P, Butt VS, Whitelegge JP, Souda P, Ausubel FM, Bolwell GP (2012) A peroxidase-dependent apoplastic oxidative burst in cultured Arabidopsis cells functions in MAMP-elicited defense. Plant Physiol 158(4):2013–2027

    PubMed Central  PubMed  Google Scholar 

  • Odell JT, Nagy F, Chua N-H (1985) Identification of DNA sequences required for activity of the cauliflower mosaic virus 35S promoter. Nature 313(6005):810–812

    CAS  PubMed  Google Scholar 

  • Pandey S, Nelson DC, Assmann SM (2009) Two novel GPCR-type g proteins are abscisic acid receptors in Arabidopsis. Cell 136(1):136–148

    CAS  PubMed  Google Scholar 

  • Papdi C, Ábrahám E, Joseph MP, Popescu C, Koncz C, Szabados L (2008) Functional identification of Arabidopsis stress regulatory genes using the controlled cDNA overexpression system. Plant Physiol 147(2):528–542

    PubMed Central  CAS  PubMed  Google Scholar 

  • Parinov S, Sevugan M, Ye D, Yang W-C, Kumaran M, Sundaresan V (1999) Analysis of flanking sequences from dissociation insertion lines: a database for reverse genetics in Arabidopsis. Plant Cell 11(12):2263–2270

    PubMed Central  CAS  PubMed  Google Scholar 

  • Park S-Y, Fung P, Nishimura N, Jensen DR, Fujii H, Zhao Y, Lumba S, Santiago J, Rodrigues A, Chow TF et al (2009) Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science 324(5930):1068–1071

    PubMed Central  CAS  PubMed  Google Scholar 

  • Pollock JD (2002) Gene expression profiling: methodological challenges, results, and prospects for addiction research. Chem Phys Lipids 121(1):241–256

    CAS  PubMed  Google Scholar 

  • Pospíšilová J (2003) Participation of phytohormones in the stomatal regulation of gas exchange during water stress. Biol Planta 46(4):491–506

    Google Scholar 

  • Qin D, Wu H, Peng H, Yao Y, Ni Z, Li Z, Zhou C, Sun Q (2008) Heat stress-responsive transcriptome analysis in heat susceptible and tolerant wheat (Triticum aestivum L.) by using Wheat Genome Array. BMC Genomics 9(1):432

    PubMed Central  PubMed  Google Scholar 

  • Qiu Q-S, Guo Y, Dietrich MA, Schumaker KS, Zhu J-K (2002) Regulation of SOS1, a plasma membrane Na+/H+ exchanger in Arabidopsis thaliana, by SOS2 and SOS3. Proc Natl Acad Sci 99(12):8436–8441

    PubMed Central  CAS  PubMed  Google Scholar 

  • Radhamony RN, Mohan Prasad A, Srinivasan R (2005) T-DNA insertional mutagenesis in Arabidopsis: a tool for functional genomics. Electron J Biotechnol 8(1):82–106

    CAS  Google Scholar 

  • Ranjan A, Pandey N, Lakhwani D, Dubey NK, Pathre UV, Sawant SV (2012) Comparative transcriptomic analysis of roots of contrasting Gossypium herbaceum genotypes revealing adaptation to drought. BMC Genomics 13(1):680

    PubMed Central  CAS  PubMed  Google Scholar 

  • Reinartz J, Bruyns E, Lin J-Z, Burcham T, Brenner S, Bowen B, Kramer M, Woychik R (2002) Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms. Brief Funct Genomic Proteomic 1(1):95–104

    CAS  PubMed  Google Scholar 

  • Rensink WA, Buell CR (2005) Microarray expression profiling resources for plant genomics. Trends Plant Sci 10(12):603–609

    CAS  PubMed  Google Scholar 

  • Rhoads DM, Umbach AL, Subbaiah CC, Siedow JN (2006) Mitochondrial reactive oxygen species. Contribution to oxidative stress and interorganellar signaling. Plant Physiol 141(2):357–366

    PubMed Central  CAS  PubMed  Google Scholar 

  • Ribaut J-M, Hoisington D, Deutsch J, Jiang C, Gonzalez-de-Leon D (1996) Identification of quantitative trait loci under drought conditions in tropical maize. 1. Flowering parameters and the anthesis-silking interval. Theor Appl Genet 92(7):905–914

    CAS  PubMed  Google Scholar 

  • Ribaut J-M, Jiang C, Gonzalez-de-Leon D, Edmeades G, Hoisington D (1997) Identification of quantitative trait loci under drought conditions in tropical maize. 2. Yield components and marker-assisted selection strategies. Theor Appl Genet 94(6–7):887–896

    Google Scholar 

  • Rizhsky L, Liang H, Shuman J, Shulaev V, Davletova S, Mittler R (2004) When defense pathways collide. The response of Arabidopsis to a combination of drought and heat stress. Plant Physiol 134(4):1683–1696

    PubMed Central  CAS  PubMed  Google Scholar 

  • Rodrigues A, Adamo M, Crozet P, Margalha L, Confraria A, Martinho C, Elias A, Rabissi A, Lumbreras V, González-Guzmán M (2013) ABI1 and PP2CA phosphatases are negative regulators of Snf1-related protein kinase1 signaling in Arabidopsis. Plant Cell 25(10):3871–3884

    PubMed Central  CAS  PubMed  Google Scholar 

  • Ruelland E, Zachowski A (2010) How plants sense temperature. Environ Exp Bot 69(3):225–232

    Google Scholar 

  • Rus A, Yokoi S, Sharkhuu A, Reddy M, B-h L, Matsumoto TK, Koiwa H, Zhu J-K, Bressan RA, Hasegawa PM (2001) AtHKT1 is a salt tolerance determinant that controls Na+ entry into plant roots. Proc Natl Acad Sci 98(24):14150–14155

    PubMed Central  CAS  PubMed  Google Scholar 

  • Sagi M, Davydov O, Orazova S, Yesbergenova Z, Ophir R, Stratmann JW, Fluhr R (2004) Plant respiratory burst oxidase homologs impinge on wound responsiveness and development in Lycopersicon esculentum. Plant Cell 16(3):616–628

    PubMed Central  CAS  PubMed  Google Scholar 

  • Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ, Vogelstein B, Kinzler KW, Velculescu VE (2002) Using the transcriptome to annotate the genome. Nat Biotechnol 20(5):508–512

    CAS  PubMed  Google Scholar 

  • Saidi Y, Finka A, Muriset M, Bromberg Z, Weiss YG, Maathuis FJ, Goloubinoff P (2009) The heat shock response in moss plants is regulated by specific calcium-permeable channels in the plasma membrane. Plant Cell 21(9):2829–2843

    PubMed Central  CAS  PubMed  Google Scholar 

  • Salekdeh G, Siopongco J, Wade LJ, Ghareyazie B, Bennett J (2002) Proteomic analysis of rice leaves during drought stress and recovery. Proteomics 2(9):1131–1145

    CAS  PubMed  Google Scholar 

  • Santiago J, Dupeux F, Round A, Antoni R, Park S-Y, Jamin M, Cutler SR, Rodriguez PL, Márquez JA (2009) The abscisic acid receptor PYR1 in complex with abscisic acid. Nature 462(7273):665–668

    CAS  PubMed  Google Scholar 

  • Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270(5235):467–470

    CAS  PubMed  Google Scholar 

  • Schwartz SH, Tan BC, Gage DA, Zeevaart JA, McCarty DR (1997) Specific oxidative cleavage of carotenoids by VP14 of maize. Science 276(5320):1872–1874

    CAS  PubMed  Google Scholar 

  • Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enju A, Sakurai T (2002) Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 31(3):279–292

    CAS  PubMed  Google Scholar 

  • Senthil-Kumar M, Mysore KS (2011) New dimensions for VIGS in plant functional genomics. Trends Plant Sci 16(12):656–665. doi:http://dx.doi.org/10.1016/j.tplants.2011.08.006

  • Shapiguzov A, Vainonen JP, Wrzaczek M, Kangasjärvi J (2012) ROS-talk–how the apoplast, the chloroplast, and the nucleus get the message through. Front Plant Sci 3

    Google Scholar 

  • Shinozaki K, Yamaguchi-Shinozaki K (2007) Gene networks involved in drought stress response and tolerance. J Exp Bot 58(2):221–227

    CAS  PubMed  Google Scholar 

  • Sreenivasulu N, Sopory S, Kavi Kishor P (2007) Deciphering the regulatory mechanisms of abiotic stress tolerance in plants by genomic approaches. Gene 388(1):1–13

    CAS  PubMed  Google Scholar 

  • Steponkus PL, Uemura M, Webb MS (1993) A contrast of the cryostability of the plasma membrane of winter rye and spring oat-two species that widely differ in their freezing tolerance and plasma membrane lipid composition. In: Steponkus PL (ed) Advances in low-temperature biology, vol 2. JAI, London, pp 211–312

    Google Scholar 

  • Sunkar R, Chinnusamy V, Zhu J, Zhu J-K (2007) Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci 12(7):301–309

    CAS  PubMed  Google Scholar 

  • Suzuki N, Bajad S, Shuman J, Shulaev V, Mittler R (2008) The transcriptional co-activator MBF1c is a key regulator of thermotolerance in Arabidopsis thaliana. J Biol Chem 283(14):9269–9275

    CAS  PubMed  Google Scholar 

  • Suzuki N, Miller G, Morales J, Shulaev V, Torres MA, Mittler R (2011) Respiratory burst oxidases: the engines of ROS signaling. Curr Opin Plant Biol 14(6):691–699

    CAS  PubMed  Google Scholar 

  • Suzuki N, Koussevitzky S, Mittler R, Miller G (2012) ROS and redox signalling in the response of plants to abiotic stress. Plant Cell Environ 35(2):259–270

    CAS  PubMed  Google Scholar 

  • Takeda S, Gapper C, Kaya H, Bell E, Kuchitsu K, Dolan L (2008) Local positive feedback regulation determines cell shape in root hair cells. Science 319(5867):1241–1244

    CAS  PubMed  Google Scholar 

  • Teige M, Scheikl E, Eulgem T, Dóczi R, Ichimura K, Shinozaki K, Dangl JL, Hirt H (2004) The MKK2 pathway mediates cold and salt stress signaling in Arabidopsis. Mol Cell 15(1):141–152

    CAS  PubMed  Google Scholar 

  • Thakur P, Kumar S, Malik JA, Berger JD, Nayyar H (2010) Cold stress effects on reproductive development in grain crops: an overview. Environ Exp Bot 67(3):429–443

    CAS  Google Scholar 

  • Till BJ, Reynolds SH, Weil C, Springer N, Burtner C, Young K, Bowers E, Codomo CA, Enns LC, Odden AR (2004) Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol 4(1):12

    PubMed Central  PubMed  Google Scholar 

  • Torres MA, Dangl JL (2005) Functions of the respiratory burst oxidase in biotic interactions, abiotic stress and development. Curr Opin Plant Biol 8(4):397–403

    CAS  PubMed  Google Scholar 

  • Tougane K, Komatsu K, Bhyan SB, Sakata Y, Ishizaki K, Yamato KT, Kohchi T, Takezawa D (2010) Evolutionarily conserved regulatory mechanisms of abscisic acid signaling in land plants: characterization of ABSCISIC ACID INSENSITIVE1-like type 2C protein phosphatase in the liverwort Marchantia polymorpha. Plant Physiol 152(3):1529–1543

    PubMed Central  CAS  PubMed  Google Scholar 

  • Uemura M, Steponkus PL (1997) Effect of cold acclimation on membrane lipid composition and freeze-induced membrane destabilization. In: Li PH, Chen THH (eds) Plant cold hardiness. Plenum, New York, pp 171–179

    Google Scholar 

  • Uozumi N, Kim EJ, Rubio F, Yamaguchi T, Muto S, Tsuboi A, Bakker EP, Nakamura T, Schroeder JI (2000) The Arabidopsis HKT1 gene homolog mediates inward Na+ currents in Xenopus laevis oocytes and Na+ uptake in Saccharomyces cerevisiae. Plant Physiol 122(4):1249–1260

    PubMed Central  CAS  PubMed  Google Scholar 

  • Urano K, Kurihara Y, Seki M, Shinozaki K (2010) ‘Omics’ analyses of regulatory networks in plant abiotic stress responses. Curr Opin Plant Biol 13(2):132–138

    CAS  PubMed  Google Scholar 

  • Utsumi Y, Tanaka M, Morosawa T, Kurotani A, Yoshida T, Mochida K, Matsui A, Umemura Y, Ishitani M, Shinozaki K (2012) Transcriptome analysis using a high-density oligomicroarray under drought stress in various genotypes of cassava: an important tropical crop. DNA Res 19(4):335–345

    PubMed Central  CAS  PubMed  Google Scholar 

  • Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270(5235):484–486

    CAS  PubMed  Google Scholar 

  • Verdel A, Vavasseur A, Le Gorrec M, Touat-Todeschini L (2009) Common themes in siRNA-mediated epigenetic silencing pathways. Int J Dev Biol 53(2):245–257

    CAS  PubMed  Google Scholar 

  • Vij S, Tyagi AK (2007) Emerging trends in the functional genomics of the abiotic stress response in crop plants. Plant Biotechnol J 5(3):361–380

    CAS  PubMed  Google Scholar 

  • Vodkin LO, Khanna A, Shealy R, Clough SJ, Gonzalez DO, Philip R, Zabala G, Thibaud-Nissen F, Sidarous M, Strömvik MV (2004) Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant. BMC Genomics 5(1):73

    PubMed Central  PubMed  Google Scholar 

  • Wahid A, Gelani S, Ashraf M, Foolad M (2007) Heat tolerance in plants: an overview. Environ Exp Bot 61(3):199–223

    Google Scholar 

  • Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng L, Wanamaker SI, Mandal J, Xu J, Cui X (2005) Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage. Plant Physiol 139(2):822–835

    PubMed Central  CAS  PubMed  Google Scholar 

  • Wang W, Vinocur B, Altman A (2003) Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta 218(1):1–14

    CAS  PubMed  Google Scholar 

  • Wang W, Vinocur B, Shoseyov O, Altman A (2004) Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. Trends Plant Sci 9(5):244–252

    CAS  PubMed  Google Scholar 

  • Wen J-Q, Oono K, Imai R (2002) Two novel mitogen-activated protein signaling components, OsMEK1 and OsMAP1, are involved in a moderate low-temperature signaling pathway in rice. Plant Physiol 129(4):1880–1891

    PubMed Central  CAS  PubMed  Google Scholar 

  • Wienkoop S, Morgenthal K, Wolschin F, Scholz M, Selbig J, Weckwerth W (2008) Integration of metabolomic and proteomic phenotypes analysis of data covariance dissects starch and RFO metabolism from low and high temperature compensation response in Arabidopsis thaliana. Mol Cell Proteomics 7(9):1725–1736

    PubMed Central  CAS  PubMed  Google Scholar 

  • Wohlbach DJ, Quirino BF, Sussman MR (2008) Analysis of the Arabidopsis histidine kinase ATHK1 reveals a connection between vegetative osmotic stress sensing and seed maturation. Plant Cell 20(4):1101–1117

    PubMed Central  CAS  PubMed  Google Scholar 

  • Wrzaczek M, Brosché M, Kangasjärvi J (2013) ROS signaling loops—production, perception, regulation. Curr Opin Plant Biol 16(5):575–582

    CAS  PubMed  Google Scholar 

  • Xia Y, Suzuki H, Borevitz J, Blount J, Guo Z, Patel K, Dixon RA, Lamb C (2004) An extracellular aspartic protease functions in Arabidopsis disease resistance signaling. EMBO J 23(4):980–988

    PubMed Central  CAS  PubMed  Google Scholar 

  • Xiong L, Zhu J-K (2003) Regulation of abscisic acid biosynthesis. Plant Physiol 133(1):29–36

    PubMed Central  CAS  PubMed  Google Scholar 

  • Xin Z, Wang ML, Barkley NA, Burow G, Franks C, Pederson G, Burke J (2008) Applying genotyping (TILLING) and phenotyping analyses to elucidate gene function in a chemically induced sorghum mutant population. BMC Plant Biology 8 (1):103

    Google Scholar 

  • Yamaguchi-Shinozaki K, Shinozaki K (1994) A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell 6(2):251–264

    PubMed Central  CAS  PubMed  Google Scholar 

  • Yamaguchi-Shinozaki K, Shinozaki K (2005) Organization of cis-acting regulatory elements in osmotic-and cold-stress-responsive promoters. Trends Plant Sci 10(2):88–94

    CAS  PubMed  Google Scholar 

  • Yamamoto K, Sasaki T (1997) Large-scale EST sequencing in rice. Plant Mol Biol 35(1–2):135–144

    CAS  PubMed  Google Scholar 

  • Yamamoto YY, Tsuhara Y, Gohda K, Suzuki K, Matsui M (2003) Gene trapping of the Arabidopsis genome with a firefly luciferase reporter. Plant J 35(2):273–283

    CAS  PubMed  Google Scholar 

  • Yan S, Tang Z, Su W, Sun W (2005) Proteomic analysis of salt stress-responsive proteins in rice root. Proteomics 5(1):235–244

    CAS  PubMed  Google Scholar 

  • Yoshida R, Hobo T, Ichimura K, Mizoguchi T, Takahashi F, Aronso J, Ecker JR, Shinozaki K (2002) ABA-activated SnRK2 protein kinase is required for dehydration stress signaling in Arabidopsis. Plant Cell Physiol 43(12):1473–1483

    CAS  PubMed  Google Scholar 

  • Yu H, Chen X, Hong Y-Y, Wang Y, Xu P, Ke S-D, Liu H-Y, Zhu J-K, Oliver DJ, Xiang C-B (2008) Activated expression of an Arabidopsis HD-START protein confers drought tolerance with improved root system and reduced stomatal density. Plant Cell 20(4):1134–1151

    PubMed Central  CAS  PubMed  Google Scholar 

  • Yu S, Liao F, Wang F, Wen W, Li J, Mei H, Luo L (2012) Identification of rice transcription factors associated with drought tolerance using the ecotilling method. PLoS One 7(2):e30765

    PubMed Central  CAS  PubMed  Google Scholar 

  • Yuan L, Liu X, Luo M, Yang S, Wu K (2013) Involvement of histone modifications in plant abiotic stress responses. J Integr Plant Biol 55(10):892–901

    CAS  PubMed  Google Scholar 

  • Zamore PD, Tuschl T, Sharp PA, Bartel DP (2000) RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101(1):25–33

    CAS  PubMed  Google Scholar 

  • Zhang H, Sreenivasulu N, Weschke W, Stein N, Rudd S, Radchuk V, Potokina E, Scholz U, Schweizer P, Zierold U (2004) Large-scale analysis of the barley transcriptome based on expressed sequence tags. Plant J 40(2):276–290

    PubMed  Google Scholar 

  • Zhang W, Zhou R-G, Gao Y-J, Zheng S-Z, Xu P, Zhang S-Q, Sun D-Y (2009) Molecular and genetic evidence for the key role of AtCaM3 in heat-shock signal transduction in Arabidopsis. Plant Physiol 149(4):1773–1784

    PubMed Central  CAS  PubMed  Google Scholar 

  • Zinn KE, Tunc-Ozdemir M, Harper JF (2010) Temperature stress and plant sexual reproduction: uncovering the weakest links. J Exp Bot 61(7):1959–1968

    PubMed Central  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Botany, University of Delhi, New Delhi, Delhi, 110 007, India

    Swati Singh, Nisha Khatri, Arpana Katiyar & Yashwanti Mudgil

Authors
  1. Swati Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nisha Khatri
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Arpana Katiyar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yashwanti Mudgil
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yashwanti Mudgil .

Editor information

Editors and Affiliations

  1. Department of Plant Molecular Biology, University of Delhi South Campus, Dhaula Kuan, India

    Girdhar K. Pandey

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this chapter

Cite this chapter

Singh, S., Khatri, N., Katiyar, A., Mudgil, Y. (2015). Molecular Approaches in Deciphering Abiotic Stress Signaling Mechanisms in Plants. In: Pandey, G. (eds) Elucidation of Abiotic Stress Signaling in Plants. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-2211-6_2

Download citation

Publish with us

Policies and ethics

Search

Navigation