Skip to main content

Different Omics Approaches in Cereals and Their Possible Implications for Developing a System Biology Approach to Study the Mechanism of Abiotic Stress Tolerance

  • Chapter
  • First Online:
Book cover Cereal Genomics II

Abstract

Cereals comprise a number of crops including rice, wheat, maize, barley, rye and sorghum. In the form of starch and proteins, the cereal grains provide nearly 60 % of the calories consumed globally as food and fodder. There is a growing challenge to meet the global demand of food security for a human population of 9 billion expected by the year 2050.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
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

  • Agarwal PK, Agarwal P, Reddy MK, Sopory SK (2006) Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Rep 25:1263–1274

    Article  PubMed  CAS  Google Scholar 

  • Agrawal GK, Rakwal R (2006) Rice proteomics: a cornerstone for cereal food crop proteomes. Mass Spectrom Rev 25:1–53

    Article  PubMed  CAS  Google Scholar 

  • Agrawal GK, Rakwal R (2011) Rice proteomics: a move toward expanded proteome coverage to comparative and functional proteomics uncovers the mysteries of rice and plant biology. Proteomics 11:1630–1649

    Article  PubMed  CAS  Google Scholar 

  • Alcazar R, Garcia-Martinez JL, Cuevas JC, Tiburcio AF, Altabella T (2005) Overexpression of ADC2 in Arabidopsis induces dwarfism and late-flowering through GA deficiency. Plant J 43:425–436

    Article  PubMed  CAS  Google Scholar 

  • Ali GM, Komatsu S (2006) Proteomic analysis of rice leaf sheath during drought stress. J Proteome Res 5:396–403

    Article  PubMed  CAS  Google Scholar 

  • Allen DK, Shachar-Hill Y, Ohlrogge JB (2007) Compartment-specific labeling information in 13C metabolic flux analysis of plants. Phytochemistry 68:2197–2210

    Article  PubMed  CAS  Google Scholar 

  • Alonso AP, Vigeolas H, Raymond P, Rolin D, Dieuaide-Noubhani M (2005) A new substrate cycle in plants. Evidence for a high glucose-phosphate-to-glucose turnover from in vivo steady-state and pulse-labeling experiments with [13C] glucose and [14C] glucose. Plant Physiol 138:2220–2232

    Article  PubMed  CAS  Google Scholar 

  • Alves SC, Worland B, Thole V, Snape JW, Bevan MW, Vain P (2009) A protocol for agrobacterium-mediated transformation of brachypodium distachyon community standard line Bd21. Nat Protoc 4:638–649

    Article  PubMed  CAS  Google Scholar 

  • Amudha J, Balasubramani G (2011) Recent molecular advances to cambat abiotic stress tolerance in crop plants. Biotech Mol Bio Rev 6:31–58

    CAS  Google Scholar 

  • An GH, Lee S, Kim SH, Kim SR (2005) Molecular genetics using T-DNA in rice. Plant Cell Physiol 46:14–22

    Article  PubMed  CAS  Google Scholar 

  • Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218

    Article  CAS  Google Scholar 

  • Bansal M, Belcastro V, Ambesi-Impiombato A, di Bernardo D (2007) How to infer gene networks from expression profiles. Mol Syst Biol 3(1):78

    PubMed  Google Scholar 

  • Bartels D, Sunkar R (2005) Drought and salt tolerance in plants. Crit Rev Plant Sci 24:23–58

    Article  CAS  Google Scholar 

  • Battisti DS, Naylor RL (2009) Historical warnings of future food insecurity with unprecedented seasonal heat. Science 323:240–244

    Article  PubMed  CAS  Google Scholar 

  • Becker J, Klopprogge C, Herold A, Zelder O, Bolten CJ, Wittmann C (2007) Metabolic flux engineering of L-lysine production in corynebacterium glutamicum: over expression and modification of G6P dehydrogenase. J Biotechnol 132:99–109

    Article  PubMed  CAS  Google Scholar 

  • Berhan AM, Hulbert SH, Butler LG, Bennetzen JL (1993) Structure and evolution of the genomes of sorghum-bicolor and zea-mays. Theor Appl Genet 86:598–604

    Article  CAS  Google Scholar 

  • Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EY, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubalakova M, Simkova H, Batley J, Fleury D, Dolezel J, Edwards D (2011) Sequencing and assembly of low copy and genic regions of isolated triticum aestivum chromosome arm 7DS. Plant Biotechnol J 9:768–775

    Article  PubMed  CAS  Google Scholar 

  • Bino RJ, Hall RD, Fiehn O, Kopka J, Saito K, Draper J, Nikolau BJ, Mendes P, Roessner-Tunali U, Beale MH, Trethewey RN, Lange BM, Wurtele ES, Sumner LW (2004) Potential of metabolomics as a functional genomics tool. Trends Plant Sci 9:418–425

    Article  PubMed  CAS  Google Scholar 

  • Boatright J, Negre F, Chen XL, Kish CM, Wood B, Peel G, Orlova I, Gang D, Rhodes D, Dudareva N (2004) Understanding in vivo benzenoid metabolism in petunia petal tissue. Plant Physiol 135:1993–2011

    Article  PubMed  CAS  Google Scholar 

  • Bombarely A, Menda N, Tecle IY, Buels RM, Strickler S, Fischer-York T, Pujar A, Leto J, Gosselin J, Mueller LA (2011) The sol genomics network (solgenomics.net): growing tomatoes using perl. Nucleic Acids Res 39:D1149–D1155

    Article  PubMed  CAS  Google Scholar 

  • Caldana C, Degenkolbe T, Cuadros-Inostroza A, Klie S, Sulpice R, Leisse A, Steinhauser D, Fernie AR, Willmitzer L, Hannah MA (2011) High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to eight environmental conditions. Plant J 67:869–884

    Article  PubMed  CAS  Google Scholar 

  • Canovas FM, Dumas-Gaudot E, Recorbet G, Jorrin J, Mock HP, Rossignol M (2004) Plant proteome analysis. Proteomics 4:285–298

    Article  PubMed  CAS  Google Scholar 

  • Carrera J, Rodrigo G, Jaramillo A, Elena SF (2009) Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions. Genome biology 10(9):R96

    Article  PubMed  CAS  Google Scholar 

  • Carro MS, Lim WK, Alvarez MJ, Bollo RJ, Zhao XD, Snyder EY, Sulman EP, Anne SL, Doetsch F, Colman H, Lasorella A, Aldape K, Califano A, Iavarone A (2010) The transcriptional network for mesenchymal transformation of brain tumours. Nature 463:318–368

    Article  PubMed  CAS  Google Scholar 

  • Caruso G, Cavaliere C, Foglia P, Gubbiotti R, Samperi R, Lagana A (2009) Analysis of drought responsive proteins in wheat (Triticum durum) by 2D-PAGE and MALDI-TOF mass spectrometry. Plant Sci 177:570–576

    Article  CAS  Google Scholar 

  • Casati P, Morrow DJ, Fernandes JF, Walbot V (2011) Rapid Maize leaf and immature ear responses to UV-B radiation. Front Plant Sci 2:33

    Article  PubMed  CAS  Google Scholar 

  • Chantret N, Salse J, Sabot F, Rahman S, Bellec A, Laubin B, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier MF, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Bernard M, Leroy P, Chalhoub B (2005) Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and aegilops). Plant Cell 17:1033–1045

    Article  PubMed  CAS  Google Scholar 

  • Charng YY, Liu HC, Liu NY, Hsu FC, Ko SS (2006) Arabidopsis Hsa32, a novel heat shock protein, is essential for acquired thermotolerance during long recovery after acclimation. Plant Physiol 140:1297–1305

    Article  PubMed  CAS  Google Scholar 

  • Christensen B, Nielsen J (2000) Metabolic network analysis. A powerful tool in metabolic engineering. Adv Biochem Eng Biotechnol 66:209–231

    PubMed  CAS  Google Scholar 

  • Collins NC, Tardieu F, Tuberosa R (2008) Quantitative trait loci and crop performance under abiotic stress: where do we stand? Plant Physiol 147:469–486

    Article  PubMed  CAS  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 USA 101:15243–15248

    Article  PubMed  CAS  Google Scholar 

  • Craigon DJ, James N, Okyere J, Higgins J, Jotham J, May S (2004) NASCArrays: a repository for microarray data generated by NASC’s transcriptomics service. Nucleic Acids Res 32:D575–D577

    Article  PubMed  CAS  Google Scholar 

  • Cramer GR, Ergul A, Grimplet J, Tillett RL, Tattersall EAR, Bohlman MC, Vincent D, Sonderegger J, Evans J, Osborne C, Quilici D, Schlauch KA, Schooley DA, Cushman JC (2007) Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles. Funct Integr Genomics 7:111–134

    Article  PubMed  CAS  Google Scholar 

  • Cramer GR, Urano K, Delrot S, Pezzotti M, Shinozaki K (2011) Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biol 11(1):63

    Article  Google Scholar 

  • de la Fuente A, Brazhnik P, Mendes P (2002) Linking the genes: inferring quantitative gene networks from microarray data. Trends Genet: TIG 18:395–398

    Article  PubMed  Google Scholar 

  • de Vienne D, Leonardi A, Damerval C, Zivy M (1999) Genetics of proteome variation for QTL characterization: application to drought-stress responses in maize. J Exp Bot 50:303–309

    Google Scholar 

  • Deeb F, van der Weele CM, Wolniak SM (2010) Spermidine is a morphogenetic determinant for cell fate specification in the male gametophyte of the water fern marsilea vestita. Plant Cell 22:3678–3691

    Article  PubMed  CAS  Google Scholar 

  • Des Rosiers C, Lloyd S, Comte B, Chatham JC (2004) A critical perspective of the use of C-13-isotopomer analysis by GCMS and NMR as applied to cardiac metabolism. Metab Eng 6:44–58

    Article  PubMed  CAS  Google Scholar 

  • Deyholos MK (2010) Making the most of drought and salinity transcriptomics. Plant Cell Environ 33:648–654

    Article  PubMed  CAS  Google Scholar 

  • Dieuaide-Noubhani M, Raffard G, Canioni P, Pradet A, Raymond P (1995) Quantification of compartmented metabolic fluxes in maize root tips using isotope distribution from 13C- or 14C-labeled glucose. J Biol Chem 270:13147–13159

    Article  PubMed  CAS  Google Scholar 

  • Dixon RA, Strack D (2003) Phytochemistry meets genome analysis, and beyond. Phytochemistry 62:815–816

    Article  PubMed  CAS  Google Scholar 

  • Dolezel J, Kubalakova M, Paux E, Bartos J, Feuillet C (2007) Chromosome-based genomics in the cereals. Chromosome Res: Int J Mol, Supramol Evol Aspects Chromosome Biol 15:51–66

    Article  CAS  Google Scholar 

  • Dooki AD, Mayer-Posner FJ, Askari H, Zaiee AA, Salekdeh GH (2006) Proteomic responses of rice young panicles to salinity. Proteomics 6:6498–6507

    Article  PubMed  CAS  Google Scholar 

  • Druka A, Franckowiak J, Lundqvist U, Bonar N, Alexander J, Houston K, Radovic S, Shahinnia F, Vendramin V, Morgante M, Stein N, Waugh R (2011) Genetic dissection of barley morphology and development. Plant Physiol 155:617–627

    Article  PubMed  CAS  Google Scholar 

  • Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman A, Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R (2006) An atlas of gene expression from seed to seed through barley development. Funct Integr Genomics 6:202–211

    Article  PubMed  CAS  Google Scholar 

  • Eastmond PJ, van Dijken AJH, Spielman M, Kerr A, Tissier AF, Dickinson HG, Jones JDG, Smeekens SC, Graham IA (2002) Trehalose-6-phosphate synthase 1, which catalyses the first step in trehalose synthesis, is essential for Arabidopsis embryo maturation. Plant J 29:225–235

    Article  PubMed  CAS  Google Scholar 

  • Edwards D, Batley J (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnol J 8:2–9

    Article  PubMed  CAS  Google Scholar 

  • Edwards S, Nguyen BT, Do B, Roberts JKM (1998) Contribution of malic enzyme, pyruvate kinase, phosphoenolpyruvate carboxylase, and the krebs cycle to respiration and biosynthesis and to intracellular pH regulation during hypoxia in maize root tips observed by nuclear magnetic resonance imaging and gas chromatography-mass spectrometry. Plant Physiol 116:1073–1081

    Article  PubMed  CAS  Google Scholar 

  • Ergen NZ, Budak H (2009) Sequencing over 13,000 expressed sequence tags from six subtractive cDNA libraries of wild and modern wheats following slow drought stress. Plant, Cell Environ 32:220–236

    Article  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Espinoza C, Degenkolbe T, Caldana C, Zuther E, Leisse A, Willmitzer L, Hincha DK, Hannah MA (2010) Interaction with diurnal and circadian regulation results in dynamic metabolic and transcriptional changes during cold acclimation in Arabidopsis. PloS one 5(11):e14101

    Article  PubMed  CAS  Google Scholar 

  • Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BO (2009) Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 7:129–143

    PubMed  CAS  Google Scholar 

  • Feuillet C, Keller B (2002) Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann Bot 89:3–10

    Article  PubMed  CAS  Google Scholar 

  • Fiehn O (2002) Metabolomics: the link between genotypes and phenotypes. Plant Mol Biol 48:155–171

    Article  PubMed  CAS  Google Scholar 

  • Filiz E, Ozdemir BS, Budak F, Vogel JP, Tuna M, Budak H (2009) Molecular, morphological, and cytological analysis of diverse Brachypodium distachyon inbred lines. Genome 52:876–890 National Research Council Canada, Conseil National de Recherches Canada

    Article  PubMed  CAS  Google Scholar 

  • Finkel E (2009) Imaging With ‘phenomics’, plant scientists hope to shift breeding into overdrive. Science 325:380–381

    Article  PubMed  CAS  Google Scholar 

  • Finnie C, Melchior S, Roepstorff P, Svensson B (2002) Proteome analysis of grain filling and seed maturation in barley. Plant Physiol 129:1308–1319

    Article  PubMed  CAS  Google Scholar 

  • Fleury D, Jefferies S, Kuchel H, Langridge P (2010) Genetic and genomic tools to improve drought tolerance in wheat. J Exp Bot 61:3211–3222

    Article  PubMed  CAS  Google Scholar 

  • Frick O, Wittmann C (2005) Characterization of the metabolic shift between oxidative and fermentative growth in Saccharomyces cerevisiae by comparative C-13 flux analysis. Microb Cell Fact 4

    Google Scholar 

  • Fujita M, Mizukado S, Fujita Y, Ichikawa T, Nakazawa M, Seki M, Matsui M, Yamaguchi-Shinozaki K, Shinozaki K (2007) Identification of stress-tolerance-related transcription-factor genes via mini-scale Full-length cDNA Over-eXpressor (FOX) gene hunting system. Biochem Bioph Res Co 364:250–257

    Article  CAS  Google Scholar 

  • Furbank RT, Tester M (2011) Phenomics: technologies to relieve the phenotyping bottleneck. Trends Plant Sci 16:635–644

    Article  PubMed  CAS  Google Scholar 

  • Gagneul D, Ainouche A, Duhaze C, Lugan R, Larher FR, Bouchereau A (2007) A reassessment of the function of the so-called compatible solutes in the halophytic Plumbaginaceae Limonium latifolium. Plant Physiol 144:1598–1611

    Article  PubMed  CAS  Google Scholar 

  • Garvin DF, McKenzie N, Vogel JP, Mockler TC, Blankenheim ZJ, Wright J, Cheema JJS, Dicks J, Huo NX, Hayden DM, Gu Y, Tobias C, Chang JH, Chu A, Trick M, Michael TP, Bevan MW, Snape JW (2010) An SSR-based genetic linkage map of the model grass Brachypodium distachyon. Genome 53:1–13 National Research Council Canada, Conseil National de Recherches Canada

    Article  PubMed  CAS  Google Scholar 

  • Geu-Flores F, Nielsen MT, Nafisi M, Moldrup ME, Olsen CE, Motawia MS, Halkier BA (2009) Glucosinolate engineering identifies a gamma-glutamyl peptidase. Nat Chem Biol 5:575–577

    Article  PubMed  CAS  Google Scholar 

  • Gibon Y, Usadel B, Blaesing OE, Kamlage B, Hoehne M, Trethewey R, Stitt M (2006) Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes. Genome Biol 7:R76

    Article  PubMed  Google Scholar 

  • Glawischnig E, Gierl A, Tomas A, Bacher A, Eisenreich W (2001) Retrobiosynthetic nuclear magnetic resonance analysis of amino acid biosynthesis and intermediary metabolism. Metabolic flux in developing maize kernels. Plant Physiol 125:1178–1186

    Article  PubMed  CAS  Google Scholar 

  • Glawischnig E, Gierl A, Tomas A, Bacher A, Eisenreich W (2002) Starch biosynthesis and intermediary metabolism in maize kernels. Quantitative analysis of metabolite flux by nuclear magnetic resonance. Plant Physiol 130:1717–1727

    Article  PubMed  CAS  Google Scholar 

  • Goda H, Sasaki E, Akiyama K, Maruyama-Nakashita A, Nakabayashi K, Li WQ, Ogawa M, Yamauchi Y, Preston J, Aoki K, Kiba T, Takatsuto S, Fujioka S, Asami T, Nakano T, Kato H, Mizuno T, Sakakibara H, Yamaguchi S, Nambara E, Kamiya Y, Takahashi H, Hirai MY, Sakurai T, Shinozaki K, Saito K, Yoshida S, Shimada Y (2008) The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. Plant Journal 55:526–542

    Article  PubMed  CAS  Google Scholar 

  • Goff SA, Ricke D, Lan TH, Presting G, Wang RL, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchinson D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong JP, Miguel T, Paszkowski U, Zhang SP, Colbert M, Sun WL, Chen LL, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu YS, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science 296:92–100

    Article  PubMed  CAS  Google Scholar 

  • Gomez-Porras JL, Riano-Pachon DM, Dreyer I, Mayer JE, Mueller-Roeber B (2007) Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC Genomics 8(1):260

    Article  PubMed  CAS  Google Scholar 

  • Gong QQ, Li PH, Ma SS, Rupassara SI, Bohnert HJ (2005) Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana. Plant J 44:826–839

    Article  PubMed  CAS  Google Scholar 

  • Grafahrend-Belau E, Schreiber F, Koschutzki D, Junker BH (2009) Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. Plant Physiol 149:585–598

    Article  PubMed  CAS  Google Scholar 

  • Gu YQ, Ma YQ, Huo NX, Vogel JP, You FM, Lazo GR, Nelson WM, Soderlund C, Dvorak J, Anderson OD, Luo MC (2009) A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. BMC Genomics 10(1):496

    Article  PubMed  CAS  Google Scholar 

  • Gupta AK, Kaur N (2005) Sugar signalling and gene expression in relation to carbohydrate metabolism under abiotic stresses in plants. J Biosciences 30:761–776

    Article  CAS  Google Scholar 

  • Gupta PK, Mir RR, Mohan A, Kumar J (2008) Wheat genomics: present status and future prospects. Int J Plant Genomics 2008:896451

    PubMed  CAS  Google Scholar 

  • Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17:994–999

    Article  PubMed  CAS  Google Scholar 

  • Haberer G, Young S, Bharti AK, Gundlach H, Raymond C, Fuks G, Butler E, Wing RA, Rounsley S, Birren B, Nusbaum C, Mayer KF, Messing J (2005) Structure and architecture of the maize genome. Plant Physiol 139:1612–1624

    Article  PubMed  CAS  Google Scholar 

  • Hache H, Lehrach H, Herwig R (2009) Reverse engineering of gene regulatory networks: a comparative study. EURASIP J Bioinf Syst Biol 2009:8

    Google Scholar 

  • Hadiarto T, Tran LS (2011) Progress studies of drought-responsive genes in rice. Plant Cell Rep 30:297–310

    Article  PubMed  CAS  Google Scholar 

  • Hagel JM, Facchini PJ (2008) Plant metabolomics: analytical platforms and integration with functional genomics. Phytochem Rev 7:479–497

    Article  CAS  Google Scholar 

  • Hajheidari M, Eivazi A, Buchanan BB, Wong JH, Majidi I, Salekdeh GH (2007) Proteomics uncovers a role for redox in drought tolerance in wheat. J Proteome Res 6:1451–1460

    Article  PubMed  CAS  Google Scholar 

  • Hall RD (2006) Plant metabolomics: from holistic hope, to hype, to hot topic. New Phytol 169:453–468

    Article  PubMed  CAS  Google Scholar 

  • Hamada K, Hongo K, Suwabe K, Shimizu A, Nagayama T, Abe R, Kikuchi S, Yamamoto N, Fujii T, Yokoyama K, Tsuchida H, Sano K, Mochizuki T, Oki N, Horiuchi Y, Fujita M, Watanabe M, Matsuoka M, Kurata N, Yano K (2011) OryzaExpress: an integrated database of gene expression networks and omics annotations in rice. Plant Cell Physiol 52:220–229

    Article  PubMed  CAS  Google Scholar 

  • Hansen BG, Kliebenstein DJ, Halkier BA (2007) Identification of a flavin-monooxygenase as the S-oxygenating enzyme in aliphatic glucosinolate biosynthesis in Arabidopsis. Plant J 50:902–910

    Article  PubMed  CAS  Google Scholar 

  • Hanzawa Y, Takahashi T, Michael AJ, Burtin D, Long D, Pineiro M, Coupland G, Komeda Y (2000) ACAULIS5 an Arabidopsis gene required for stem elongation, encodes a spermine synthase. EMBO J 19:4248–4256

    Article  PubMed  CAS  Google Scholar 

  • Harrigan GG, Stork LG, Riordan SG, Ridley WP, Macisaac S, Halls SC, Orth R, Rau D, Smith RG, Wen L, Brown WE, Riley R, Sun D, Modiano S, Pester T, Lund A, Nelson D (2007) Metabolite analyses of grain from maize hybrids grown in the United States under drought and watered conditions during the 2002 field season. J Agricu Food Chem 55:6169–6176

    Article  CAS  Google Scholar 

  • Hasegawa PM, Bressan RA, Zhu JK, Bohnert HJ (2000) Plant cellular and molecular responses to high salinity. Ann Rev Plant Physiol Plant Mol Biol 51:463–499

    Article  CAS  Google Scholar 

  • Hayes PM, Castro A, Marquez-Cedillo L, Corey A, Henson C, Jones B, Kling J, Mather D, Matus I, Rossi C, Sato K (2003) Genetic diversity for quantitatively inherited agronomic and malting quality traits. In: Von Bothmer R, Knupfeer H, van Hintum T, Sato K (eds) Diversity barley. Elsevier Science Publishers, Amsterdam

    Google Scholar 

  • Helmy M, Tomita M, Ishihama Y (2011) OryzaPG-DB: rice proteome database based on shotgun proteogenomics. BMC Plant Biol 11:63

    Article  PubMed  CAS  Google Scholar 

  • Hirai MY, Sugiyama K, Sawada Y, Tohge T, Obayashi T, Suzuki A, Araki R, Sakurai N, Suzuki H, Aoki K, Goda H, Nishizawa OI, Shibata D, Saito K (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc Natl Acad Sci USA 104:6478–6483

    Article  PubMed  CAS  Google Scholar 

  • Hirai MY, Yano M, Goodenowe DB, Kanaya S, Kimura T, Awazuhara M, Arita M, Fujiwara T, Saito K (2004) Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc Natl Acad Sci USA 101:10205–10210

    Article  PubMed  CAS  Google Scholar 

  • Horan K, Jang C, Bailey-Serres J, Mittler R, Shelton C, Harper JF, Zhu JK, Cushman JC, Gollery M, Girke T (2008) Annotating genes of known and unknown function by large-scale coexpression analysis. Plant Physiol 147:41–57

    Article  PubMed  CAS  Google Scholar 

  • Hu WH, Hu GC, Han B (2009) Genome-wide survey and expression profiling of heat shock proteins and heat shock factors revealed overlapped and stress specific response under abiotic stresses in rice. Plant Sci 176:583–590

    Article  CAS  Google Scholar 

  • Huo CM, Zhao BC, Ge RC, Shen YZ, Huang ZJ (2004) Proteomic analysis of the salt tolerance mutant of wheat under salt stress. Acta Genetica Sinica 31:1408–1414 Yi chuan xue bao

    PubMed  CAS  Google Scholar 

  • Huo NX, Gu YQ, Lazo GR, Vogel JP, Coleman-Derr D, Luo MC, Thilmony R, Garvin DF, Anderson OD (2006) Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome 49(9):1099–1108 National Research Council Canada, Conseil National de Recherches Canada

    Article  PubMed  CAS  Google Scholar 

  • Huo NX, Lazo GR, Vogel JP, You FM, Ma YQ, Hayde DM, Coleman-Derr D, Hill TA, Dvorak J, Anderson OD, Luo MC, Gu YQ (2008) The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Funct Integr Genomics 8:135–147

    Article  PubMed  CAS  Google Scholar 

  • Imai A, Matsuyama T, Hanzawa Y, Akiyama T, Tamaoki M, Saji H, Shirano Y, Kato T, Hayashi H, Shibata D, Tabata S, Komeda Y, Takahashi T (2004) Spermidine synthase genes are essential for survival of Arabidopsis. Plant Physiol 135:1565–1573

    Article  PubMed  CAS  Google Scholar 

  • Ingram J, Bartels D (1996) The molecular basis of dehydration tolerance in plants. Ann Rev Plant Physiol Plant Mol Biol 47:377–403

    Article  CAS  Google Scholar 

  • Intergovernmental Panel on Climate Change (IPCC) (2007) In: Pachauri RK, Reisinger A (eds) Climate change 2007 synthesis report. IPCC, Geneva

    Google Scholar 

  • Izawa T, Mihara M, Suzuki Y, Gupta M, Itoh H, Nagano AJ, Motoyama R, Sawada Y, Yano M, Hirai MY, Makino A, Nagamura Y (2011) Os-GIGANTEA confers robust diurnal rhythms on the global transcriptome of rice in the field. Plant Cell 23:1741–1755

    Article  PubMed  CAS  Google Scholar 

  • Janz D, Behnke K, Schnitzler JP, Kanawati B, Schmitt-Kopplin P, Polle A (2010) Pathway analysis of the transcriptome and metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms. BMC Plant Biol 10:150

    Article  PubMed  CAS  Google Scholar 

  • Jeanneau M, Gerentes D, Foueillassar X, Zivy M, Vidal J, Toppan A, Perez P (2002) Improvement of drought tolerance in maize: towards the functional validation of the Zm-Asr1 gene and increase of water use efficiency by over-expressing C4-PEPC. Biochimie 84:1127–1135

    Article  PubMed  CAS  Google Scholar 

  • Jordan KW, Nordenstam J, Lauwers GY, Rothenberger DA, Alavi K, Garwood M, Cheng LL (2009) Metabolomic characterization of human rectal adenocarcinoma with intact tissue magnetic resonance spectroscopy. Dis Colon Rectum 52:520–525

    Article  PubMed  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 136:4159–4168

    Article  PubMed  CAS  Google Scholar 

  • Kaplan F, Kopka J, Sung DY, Zhao W, Popp M, Porat R, Guy CL (2007) Transcript and metabolite profiling during cold acclimation of Arabidopsis reveals an intricate relationship of cold-regulated gene expression with modifications in metabolite content. Plant Journal 50:967–981

    Article  PubMed  CAS  Google Scholar 

  • Kell DB, Brown M, Davey HM, Dunn WB, Spasic I, Oliver SG (2005) Metabolic footprinting and systems biology: the medium is the message. Nat Rev Microbiol 3:557–565

    Article  PubMed  CAS  Google Scholar 

  • Kempa S, Krasensky J, Dal Santo S, Kopka J, Jonak C (2008) A central role of abscisic acid in stress-regulated carbohydrate metabolism. PLoS ONE 3:e3935

    Article  PubMed  CAS  Google Scholar 

  • Kempa S, Rozhon W, Samaj J, Erban A, Baluska F, Becker T, Haselmayer J, Schleiff E, Kopka J, Hirt H, Jonak C (2007) A plastid-localized glycogen synthase kinase 3 modulates stress tolerance and carbohydrate metabolism. Plant J 49:1076–1090

    Article  PubMed  CAS  Google Scholar 

  • Kholodenko BN, Kiyatkin A, Bruggeman FJ, Sontag E, Westerhoff HV, Hoek JB (2002) Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. Proc Natl Acad Sci USA 99:12841–12846

    Article  PubMed  CAS  Google Scholar 

  • Kiba T, Kudo T, Kojima M, Sakakibara H (2011) Hormonal control of nitrogen acquisition: roles of auxin, abscisic acid, and cytokinin. J Exp Bot 62:1399–1409

    Article  PubMed  CAS  Google Scholar 

  • Kiefer P, Heinzle E, Zelder O, Wittmann C (2004) Comparative metabolic flux analysis of lysine-producing Corynebacterium glutamicum cultured on glucose or fructose. Appl Environ Microbiol 70:229–239

    Article  PubMed  CAS  Google Scholar 

  • Kim ST, Cho KS, Yu S, Kim SG, Hong JC, Han CD, Bae DW, Nam MH, Kang KY (2003) Proteomic analysis of differentially expressed proteins induced by rice blast fungus and elicitor in suspension-cultured rice cells. Proteomics 3:2368–2378

    Article  PubMed  CAS  Google Scholar 

  • Kimura M, Yamamoto YY, Seki M, Sakurai T, Sato M, Abe T, Yoshida S, Manabe K, Shinozaki K, Matsui M (2003) Identification of Arabidopsis genes regulated by high light-stress using cDNA microarray. Photochem Photobiol 77:226–233

    PubMed  CAS  Google Scholar 

  • Kishor PBK, Sangam S, Amrutha RN, Laxmi PS, Naidu KR, Rao KRSS, Rao S, Reddy KJ, Theriappan P, Sreenivasulu N (2005) Regulation of proline biosynthesis, degradation, uptake and transport in higher plants: Its implications in plant growth and abiotic stress tolerance. Curr Sci India 88:424–438

    CAS  Google Scholar 

  • Kitano H (2000) Perspectives on systems biology. New Generat Comput 18:199–216

    Article  Google Scholar 

  • Kogel KH, Voll LM, Schafer P, Jansen C, Wu YC, Langen G, Imani J, Hofmann J, Schmiedl A, Sonnewald S, von Wettstein D, Cook RJ, Sonnewald U (2010) Transcriptome and metabolome profiling of field-grown transgenic barley lack induced differences but show cultivar-specific variances. Proc Natl Acad Sci USA 107:6198–6203

    Article  PubMed  CAS  Google Scholar 

  • Kohli A, Narciso JO, Miro B, Raorane M (2012) Root proteases: reinforced links between nitrogen uptake and mobilization and drought tolerance. Physiol Plant 145:165–179

    Article  PubMed  CAS  Google Scholar 

  • Komatsu S, Yano H (2006) Update and challenges on proteomics in rice. Proteomics 6:4057–4068

    Article  PubMed  CAS  Google Scholar 

  • Kondou Y, Higuchi M, Takahashi S, Sakurai T, Ichikawa T, Kuroda H, Yoshizumi T, Tsumoto Y, Horii Y, Kawashima M, Hasegawa Y, Kuriyama T, Matsui K, Kusano M, Albinsky D, Takahashi H, Nakamura Y, Suzuki M, Sakakibara H, Kojima M, Akiyama K, Kurotani A, Seki M, Fujita M, Enju A, Yokotani N, Saitou T, Ashidate K, Fujimoto N, Ishikawa Y, Mori Y, Nanba R, Takata K, Uno K, Sugano S, Natsuki J, Dubouzet JG, Maeda S, Ohtake M, Mori M, Oda K, Takatsuji H, Hirochika H, Matsui M (2009) Systematic approaches to using the FOX hunting system to identify useful rice genes. Plant J 57:883–894

    Article  PubMed  CAS  Google Scholar 

  • Koornneef M, AlonsoBlanco C, Peeters AJM (1997) Genetic approaches in plant physiology. New Phytol 137:1–8

    Article  Google Scholar 

  • Kremling A, Fischer S, Gadkar K, Doyle FJ, Sauter T, Bullinger E, Allgower F, Gilles ED (2004) A benchmark for methods in reverse engineering and model discrimination: Problem formulation and solutions. Genome Res 14:1773–1785

    Article  PubMed  CAS  Google Scholar 

  • Kreps JA, Wu Y, Chang HS, Zhu T, Wang X, Harper JF (2002) Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol 130:2129–2141

    Article  PubMed  CAS  Google Scholar 

  • Krishnan A, Guiderdoni E, An G, Hsing YIC, Han CD, Lee MC, Yu SM, Upadhyaya N, Ramachandran S, Zhang QF, Sundaresan V, Hirochika H, Leung H, Pereira A (2009) Mutant resources in rice for functional genomics of the grasses. Plant Physiol 149:165–170

    Article  PubMed  CAS  Google Scholar 

  • Kruger NJ, Le Lay P, Ratcliffe RG (2007) Vacuolar compartmentation complicates the steady-state analysis of glucose metabolism and forces reappraisal of sucrose cycling in plants. Phytochemistry 68:2189–2196

    Article  PubMed  CAS  Google Scholar 

  • Kumar CS, Wing RA, Sundaresan V (2005) Efficient insertional mutagenesis in rice using the maize En/Spm elements. Plant J 44:879–892

    Article  PubMed  CAS  Google Scholar 

  • Kuromori T, Takahashi S, Kondou Y, Shinozaki K, Matsui M (2009) phenome analysis in plant species using loss-of-function and gain-of-function mutants. Plant Cell Physiol 50:1215–1231

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Lee TH, Kim YK, Pham TT, Song SI, Kim JK, Kang KY, An G, Jung KH, Galbraith DW, Kim M, Yoon UH, Nahm BH (2009) RiceArrayNet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice. Plant Physiol 151:16–33

    Article  PubMed  CAS  Google Scholar 

  • Li Y, Shrestha B, Vertes A (2008) Atmospheric pressure infrared MALDI imaging mass spectrometry for plant metabolomics. Anal Chem 80:407–420

    Article  PubMed  CAS  Google Scholar 

  • Lim CJ, Yang KA, Hong JK, Choi JS, Yun DJ, Hong JC, Chung WS, Lee SY, Cho MJ, Lim CO (2006) Gene expression profiles during heat acclimation in Arabidopsis thaliana suspension-culture cells. J Plant Res 119:373–383

    Article  PubMed  CAS  Google Scholar 

  • Lugan R, Niogret MF, Leport L, Guegan JP, Larher FR, Savoure A, Kopka J, Bouchereau A (2010) Metabolome and water homeostasis analysis of Thellungiella salsuginea suggests that dehydration tolerance is a key response to osmotic stress in this halophyte. Plant J 64:215–229

    Article  PubMed  CAS  Google Scholar 

  • Majoul T, Bancel E, Triboi E, Ben Hamida J, Branlard G (2003) Proteomic analysis of the effect of heat stress on hexaploid wheat grain: characterization of heat-responsive proteins from total endosperm. Proteomics 3:175–183

    Article  PubMed  CAS  Google Scholar 

  • Majoul T, Bancel E, Triboi E, Ben Hamida J, Branlard G (2004) Proteomic analysis of the effect of heat stress on hexaploid wheat grain: characterization of heat-responsive proteins from non-prolamins fraction. Proteomics 4:505–513

    Article  PubMed  CAS  Google Scholar 

  • Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G (2010) Revealing strengths and weaknesses of methods for gene network inference. Proc Natl Acad Sci USA 107:6286–6291

    Article  PubMed  CAS  Google Scholar 

  • Masoudi-Nejad A, Goto S, Jauregui R, Ito M, Kawashima S, Moriya Y, Endo TR, Kanehisa M (2007) EGENES: transcriptome-based plant database of genes with metabolic pathway information and expressed sequence tag indices in KEGG. Plant Physiol 144:857–866

    Article  PubMed  CAS  Google Scholar 

  • Matsuda F, Morino K, Ano R, Kuzawa M, Wakasa K, Miyagawa H (2005) Metabolic flux analysis of the phenylpropanoid pathway in elicitor-treated potato tuber tissue. Plant Cell Physiol 46:454–466

    Article  PubMed  CAS  Google Scholar 

  • Matsuda F, Shinbo Y, Oikawa A, Hirai MY, Fiehn O, Kanaya S, Saito K (2009) Assessment of metabolome annotation quality: a method for evaluating the false discovery rate of elemental composition searches. PloS One 4(10):e7490

    Article  PubMed  CAS  Google Scholar 

  • Mattioli R, Falasca G, Sabatini S, Altamura MM, Costantino P, Trovato M (2009) The proline biosynthetic genes P5CS1 and P5CS2 play overlapping roles in Arabidopsis flower transition but not in embryo development. Physiol Plant 137:72–85

    Article  PubMed  CAS  Google Scholar 

  • Mattioli R, Marchese D, D’Angeli S, Altamura MM, Costantino P, Trovato M (2008) Modulation of intracellular proline levels affects flowering time and inflorescence architecture in Arabidopsis. Plant Mol Biol 66:277–288

    Article  PubMed  CAS  Google Scholar 

  • Mayer KF, Martis M, Hedley PE, Simkova H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubalakova M, Suchankova P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Dolezel J, Waugh R, Stein N (2011) Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23:1249–1263

    Article  PubMed  CAS  Google Scholar 

  • Mechin V, Balliau T, Chateau-Joubert S, Davanture M, Langella O, Negroni L, Prioul JL, Thevenot C, Zivy M, Damerval C (2004) A two-dimensional proteome map of maize endosperm. Phytochemistry 65:1609–1618

    Article  PubMed  CAS  Google Scholar 

  • Mir RR, Zaman-Allah M, Sreenivasulu N, Trethowan R, Varshney RK (2012) Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops. Theor Appl Genet 125:625–645

    Article  PubMed  CAS  Google Scholar 

  • Mittler R (2006) Abiotic stress, the field environment and stress combination. Trends Plant Sci 11:15–19

    Article  PubMed  CAS  Google Scholar 

  • Miyao A, Iwasaki Y, Kitano H, Itoh J, Maekawa M, Murata K, Yatou O, Nagato Y, Hirochika H (2007) A large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes. Plant Mol Biol 63:625–635

    Article  PubMed  CAS  Google Scholar 

  • Mochida K, Uehara-Yamaguchi Y, Yoshida T, Sakurai T, Shinozaki K (2011) Global landscape of a co-expressed gene network in barley and its application to gene discovery in triticeae crops. Plant Cell Physiol 52:785–803

    Article  PubMed  CAS  Google Scholar 

  • Mohammadi M, Kav NN, Deyholos MK (2007) Transcriptional profiling of hexaploid wheat (Triticum aestivum L.) roots identifies novel, dehydration-responsive genes. Plant Cell Environ 30:630–645

    Article  PubMed  CAS  Google Scholar 

  • Moles CG, Mendes P, Banga JR (2003) Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Res 13:2467–2474

    Article  PubMed  CAS  Google Scholar 

  • Montero-Barrientos M, Hermosa R, Cardoza RE, Gutierrez S, Nicolas C, Monte E (2010) Transgenic expression of the Trichoderma harzianum hsp70 gene increases Arabidopsis resistance to heat and other abiotic stresses. J Plant Physiol 167:659–665

    Article  PubMed  CAS  Google Scholar 

  • Mullarkey M, Jones P (2000) Isolation and analysis of thermotolerant mutants of wheat. J Exp Bot 51:139–146

    Article  PubMed  CAS  Google Scholar 

  • Mutwil M, Klie S, Tohge T, Giorgi FM, Wilkins O, Campbell MM, Fernie AR, Usadel B, Nikoloski Z, Persson S (2011) PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell 23:895–910

    Article  PubMed  CAS  Google Scholar 

  • Nakagami H, Sugiyama N, Ishihama Y, Shirasu K (2012) Shotguns in the front line: phosphoproteomics in plants. Plant Cell Physiol 53:118–124

    Article  PubMed  CAS  Google Scholar 

  • Nakagami H, Sugiyama N, Mochida K, Daudi A, Yoshida Y, Toyoda T, Tomita M, Ishihama Y, Shirasu K (2010) Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants. Plant Physiol 153:1161–1174

    Article  PubMed  CAS  Google Scholar 

  • Needham CJ, Manfield IW, Bulpitt AJ, Gilmartin PM, Westhead DR (2009) From gene expression to gene regulatory networks in Arabidopsis thaliana. BMC Syst Biol 3(1):85

    Article  PubMed  CAS  Google Scholar 

  • Nishiyama R, Watanabe Y, Fujita Y, Le DT, Kojima M, Werner T, Vankova R, Yamaguchi-Shinozaki K, Shinozaki K, Kakimoto T, Sakakibara H, Schmulling T, Tran LS (2011) Analysis of cytokinin mutants and regulation of cytokinin metabolic genes reveals important regulatory roles of cytokinins in drought, salt and abscisic acid responses, and abscisic acid biosynthesis. Plant Cell 23:2169–2183

    Article  PubMed  CAS  Google Scholar 

  • Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H (2007) ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res 35:D863–D869

    Article  PubMed  CAS  Google Scholar 

  • Obayashi T, Nishida K, Kasahara K, Kinoshita K (2011) ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Plant Cell Physiol 52:213–219

    Article  PubMed  CAS  Google Scholar 

  • Okazaki Y, Shimojima M, Sawada Y, Toyooka K, Narisawa T, Mochida K, Tanaka H, Matsuda F, Hirai A, Hirai MY, Ohta H, Saito K (2009) A chloroplastic UDP-glucose pyrophosphorylase from arabidopsis is the committed enzyme for the first step of sulfolipid biosynthesis. Plant Cell 21:892–909

    Article  PubMed  CAS  Google Scholar 

  • Oksman-Caldentey KM, Saito K (2005) Integrating genomics and metabolomics for engineering plant metabolic pathways. Curr Opin Biotechnol 16:174–179

    Article  PubMed  CAS  Google Scholar 

  • Oliver SG, Winson MK, Kell DB, Baganz F (1998) Systematic functional analysis of the yeast genome. Trends Biotechnol 16:373–378

    Article  PubMed  CAS  Google Scholar 

  • O’Malley RC, Ecker JR (2010) Linking genotype to phenotype using the Arabidopsis unimutant collection. Plant J 61:928–940

    Article  PubMed  CAS  Google Scholar 

  • Oono Y, Seki M, Nanjo T, Narusaka M, Fujita M, Satoh R, Satou M, Sakurai T, Ishida J, Akiyama K, Iida K, Maruyama K, Satoh S, Yamaguchi-Shinozaki K, Shinozaki K (2003) Monitoring expression profiles of Arabidopsis gene expression during rehydration process after dehydration using ca 7000 full-length cDNA microarray. Plant J: Cell Mol Biol 34:868–887

    Article  CAS  Google Scholar 

  • Osuna D, Usadel B, Morcuende R, Gibon Y, Blasing OE, Hohne M, Gunter M, Kamlage B, Trethewey R, Scheible WR, Stitt M (2007) Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings. Plant J 49:463–491

    Article  PubMed  CAS  Google Scholar 

  • Palanivelu R, Brass L, Edlund AF, Preuss D (2003) Pollen tube growth and guidance is regulated by POP2, an Arabidopsis gene that controls GABA levels. Cell 114:47–59

    Article  PubMed  CAS  Google Scholar 

  • Pasam RK, Sharma R, Malosetti M, van Eeuwijk FA, Haseneyer G, Kilian B, Graner A (2012) Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biol 12:16

    Article  PubMed  Google Scholar 

  • Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboobur R, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556

    Article  PubMed  CAS  Google Scholar 

  • Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, Korol A, Michalak M, Kianian S, Spielmeyer W, Lagudah E, Somers D, Kilian A, Alaux M, Vautrin S, Berges H, Eversole K, Appels R, Safar J, Simkova H, Dolezel J, Bernard M, Feuillet C (2008) A physical map of the 1-gigabase bread wheat chromosome 3B. Science 322:101–104

    Article  PubMed  CAS  Google Scholar 

  • Peleg Z, Blumwald E (2011) Hormone balance and abiotic stress tolerance in crop plants. Curr Opin Plant Biol 14:290–295

    Article  PubMed  CAS  Google Scholar 

  • Peleg Z, Reguera M, Tumimbang E, Walia H, Blumwald E (2011) Cytokinin-mediated source/sink modifications improve drought tolerance and increase grain yield in rice under water-stress. Plant Biotechnol J 9:747–758

    Article  PubMed  CAS  Google Scholar 

  • Pennisi E (2008) Plant genetics: the blue revolution, drop by drop, gene by gene. Science 320:171–173

    Article  PubMed  CAS  Google Scholar 

  • Persson S, Wei HR, Milne J, Page GP, Somerville CR (2005) Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc Natl Acad Sci USA 102:8633–8638

    Article  PubMed  CAS  Google Scholar 

  • Pinheiro C, Chaves MM (2011) Photosynthesis and drought: can we make metabolic connections from available data? J Exp Bot 62:869–882

    Article  PubMed  CAS  Google Scholar 

  • Qureshi MI, Qadir S, Zolla L (2007) Proteomics-based dissection of stress-responsive pathways in plants. J Plant Physiol 164:1239–1260

    Article  PubMed  CAS  Google Scholar 

  • Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol 133:1755–1767

    Article  PubMed  CAS  Google Scholar 

  • Rajendran K, Tester M, Roy SJ (2009) Quantifying the three main components of salinity tolerance in cereals. Plant, Cell Environ 32:237–249

    Article  CAS  Google Scholar 

  • Ratcliffe RG, Shachar-Hill Y (2006) Measuring multiple fluxes through plant metabolic networks. Plant J 45:490–511

    Article  PubMed  CAS  Google Scholar 

  • Reynolds TL, Nemeth MA, Glenn KC, Ridley WP, Astwood JD (2005) Natural variability of metabolites in maize grain: differences due to genetic background. J Agric Food Chem 53:10061–10067

    Article  PubMed  CAS  Google Scholar 

  • Riccardi F, Gazeau P, de Vienne D, Zivy M (1998) Protein changes in response to progressive water deficit in maize. Quantitative variation and polypeptide identification. Plant Physiol 117:1253–1263

    Article  PubMed  CAS  Google Scholar 

  • Rizhsky L, Liang HJ, 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 134:1683–1696

    Article  PubMed  CAS  Google Scholar 

  • Rohlig RM, Eder J, Engel KH (2009) Metabolite profiling of maize grain: differentiation due to genetics and environment. Metabolomics 5:459–477

    Article  CAS  Google Scholar 

  • Rolletschek H, Melkus G, Grafahrend-Belau E, Fuchs J, Heinzel N, Schreiber F, Jakob PM, Borisjuk L (2011) Combined noninvasive imaging and modeling approaches reveal metabolic compartmentation in the barley endosperm. Plant Cell 23:3041–3054

    Article  PubMed  CAS  Google Scholar 

  • Roscher A, Kruger NJ, Ratcliffe RG (2000) Strategies for metabolic flux analysis in plants using isotope labelling. J Biotechnol 77:81–102

    Article  PubMed  CAS  Google Scholar 

  • Rossel JB, Wilson IW, Pogson BJ (2002) Global changes in gene expression in response to high light in Arabidopsis. Plant Physiol 130:1109–1120

    Article  PubMed  CAS  Google Scholar 

  • Rostoks N, Mudie S, Cardle L, Russell J, Ramsay L, Booth A, Svensson JT, Wanamaker SI, Walia H, Rodriguez EM, Hedley PE, Liu H, Morris J, Close TJ, Marshall DF, Waugh R (2005) Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol Genet Genomics 274:515–527

    Article  PubMed  CAS  Google Scholar 

  • Royal Society (2009) Reaping the benefits: science and the sustainable intensification of global agriculture. London (The Royal Society; Policy Document 11/09)

    Google Scholar 

  • Safar J, Bartos J, Janda J, Bellec A, Kubalakova M, Valarik M, Pateyron S, Weiserova J, Tuskova R, Cihalikova J, Vrana J, Simkova H, Faivre-Rampant P, Sourdille P, Caboche M, Bernard M, Dolezel J, Chalhoub B (2004) Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat. Plant J: Cell Mol Biol 39:960–968

    Article  CAS  Google Scholar 

  • Safar J, Simkova H, Kubalakova M, Cihalikova J, Suchankova P, Bartos J, Dolezel J (2010) Development of chromosome-specific BAC resources for genomics of bread wheat. Cytogenet Genome Res 129:211–223

    Article  PubMed  CAS  Google Scholar 

  • Saisho D, Takeda K (2011) Barley: emergence as a new research material of crop science. Plant Cell Physiol 52:724–727

    Article  PubMed  CAS  Google Scholar 

  • Saito K, Hirai MY, Yonekura-Sakakibara K (2008) Decoding genes with coexpression networks and metabolomics: ‘majority report by precogs’. Trends Plant Sci 13:36–43

    Article  PubMed  CAS  Google Scholar 

  • Sakurai T, Kondou Y, Akiyama K, Kurotani A, Higuchi M, Ichikawa T, Kuroda H, Kusano M, Mori M, Saitou T, Sakakibara H, Sugano S, Suzuki M, Takahashi H, Takahashi S, Takatsuji H, Yokotani N, Yoshizumi T, Saito K, Shinozaki K, Oda K, Hirochika H, Matsui M (2011) RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function. Plant Cell Physiol 52:265–273

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Samach A, Onouchi H, Gold SE, Ditta GS, Schwarz-Sommer Z, Yanofsky MF, Coupland G (2000) Distinct roles of CONSTANS target genes in reproductive development of Arabidopsis. Science 288:1613–1616

    Article  PubMed  CAS  Google Scholar 

  • Sanchez DH, Siahpoosh MR, Roessner U, Udvardi M, Kopka J (2008) Plant metabolomics reveals conserved and divergent metabolic responses to salinity. Physiol Plant 132:209–219

    PubMed  CAS  Google Scholar 

  • Sangam S, Jayasree D, Reddy KJ, Chari PVB, Sreenivasulu N, Kavi Kishor PB (2005) Salt tolerance in plants-transgenic approaches. J Plant Biotechnol. 7:1–15

    Google Scholar 

  • SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20:43–45

    Article  PubMed  CAS  Google Scholar 

  • Sato S, Arita M, Soga T, Nishioka T, Tomita M (2008) Time-resolved metabolomics reveals metabolic modulation in rice foliage. BMC Syst Biol 2(1):51

    Article  PubMed  CAS  Google Scholar 

  • Satoh-Nagasawa N, Nagasawa N, Malcomber S, Sakai H, Jackson D (2006) A trehalose metabolic enzyme controls inflorescence architecture in maize. Nature 441:227–230

    Article  PubMed  CAS  Google Scholar 

  • Sauer U, Lasko DR, Fiaux J, Hochuli M, Glaser R, Szyperski T, Wuthrich K, Bailey JE (1999) Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J Bacteriol 181:6679–6688

    PubMed  CAS  Google Scholar 

  • Sawada Y, Akiyama K, Sakata A, Kuwahara A, Otsuki H, Sakurai T, Saito K, Hirai MY (2009) Widely targeted metabolomics based on large-scale MS/MS data for elucidating metabolite accumulation patterns in plants. Plant Cell Physiol 50:37–47

    Article  PubMed  CAS  Google Scholar 

  • Schaeffer ML, Harper LC, Gardiner JM, Andorf CM, Campbell DA, Cannon EKS, Sen TZ, Lawrence CJ (2011) MaizeGDB: curation and outreach go hand-in-hand. Database-Oxford

    Google Scholar 

  • Schauer N, Fernie AR (2006) Plant metabolomics: towards biological function and mechanism. Trends Plant Sci 11:508–516

    Article  PubMed  CAS  Google Scholar 

  • Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37:501–506

    Article  PubMed  CAS  Google Scholar 

  • Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115

    Article  PubMed  CAS  Google Scholar 

  • Schulte D, Ariyadasa R, Shi B, Fleury D, Saski C, Atkins M, de Jong P, Wu CC, Graner A, Langridge P, Stein N (2011) BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.). BMC Genomics 12(1):247

    Article  PubMed  CAS  Google Scholar 

  • Schwab W (2003) Metabolome diversity: too few genes, too many metabolites? Phytochemistry 62:837–849

    Article  PubMed  CAS  Google Scholar 

  • Seebauer JR, Moose SP, Fabbri BJ, Crossland LD, Below FE (2004) Amino acid metabolism in maize earshoots. Implications for assimilate preconditioning and nitrogen signaling. Plant Physiol 136:4326–4334

    Article  PubMed  CAS  Google Scholar 

  • Seiler C, Harshavardhan VT, Rajesh K, Reddy PS, Strickert M, Rolletschek H, Scholz U, Wobus U, Sreenivasulu N (2011) ABA biosynthesis and degradation contributing to ABA homeostasis during barley seed development under control and terminal drought-stress conditions. J Exp Bot 62:2615–2632

    Article  PubMed  CAS  Google Scholar 

  • Seki M, Ishida J, Narusaka M, Fujita M, Nanjo T, Umezawa T, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K (2002a) Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray. Funct Integr Genomics 2:282–291

    Article  PubMed  CAS  Google Scholar 

  • Seki M, Narusaka M, Abe H, Kasuga M, Yamaguchi-Shinozaki K, Carninci P, Hayashizaki Y, Shinozaki K (2001) Monitoring the expression pattern of 1,300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 13:61–72

    PubMed  CAS  Google Scholar 

  • Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Taji T, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K (2002b) Monitoring the expression profiles of 7,000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J: Cell Mol Biol 31:279–292

    Article  CAS  Google Scholar 

  • Shingaki-Wells RN, Huang SB, Taylor NL, Carroll AJ, Zhou WX, Millar AH (2011) Differential molecular responses of rice and wheat coleoptiles to anoxia reveal novel metabolic adaptations in amino acid metabolism for tissue tolerance. Plant Physiol 156:1706–1724

    Article  PubMed  CAS  Google Scholar 

  • Shulaev V, Cortes D, Miller G, Mittler R (2008) Metabolomics for plant stress response. Physiol Plant 132:199–208

    Article  PubMed  CAS  Google Scholar 

  • Smit B, Ludlow L, Brklacich M (1988) Implications of a global climatic warming for agriculture: a review and appraisal. J Environ Qual 17:519–527

    Article  Google Scholar 

  • Sreenivasulu N, Altschmied L, Radchuk V, Gubatz S, Wobus U, Weschke W (2004a) Transcript profiles and deduced changes of metabolic pathways in maternal and filial tissues of developing barley grains. Plant J: Cell Mol Biol 37:539–553

    Article  CAS  Google Scholar 

  • Sreenivasulu N, Miranda M, Prakash HS, Wobus U, Weschke W (2004b) Transcriptome changes in foxtail millet genotypes at high salinity: Identification and characterization of a PHGPX gene specifically up-regulated by NaCl in a salt-tolerant line. J Plant Physiol 161:467–477

    Article  PubMed  CAS  Google Scholar 

  • Sreenivasulu N, Radchuk V, Strickert M, Miersch O, Weschke W, Wobus U (2006) Gene expression patterns reveal tissue-specific signaling networks controlling programmed cell death and ABA- regulated maturation in developing barley seeds. Plant J: Cell Mol Biol 47:310–327

    Article  CAS  Google Scholar 

  • Sreenivasulu N, Schnurbusch T (2012) A genetic playground for enhancing grain number in cereals. Trends Plant Sci 17:91–101

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Sreenivasulu N, Graner A, Wobus U (2008a) Barley genomics: an overview. Int J Plant Genomics 2008:486258

    Article  PubMed  CAS  Google Scholar 

  • Sreenivasulu N, Usadel B, Winter A, Radchuk V, Scholz U, Stein N, Weschke W, Strickert M, Close TJ, Stitt M, Graner A, Wobus U (2008b) Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools. Plant Physiol 146:1738–1758

    Article  PubMed  CAS  Google Scholar 

  • Sreenivasulu N, Sunkar R, Wobus U, Strickert M (2010) Array platforms and bioinformatics tools for the analysis of plant transcriptome in response to abiotic stress. Methods Mol Biol 639:71–93

    Article  PubMed  CAS  Google Scholar 

  • Sreenivasulu N, Harshavardhan VT, Govind G, Seiler C, Kohli A (2012) Contrapuntal role of ABA: does it mediate stress tolerance or plant growth retardation under long-term drought stress? Gene 125:625–645

    Google Scholar 

  • Styczynski MP, Stephanopoulos G (2005) Overview of computational methods for the inference of gene regulatory networks. Comput Chem Eng 29:519–534

    Article  CAS  Google Scholar 

  • Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E (2008) The Arabidopsis information resource (TAIR): gene structure and function annotation. Nucleic Acid Res 36:D1009–D1014

    Article  PubMed  CAS  Google Scholar 

  • Sweetlove LJ, Fell D, Fernie AR (2008) Getting to grips with the plant metabolic network. Biochem J 409:27–41

    Article  PubMed  CAS  Google Scholar 

  • Szekely G, Abraham E, Cseplo A, Rigo G, Zsigmond L, Csiszar J, Ayaydin F, Strizhov N, Jasik J, Schmelzer E, Koncz C, Szabados L (2008) Duplicated P5CS genes of Arabidopsis play distinct roles in stress regulation and developmental control of proline biosynthesis. Plant J: Cell Mol Biol 53:11–28

    Article  CAS  Google Scholar 

  • Takahashi S, Seki M, Ishida J, Satou M, Sakurai T, Narusaka M, Kamiya A, Nakajima M, Enju A, Akiyama K, Yamaguchi-Shinozaki K, Shinozaki K (2004) Monitoring the expression profiles of genes induced by hyperosmotic, high salinity, and oxidative stress and abscisic acid treatment in Arabidopsis cell culture using a full-length cDNA microarray. Plant Mol Biol 56:29–55

    Article  PubMed  CAS  Google Scholar 

  • Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda JI, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O’Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M (2008) The rice annotation project database (RAP-DB): 2008 update. Nucleic Acid Res 36:D1028–D1033

    PubMed  CAS  Google Scholar 

  • Thimm O, Essigmann B, Kloska S, Altmann T, Buckhout TJ (2001) Response of Arabidopsis to iron deficiency stress as revealed by microarray analysis. Plant Physiol 127:1030–1043

    Article  PubMed  CAS  Google Scholar 

  • Thole V, Worland B, Wright J, Bevan MW, Vain P (2010) Distribution and characterization of more than 1000 T-DNA tags in the genome of Brachypodium distachyon community standard line Bd21. Plant Biotechnol J 8:734–747

    Article  PubMed  CAS  Google Scholar 

  • Umezawa T, Fujita M, Fujita Y, Yamaguchi-Shinozaki K, Shinozaki K (2006) Engineering drought tolerance in plants: discovering and tailoring genes to unlock the future. Curr Opin Biotech 17:113–122

    Article  PubMed  CAS  Google Scholar 

  • Urano K, Maruyama K, Ogata Y, Morishita Y, Takeda M, Sakurai N, Suzuki H, Saito K, Shibata D, Kobayashi M, Yamaguchi-Shinozaki K, Shinozaki K (2009) Characterization of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics. Plant J: Cell Mol Biol 57:1065–1078

    Article  CAS  Google Scholar 

  • Usadel B, Blasing OE, Gibon Y, Poree F, Hohne M, Gunter M, Trethewey R, Kamlage B, Poorter H, Stitt M (2008) Multilevel genomic analysis of the response of transcripts, enzyme activities and metabolites in Arabidopsis rosettes to a progressive decrease of temperature in the non-freezing range. Plant, Cell Environ 31:518–547

    Article  CAS  Google Scholar 

  • Vain P, Worland B, Thole V, McKenzie N, Alves SC, Opanowicz M, Fish LJ, Bevan MW, Snape JW (2008) Agrobacterium-mediated transformation of the temperate grass Brachypodium distachyon (genotype Bd21) for T-DNA insertional mutagenesis. Plant Biotechnol J 6:236–245

    Article  PubMed  CAS  Google Scholar 

  • Van Baarlen P, Van Esse HP, Siezen RJ, Thomma BPHJ (2008) Challenges in plant cellular pathway reconstruction based on gene expression profiling. Trends Plant Sci 13:44–50

    Article  PubMed  CAS  Google Scholar 

  • van Dijken AJH, Schluepmann H, Smeekens SCM (2004) Arabidopsis trehalose-6-phosphate synthase 1 is essential for normal vegetative growth and transition to flowering. Plant Physiol 135:969–977

    Article  PubMed  Google Scholar 

  • Vensel WH, Tanaka CK, Cai N, Wong JH, Buchanan BB, Hurkman WJ (2005) Developmental changes in the metabolic protein profiles of wheat endosperm. Proteomics 5:1594–1611

    Article  PubMed  CAS  Google Scholar 

  • Verpoorte R, Memelink J (2002) Engineering secondary metabolite production in plants. Curr Opin Biotech 13:181–187

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Vinocur B, Altman A (2005) Recent advances in engineering plant tolerance to abiotic stress: achievements and limitations. Curr Opin Biotech 16:123–132

    Article  PubMed  CAS  Google Scholar 

  • Vlad MO, Arkin A, Ross J (2004) Response experiments for nonlinear systems with application to reaction kinetics and genetics. Proc Natl Acad Sci USA 101:7223–7228

    Article  PubMed  CAS  Google Scholar 

  • Vogel J, Hill T (2008) High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3. Plant Cell Rep 27:471–478

    Article  PubMed  CAS  Google Scholar 

  • Vogel JP, Tuna M, Budak H, Huo N, Gu YQ, Steinwand MA (2009) Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC Plant Biol 9:88

    Article  PubMed  CAS  Google Scholar 

  • Walia H, Wilson C, Condamine P, Ismail AM, Xu J, Cui X, Close TJ (2007) Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise. BMC genomics 8:87

    Article  PubMed  CAS  Google Scholar 

  • Walia H, Wilson C, Wahid A, Condamine P, Cui X, Close TJ (2006) Expression analysis of barley (Hordeum vulgare L.) during salinity stress. Funct Integr Genomics 6:143–156

    Article  PubMed  CAS  Google Scholar 

  • Wan JX, Griffiths R, Ying JF, McCourt P, Huang YF (2009) Development of drought-tolerant canola (Brassica napus L.) through genetic modulation of ABA-mediated stomatal responses. Crop Sci 49:1539–1554

    Article  CAS  Google Scholar 

  • Wang H, Schauer N, Usadel B, Frasse P, Zouine M, Hernould M, Latche A, Pech JC, Fernie AR, Bouzayen M (2009) Regulatory features underlying pollination-dependent and -independent tomato fruit set revealed by transcript and primary metabolite profiling. Plant Cell 21:1428–1452

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Wanjugi H, Coleman-Derr D, Huo N, Kianian SF, Luo MC, Wu J, Anderson O, Gu YQ (2009) Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat. Genome 52:576–587 National Research Council Canada, Conseil National de Recherches Canada

    Article  PubMed  CAS  Google Scholar 

  • Wasinger VC, Cordwell SJ, Cerpa-Poljak A, Yan JX, Gooley AA, Wilkins MR, Duncan MW, Harris R, Williams KL, Humphery-Smith I (1995) Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 16:1090–1094

    Article  PubMed  CAS  Google Scholar 

  • Wei F, Zhang J, Zhou S, He R, Schaeffer M, Collura K, Kudrna D, Faga BP, Wissotski M, Golser W, Rock SM, Graves TA, Fulton RS, Coe E, Schnable PS, Schwartz DC, Ware D, Clifton SW, Wilson RK, Wing RA (2009) The physical and genetic framework of the maize B73 genome. PLoS Genet 5:e1000715

    Article  PubMed  CAS  Google Scholar 

  • Weigel D, Ahn JH, Blazquez MA, Borevitz JO, Christensen SK, Fankhauser C, Ferrandiz C, Kardailsky I, Malancharuvil EJ, Neff MM, Nguyen JT, Sato S, Wang ZY, Xia YJ, Dixon RA, Harrison MJ, Lamb CJ, Yanofsky MF, Chory J (2000) Activation tagging in Arabidopsis. Plant Physiol 122:1003–1013

    Article  PubMed  CAS  Google Scholar 

  • Westerhoff HV, Palsson BO (2004) The evolution of molecular biology into systems biology. Nat Biotechnol 22:1249–1252

    Article  PubMed  CAS  Google Scholar 

  • Wicker T, Mayer KFX, Gundlach H, Martis M, Steuernagel B, Scholz U, Simkova H, Kubalakova M, Choulet F, Taudien S, Platzer M, Feuillet C, Fahima T, Budak H, Dolezel J, Keller B, Stein N (2011) Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 23:1706–1718

    Article  PubMed  CAS  Google Scholar 

  • Wiechert W, Mollney M, Petersen S, de Graaf AA (2001) A universal framework for 13C metabolic flux analysis. Metab Eng 3:265–283

    Article  PubMed  CAS  Google Scholar 

  • Williams TC, Poolman MG, Howden AJ, Schwarzlander M, Fell DA, Ratcliffe RG, Sweetlove LJ (2010) A genome-scale metabolic model accurately predicts fluxes in central carbon metabolism under stress conditions. Plant Physiol 154:311–323

    Article  PubMed  CAS  Google Scholar 

  • Wittmann C, Kiefer P, Zelder O (2004) Metabolic fluxes in Corynebacterium glutamicum during lysine production with sucrose as carbon source. Appl Environ Microbiol 70:7277–7287

    Article  PubMed  CAS  Google Scholar 

  • Worch S, Rajesh K, Harshavardhan VT, Pietsch C, Korzun V, Kuntze L, Borner A, Wobus U, Roder MS, Sreenivasulu N (2011) Haplotyping, linkage mapping and expression analysis of barley genes regulated by terminal drought stress influencing seed quality. BMC Plant Biol 11:1

    Article  PubMed  CAS  Google Scholar 

  • Xu J, Tian J, Belanger FC, Huang B (2007) Identification and characterization of an expansin gene AsEXP1 associated with heat tolerance in C3 Agrostis grass species. J Exp Bot 58:3789–3796

    Article  PubMed  CAS  Google Scholar 

  • Xue GP, McIntyre CL, Chapman S, Bower NI, Way H, Reverter A, Clarke B, Shorter R (2006) Differential gene expression of wheat progeny with contrasting levels of transpiration efficiency. Plant Mol Biol 61:863–881

    Article  PubMed  CAS  Google Scholar 

  • Yamaguchi T, Nakayama K, Hayashi T, Yazaki J, Kishimoto N, Kikuchi S, Koike S (2004) cDNA microarray analysis of rice anther genes under chilling stress at the microsporogenesis stage revealed two genes with DNA transposon Castaway in the 5’-flanking region. Biosci Biotech Bioch 68:1315–1323

    Article  CAS  Google Scholar 

  • Yamakawa H, Hakata M (2010) Atlas of rice grain filling-related metabolism under high temperature: joint analysis of metabolome and transcriptome demonstrated inhibition of starch accumulation and induction of amino acid accumulation. Plant Cell Physiol 51:795–809

    Article  PubMed  CAS  Google Scholar 

  • Yang S, Vanderbeld B, Wan J, Huang Y (2010) Narrowing down the targets: towards successful genetic engineering of drought-tolerant crops. Mol Plant 3:469–490

    Article  PubMed  CAS  Google Scholar 

  • Youens-Clark K, Buckler E, Casstevens T, Chen C, DeClerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren LY, Spooner W, Stein JC, Thomason J, Wei S, Ware D (2011) Gramene database in 2010: updates and extensions. Nucleic Acids Res 39:D1085–D1094

    Article  PubMed  CAS  Google Scholar 

  • Yu J, Hu SN, Wang J, Wong GKS, Li SG, Liu B, Deng YJ, Dai L, Zhou Y, Zhang XQ, Cao ML, Liu J, Sun JD, Tang JB, Chen YJ, Huang XB, Lin W, Ye C, Tong W, Cong LJ, Geng JN, Han YJ, Li L, Li W, Hu GQ, Huang XG, Li WJ, Li J, Liu ZW, Li L, Liu JP, Qi QH, Liu JS, Li L, Li T, Wang XG, Lu H, Wu TT, Zhu M, Ni PX, Han H, Dong W, Ren XY, Feng XL, Cui P, Li XR, Wang H, Xu X, Zhai WX, Xu Z, Zhang JS, He SJ, Zhang JG, Xu JC, Zhang KL, Zheng XW, Dong JH, Zeng WY, Tao L, Ye J, Tan J, Ren XD, Chen XW, He J, Liu DF, Tian W, Tian CG, Xia HG, Bao QY, Li G, Gao H, Cao T, Wang J, Zhao WM, Li P, Chen W, Wang XD, Zhang Y, Hu JF, Wang J, Liu S, Yang J, Zhang GY, Xiong YQ, Li ZJ, Mao L, Zhou CS, Zhu Z, Chen RS, Hao BL, Zheng WM, Chen SY, Guo W, Li GJ, Liu SQ, Tao M, Wang J, Zhu LH, Yuan LP, Yang HM (2002) A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science 296:79–92

    Article  PubMed  CAS  Google Scholar 

  • Zamboni N, Sauer U (2004) Model-independent fluxome profiling from 2H and 13C experiments for metabolic variant discrimination. Genome Biol 5:R99

    Article  PubMed  Google Scholar 

  • Zeller G, Henz SR, Widmer CK, Sachsenberg T, Ratsch G, Weigel D, Laubinger S (2009) Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. Plant J: Cell Mol Biol 58:1068–1082

    Article  CAS  Google Scholar 

  • Zhang HX, Lian CL, Shen ZG (2009) Proteomic identification of small, copper-responsive proteins in germinating embryos of Oryza sativa. Ann Bot 103:923–930

    Article  PubMed  CAS  Google Scholar 

  • Zhang YX, Wu RH, Qin GJ, Chen ZL, Gu HY, Qu LJ (2011) Over-expression of WOX1 leads to defects in meristem development and polyamine homeostasis in Arabidopsis. J Integr Plant Biol 53:493–506

    Article  PubMed  CAS  Google Scholar 

  • Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, Goldstein S, Pape L, Mehan MR, Churas C, Pasternak S, Forrest DK, Wise R, Ware D, Wing RA, Waterman MS, Livny M, Schwartz DC (2009) A single molecule scaffold for the maize genome. PLoS Genet 5:e1000711

    Article  PubMed  CAS  Google Scholar 

  • Zhu H, Bilgin M, Snyder M (2003) Proteomics. Annu Rev Biochem 72:783–812

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

NS is thankful to research funding obtained through BMBF (IND 09/526), BLE grant 511-06.01-28-1-45.041-10, BMZ grant 81131833 and from the Ministry of Education Saxony-Anhalt (IZN). PS acknowledge the Leibniz-DAAD post doctoral fellowship award (Number: A/11/94309) from Germany Academic Exchange programme (DAAD), Germany. We acknowledge the help of Prof. P.K. Gupta for the editorial changes which helped to improve the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Nese Sreenivasulu .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Reddy, P.S., Sreenivasulu, N. (2013). Different Omics Approaches in Cereals and Their Possible Implications for Developing a System Biology Approach to Study the Mechanism of Abiotic Stress Tolerance. In: Gupta, P., Varshney, R. (eds) Cereal Genomics II. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6401-9_8

Download citation

Publish with us

Policies and ethics