Nothing Special   »   [go: up one dir, main page]
Skip to main content

Advertisement

Springer Nature Link
Log in

Unrevealing metabolomics for abiotic stress adaptation and tolerance in plants

  • Review Article
  • Published:
Journal of Crop Science and Biotechnology Aims and scope Submit manuscript

Abstract

The post-genomic era has witnessed several new possibilities to understand diverse functional aspects of plants quite precisely. From genomics to metabolomics and now phenomics, the complex interplay of these biological networks has been successfully elucidated. Abiotic stresses, such as drought, flooding, exposure to heavy metals and metalloids, and high or low temperature are foremost constraints in agriculture, and remains as the major reason for poor crop productivity and low yield globally. The primary aim of metabolomics is to identify final gene products, the metabolites, which serve as prospective markers (or traits) to comprehend abiotic stress adaptation and tolerance in plants. This review provides an overview on the application of metabolomics as a comprehensive tool for “Systems Biology Approach” to unravel the complex interaction of networks and components in plants towards abiotic stress adaptation and tolerance.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

Abbreviations

APCI:

Atmospheric pressure chemical ionization

APPI:

Atmospheric pressure photoionization

COSY:

Correlation spectroscopy (1H–1H)

DNA:

Deoxyribonucleic acid

ESI:

Electron ionization spray

EST:

Expressed sequence tags

GABA:

γ—Amino butyric acid

GC:

Gas chromatography

GWAS:

Genome wide association studies

HCA:

Hierarchical cluster analysis

HTS:

High throughput screening

IT:

Ion trap

LC:

Liquid chromatography

MALDI:

Matrix assisted laser desorption ionization

MS:

Mass spectrometry

MSI:

Mass spectrometry imaging

NGS:

Next genome sequencing

NIST:

National institute of standards and technology

NMR:

Nuclear magnetic resonance

OT:

Orbitrap

PCA:

Principal component analysis

Q:

Single quadrupole

QTL:

Quantitative trait loci

QqQ:

Triple quadrupole

RFO:

Raffinose family oligosaccharides

RNA:

Ribonucleic acid

ROS:

Reactive oxygen species

SAGE:

Serial analysis of gene expression

SOM:

Self organizing mapping

TCA:

Tricarboxylic acid

TOCSY:

Total correlation spectroscopy

ToF:

Time of flight

References

  • Abbasi F, Komatsu S (2004) A proteomic approach to analyze salt responsive proteins in rice leaf sheath. Proteom 4:2072–2081

    Article  CAS  Google Scholar 

  • Aebersold R, Mann M (2016) Mass-spectrometric exploration of proteome structure and function. Nature 537(7620):347–355

    Article  CAS  PubMed  Google Scholar 

  • Ahsan N, Renaut J, Komatsu S (2009) Recent developments in the application of proteomics to the analysis of plant responses to heavy metals. Proteom 9:2602–2621

    Article  CAS  Google Scholar 

  • Ahsan NDG, Alam I, Kim PJ, Lee JJ, Ahn YO, Kwak SS, Lee IJ, Bahk JD, Kang KY, Renaut J, Komatsu S, Lee BH (2008) Comparative proteomic study of arsenic-induced differentially expressed proteins in rice roots reveals glutathione plays a central role during As stress. Proteom 8:3561–3576

    Article  CAS  Google Scholar 

  • Alam I, Sharmin SA, Kim KH, Yang JK, Choi MS, Lee BH (2010) Proteome analysis of soybean roots subjected to short-term drought stress. Plant Soil 333:491–505

    Article  CAS  Google Scholar 

  • Alexanderson E, Jacobson D, Vivier MA, Weckwerth W, Andresson E (2014) Field-omics—understanding large scale molecular data from field. Front Plant Sci 5:286

    Article  Google Scholar 

  • Amiard V, Morvan-Bertrand A, Billard JP, Huault C, Keller F, Prud’homme MP (2003) Fructans, but not the sucrosyl–galactosidase, raffinose and loliose, are affected by drought stress in perennial ryegrass. Plant Physiol 132:2218–2229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Amstalden van Hove ER, Smith DF, Heeren RMA (2010) A concise review of mass spectrometry imaging. J Chromatogr A 1217:3946–3954

    Article  CAS  PubMed  Google Scholar 

  • Arbona V, Manzi M, de Ollas C, Gómez-Cadenas A (2013) Metabolomics as a tool to investigate abiotic stress tolerance in plants. Int J Mol Sci 14(3):4885–4911

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arya M, Bhartiya A, Aditya JP, Satpute G, Ratnaparkhe M (2019) Unrevealing complex networks involved in plant stress tolerance through metabolomics. In: Wani SH (ed) Recent approaches in omics for plant resilience to climate change. Springer Nature, Singapore, pp 313–325

    Chapter  Google Scholar 

  • Avila WF, Yang Y, Faquin V, Ramos SJ, Guilherme LRG, Thannhauser TW, Li L (2014) Impact of selenium supply on Se-methylselenocysteine and glucosinolate accumulation in selenium-biofortified Brassica sprouts. Food Chem 165:578–586

    Article  CAS  PubMed  Google Scholar 

  • Bae MS, Chop EJ, Choi E-Y, Park OK (2003) Analysis of the Arabidopsis nuclear proteome and its response to cold stress. The Plant J 36:652–663

    Article  CAS  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 

  • Bernat P, Gajewska E, Bernat T, Wielanek M (2014) Characterisation of the wheat phospholipid fraction in the presence of nickel and/or selenium. Plant Growth Regul 72:163–170

    Article  CAS  Google Scholar 

  • Bino RJ, Hall RD, Fiehn O, Kopka J, Saito K, Draper J, Nikolau BJ, Mendes P, Roessner-Tunali U, Beale MH et al (2004) Potential of metabolomics as a functional genomics tool. Trends in Plant Sci 9:418–425

    Article  CAS  Google Scholar 

  • Bolouri-Moghaddam MR, Le Roy K, Xiang L, Roland F, Van der Ende W (2010) Sugar signalling and antioxidant network connections in plant cells. FEBS J 277:2022–2037

    Article  CAS  PubMed  Google Scholar 

  • Bueno PCP, Lopes NP (2020) Metabolomics to characterize adaptive and signaling responses in legume crops under abiotic stresses. ACS Omega 5:1752–1763

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Caron E, Vincent K, Fortier MH, Laverdure JP, Bramoulle A, Hardy MP, Voisin G, Roux PP, Lemieux S, Thibault P (2011) The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation. Mol Syst Biol 7:533

    Article  PubMed  PubMed Central  Google Scholar 

  • Carillo P (2018) GABA shunt in durum wheat. Front Plant Sci 9:100

    Article  PubMed  PubMed Central  Google Scholar 

  • Chain PSG, Grafham DV, Fulton RS, FitzGerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C et al (2009) Genomic Standards consortium, human microbiome project jumpstart consortium, J. C. Detter, genome project standards in new era of sequencing. Science 326:236–237

    Article  CAS  PubMed  Google Scholar 

  • Chen Y, Weckwerth W (2020) Mass spectrometry untangles plant membrane protein signalling network. Trends Plant Sci 25(9):930–944

    Article  CAS  PubMed  Google Scholar 

  • Chen B, Zhou L, Liang L, Cao Y, Zheng W, Zhang X, Ma X, Huang L, Nei G, Liu W, Peng Y (2018) The γ-aminobutyric acid (GABA) alleviates salt stress damage during seed germination of white clover associated with Na+/K+ transportation, dehydrins accumulation, and stress related genes expression in white clover. Int J Mol Sci 19(9):2520

    Article  Google Scholar 

  • Choi HK, Choi YH, Verberne M, Lefeber AWM, Erkelens C, Verpoorte R (2004) Metabolic fingerprinting of wild type and transgenic tobacco plants by 1H NMR and multivariate analysis technique. Phytochem 65:857–864

    Article  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  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  Google Scholar 

  • Denoroy L, Zimmer L, Renaud B, Parrot S (2013) Ultra high performance liquid chromatography as a tool for the discovery and the analysis of biomarkers of diseases: a review. J Chromatogr B Analyt Technol Biomed Life Sci 927:37–53

    Article  CAS  PubMed  Google Scholar 

  • Dixon RA, Gang DR, Charlton AJ, Fiehn O, Kuiper HA, Reynolds TL, Tjeerdema RS, Jeffery EH, German BJ, Ridley WP, Seiber JN (2006) Application of metabolomics in agriculture. J Agric Food Chem 54:8984–8994

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  • ElSayed AI, Rafudeen MS, Golldack D (2014) Physiological aspects of raffinose family oligosaccharides in plants: protection against abiotic stress. Plant Biol 16:1–8

    Article  CAS  PubMed  Google Scholar 

  • Feuillet C, Leach JE, Rogers J, Schnable PS, Eversole K (2010) Crop genome sequencing: lessons and rationales. Trends Plant Sci 16(2):77–88

    Article  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Francavilla C, Lupia M, Tsafou K, Villa A, Kowalczyk K, Rakownikow Jersie-Christensen R, Bertalot G, Confalonieri S, Brunak S (2017) Phosphoproteomics of primary cells reveals druggable kinase signatures in ovarian cancer. Cell Rep 18:3242–3256

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fukusaki E, Kobayashi A (2005) Plant metabolomics: potential for practical operation. J Biosci Bioeng 100:347–354

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Ghosh N, Adal MK, Ghosh PD, Gupta S, Sengupta DN, Mandal C (2011) Differential responses of two varieties to salt-stress. Plant Biotech Rep 5:89–103

    Article  Google Scholar 

  • Gokce ZNO, Akbas S, Ayten S, Azimi MH, Das R, Guven SB, Karabulut E, Omezli S, Uzer Z, Yerlikaya BA, Bakhsh A (2020) Abiotic stress tolerance in field crops: integration of omics approaches. In: Hasanuzzaman M (ed) Agronomic crops. Springer Nature, Singapore, pp 503–526

    Chapter  Google Scholar 

  • Goufo P, Moutinho-Pereira JM, Jorge TF, Correia CM, Oliviera MT, Rosa EAS, Antonio C, Trindade H (2017) Cowpea (Vigna unguiculata L. Walp.) metabolomics: osmoprotection as a physiological strategy for drought stress resistance and improved yield. Front Plant Sci 8:1–22

    Article  Google Scholar 

  • Guardado-Felix D, Serna-Saldivar SO, Cuevas-Rodriguez EO, Jacobo-Velazquez DA, Gutierrez-Uribe JA (2017) Effect of sodium selenite on isoflavonoid contents and antioxidant capacity of chickpea (Cicer arietinum L.) sprouts. Food Chem 226:69–74

    Article  CAS  PubMed  Google Scholar 

  • Guardado-Felix D, Serna-Saldivar SO, Gutierrez-Uribe JA, Chuck-Harnendez C (2019) Selenium in germinated chickpea (Cicer arietinum L.) increases stability of its oil fraction. Plants 8:113

    Article  CAS  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Hannah MA, Wiese D, Freund S, Fiehn O, Heyer AG, Hincha DK (2006) Natural genetic variation of freezing tolerance in Arabidopsis. Plant Physiol 142:98–112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Heyman HM, Dubery IA (2015) The potential of mass spectrometry imaging in plant metabolomics: a review. Phytochem Rev 14:1–20

    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  CAS  PubMed  PubMed Central  Google Scholar 

  • Hong J, Yang L, Zhang D, Jianxin S (2016) Plant metabolomics: an indispensable system biology tool for plant science. Int J Mol Sci 17:767

    Article  PubMed Central  Google Scholar 

  • Humplik JF, Lazar D, Husickova A, Spichal L (2015) Automated phenotyping of plant shoots using imaging methods for analysis of plant stress responses—a review. Plant Method 11:29

    Article  Google Scholar 

  • Iwamoto N, Shimada T (2018) Recent advances in mass spectrometry-based approaches for proteomics and biologics: Great contribution for developing therapeutic antibodies. Pharmacol Therap 185:147–154

    Article  CAS  Google Scholar 

  • Jorge TF, Rodrigues JA, Caldana C, Schmidt R, van Dongen JT, Thomas Oates J, Antonio C (2016) Mass spectrometry-based plant metabolomics: metabolite responses to abiotic stress. Mass Spec Rev 35:620–649

    Article  CAS  Google Scholar 

  • Kaplan F, Guy CL (2004) Beta-amylase induction and the protective role of maltose during temperature shock. Plant Physiol 135:1674–1684

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kawamura Y, Uemura M (2003) Mass spectrometric approach for identifying putative plasma membrane proteins of Arabidopsis leaves associated with cold acclimation. Plant J 36:141–154

    Article  CAS  PubMed  Google Scholar 

  • Kim HK, Choi YH, Verpoorte R (2010) NMR-based metabolomic analysis of plants. Nat Prot 5(3):536–549

    Article  CAS  Google Scholar 

  • Kim JK, Bamba T, Harada K, Fukusaki E, Kobayashi A (2007) Time-course metabolic profiling in Arabidopsis thaliana cell cultures after salt stress treatment. J Exp Bot 58:415–424

    Article  CAS  PubMed  Google Scholar 

  • Koek MM, Jellema RH, van der Greef J, Tas AC, Hankemeier T (2011) Quantitative metabolomics based on gas chromatography mass spectrometry: status and perspectives. Metabolom 7(3):307–328

    Article  CAS  Google Scholar 

  • Kosová K, Vítámvás P, Prášil IT, Renaut J (2011) Plant proteome changes under abiotic stress—contribution of proteomics studies to understanding plant stress response. J Proteom 74(8):1301–1322

    Article  Google Scholar 

  • Krishnan P, Kruger NJ, Ratcliffe RG (2005) Metabolite fingerprinting and profiling in plants using NMR. J Exp Bot 56(410):255–265

    Article  CAS  PubMed  Google Scholar 

  • Kruger NJ, Adrian Troncoso-Ponce M, George Ratcliffe R (2008) 1H NMR metabolite fingerprinting and metabolomic analysis of perchloric acid extracts from plant tissues. Nat Prot 3:1001–1012

    Article  CAS  Google Scholar 

  • Lazo-Vélez MA, Guardado-Félix D, Avilés-González J, Romo-López I, Serna-Saldívar SO (2018) Effect of germination with sodium selenite on the isoflavones and cellular antioxidant activity of soybean (Glycine max). LWT Food Sci Technol 93:64–70

    Article  Google Scholar 

  • Le DT, Nishiyama R, Watanabe Y, Tanaka M, Seki M, Ham LH, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP (2012) Differential gene expression in soybean leaf tissues at late developmental stage under drought stress revealed by genome wide transcriptome analysis. PLoS ONE 7:e49522

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee J, Finley JW, Harnly JM (2005) Effect of selenium fertilizer on free amino acid composition of broccoli (Brassica oleracea Cv. Majestic) determined by gas chromatography with flame ionization and mass selective detection. J Agric Food Chem 53:9105–9111

    Article  CAS  PubMed  Google Scholar 

  • Li K, Wang X, Pidalala VR, Chang CP, Cao X (2014) Novel quantitative metabolomics approach for study of stress response of plant root metabolism. J Proteom Res 13:5879–5887

    Article  CAS  Google Scholar 

  • Li D, Gaquerel E (2021) Next generation mass spectrometry metabolomics revises the functional analysis of plant metabolic diversity. Ann Rev Plant Biol 72:25.1-25.25

    Article  Google Scholar 

  • Lisec J, Schauer N, Kopka J, Willmitzer L, Fernie AR (2006) Gas chromatography mass spectrometry-based metabolite profiling in plants. Nat Prot 1:387–396

    Article  CAS  Google Scholar 

  • Liu X, Locasale JW (2017) Metabolomics: a primer. Trends Biochem Sci 42(4):274–284

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu D, Ford KL, Roessner U, Natera S, Cassin AM, Paterson JH, Bacic A (2013) Rice suspension culture are evaluated as model system to study salt responsive netwroks in plants using a combined proteomic and metabolomic profiling approach. Proteom 13:2046–2062

    Article  CAS  Google Scholar 

  • Lopes AS, Santa Cruz ES, Sussulini A, Klassen A (2017) Metabolomic Strategies Involving mass spectrometry combined with liquid and gas chromatography. In: A Sussulini (ed) Metabolomics: from fundamentals to clinical applications, advances in experimental medicine and biology, pp 77–98

  • Malheiros RS, Costa LC, Ávila RT, Pimenta TM, Teixeira LS, Brito FA, Zsögön A, Araújo WL, Ribeiro DM (2019) Selenium downregulates auxin and ethylene biosynthesis in rice seedlings to modify primary metabolism and root architecture. Planta 250:333–345

    Article  CAS  PubMed  Google Scholar 

  • Marques MC, Alonso-Cantabrana H, Forment J, Arribas R, Alamar S, Conejero V, Perez-Amador MA (2009) A new set of ESTs and cDNA clones from full length and nromalized libraries for gene discovery and functional characterization of citrus. BMC Genom 10:428

    Article  Google Scholar 

  • Martin FP, Dumas ME, Wang Y, Legido-Quigley C, Yap IK, Tang H, Zirah S, Murphy GM, Cloarec O et al (2007) A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol Syst Biol 3:112

    Article  PubMed  PubMed Central  Google Scholar 

  • Maruyama K, Takeda M, Kidokoro S, Yamada K, Sakuma Y, Urano K, Fujita M, Yoshiwara K, Matsukura S, Morishita Y, Sasaki R, Suzuki H, Saito K, Shibata D, Shinozaki K, Yamaguchi-Shinozaki K (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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mostofa MG, Hossain MA, Siddiqui N, Fujita M, Tran LS (2017) Phenotypical, physiological and biochemical analyses provide insight into selenium-induced phytotoxicity in rice plants. Chemosphere 178:212–223

    Article  CAS  PubMed  Google Scholar 

  • Nishizawa A, Yabuta Y, Shigeoka S (2008) Galactinol and raffinose constitute a novel function to protect plants from oxidative damage. Plant Physiol 147:1251–1263

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Obata T, Fernie AR (2012) The use of metabolomics to dissect plant responses to abiotic stresses. Cell Mol Life Sci 69:3225–3243

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Oliver DJ, Nikolau B, Wurtele ES (2002) Functional genomics: high-throughput mRNA, protein, and metabolite analyses. Metabol Eng 4:98–106

    Article  CAS  Google Scholar 

  • Pandey A, Chakraborty S, Datta A, Chakraborty N (2008) Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.). Mol Cell Proteom 7:88–107

    Article  CAS  Google Scholar 

  • Pasikanti KK, Ho PC, Chan EC (2008) Development and validation of a gas chromatography/mass spectrometry metabonomic platform for the global profiling of urinary metabolites. Rap Comm Mass Spect 22:2984–2992

    Article  CAS  Google Scholar 

  • Peck SC, Nuhse TS, Hess D, Iglesias A, Meins F, Boller T (2001) Directed proteomics identifies a plant specific protein rapidly phosphorylated in response to bacterial and fungal elicitors. Plant Cell 13:1467–1475

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Petersen AK, Zielinger S, Kastenmuller G, Romisch-Margl W, Brugger M, Peters A, Meisinger C, Strauch K, Hengstenberg C, Pagel P et al (2014) Epigenetic meets metabolomics an epigenome-wide association study with blood serum metabolic traits. Hum Mol Gent 23:534–545

    Article  CAS  Google Scholar 

  • Ramani AK, Li Z, Hart GT, Carlson MW, Boutz DR, Marcotte EM (2008) A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. Mol Syst Biol 4:180

    Article  PubMed  PubMed Central  Google Scholar 

  • Ratcliffe RG (1994) In vivo NMR studies of higher plants and algae. Adv Bot Res 20:43–123

    Article  CAS  Google Scholar 

  • Ratcliffe RG (1996) In vivo NMR spectroscopy: biochemical and physiological applications to plants. In: Shachar-Hill Y, Pfeffer PE (eds) Nuclear magnetic resonance in plant biology. American Society of Plant Physiologists, Rockville, pp 1–32

    Google Scholar 

  • Ratcliffe RG, Shachar-Hill Y (2001) Probing plant metabolism with NMR. Ann Rev Plant Physiol 52:499–526

    Article  CAS  Google Scholar 

  • Roberts JKM, Xia JH (1995) High-resolution NMR methods for study of higher plants. In: Galbraith DW, Bohnert HJ, Bourque DP (eds) Methods in plant cell biology, Vol 49, Part A. Academic Press, San Diego, pp 245–258

    Google Scholar 

  • Roberts J, Ray P, Wade-Jardetzky N, Jardetzky O (1980) Estimation of cytoplasmic and vacuolar pH in higher plant cells by 31P NMR. Nat 283:870–872

    Article  CAS  Google Scholar 

  • Roberts MR (2007) Does GABA acts as a signal in plants? Hints from molecular studies. Plant Signal Behav 2:408–409

    Article  PubMed  PubMed Central  Google Scholar 

  • Rocheta M, Coito JL, Ramos MJM, Carvalho L, Becket JD, Carbonell-Bejerano P, Amancio S (2016) Transcriptomic comparison between two Vitis vinifera L. varieties (Trincaderia and Touriga Nacional) in abiotic stress conditions. BMC Plant Biol 16:224

    Article  PubMed  PubMed Central  Google Scholar 

  • Roessner U, Bowne J (2009) What is metabolomics all about? Beyond Darwin: the future of molecular biology. Bio Tech 46(5):363–365

    CAS  Google Scholar 

  • Sanchez DH, Schwabe F, Erban A, Udvardi MK, Koka J (2012) Comparative metabolomics for drought acclimation in model and forage legumes. Plant Cell Environ 35:136–149

    Article  CAS  PubMed  Google Scholar 

  • Scherling C, Roscher C, Giavalisco P, Schulze E-D, Weckwerth W (2010) Metabolomics unravel contrasting effects of biodiversity on the performance of individual plant species. PLoS ONE 5(9):e12569

    Article  PubMed  PubMed Central  Google Scholar 

  • Seger C, Sturm S (2006) Analytical aspect of plant metabolite profiling platform: current standing and future aims. J Proteome Res 6:480–497

    Google Scholar 

  • Shachar-Hill Y, Pfeffer PE (1996) Nuclear magnetic resonance in plant biology. American Society of Plant Physiologists, Rockville

    Google Scholar 

  • Shelp BJ, Brown AW, McLean MD (1999) Metabolism and function of gamma aminobutyric acid. Trend Plant Sci 4(11):446–452

    Article  CAS  Google Scholar 

  • Shi SQ, Shi Z, Jiang ZP, Qi LW, Sun XM, Li CX, Lui JF, Xiao WF, Zhang SG (2010) Effect of exogenous GABA on gene expression of Caragana intermedia roots under NaCl stress: regulatory role of H2O2 and ethylene production. Plant Cell Environ 33(2):149–162

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Singh S, Parihar P, Singh R, Singh VP, Prasad SM (2015) Heavy metal tolerance in plants: role of transcriptomics, proteomics, metabolomics, and Ionomics. Front Plant Sci 6:1143

    PubMed  Google Scholar 

  • Skirycz A, Claeys H, De Bodt S, Oikawa A, Shinoda S, Andriankaja M, Maleux K, Eloy NB, Coppens F, Yoo SD, Saito K, Inze D (2011) Pause-and-stop: the effects of osmotic stress on cell proliferation during early leaf development in arabidopsis and a role for ethylene signaling in cell cycle arrest. Plant Cell 23:1876–1888

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Skylas DJ, Cordwell SJ, Hains PG, Larsen MR, Basseal DJ, Walsh BJ, Blumenthal C, Rathmell W, Copeland L, Wrigley CW (2002) Heat shock of wheat during grain filling: proteins associated with heat-tolerance. J Cereal Sci 35:175–188

    Article  CAS  Google Scholar 

  • Smith AR, Johnson HE, Hall M (2003) Metabolomic fingerprinting for salt stressed tomatoes. Bulg J Plant Physiol 29(3–4):153–163

    Google Scholar 

  • Soni P, Nutan KK, Soda N, Nongpiur RC, Roy S, Singla-Pareek SL, Pareek A (2015) Towards understanding abiotic stress signalling in plants: convergence of genomics, proteomic, and metabolomic approaches. In: Pandey GK (ed) Elucidation of abiotic stress signalling in plants. Springer Science, New York, pp 3–40

    Chapter  Google Scholar 

  • Tenenboim H, Burgos A, Willmitzer L, Brotman Y (2016) Using lipidomics for expanding the knowledge on lipid metabolism in plants. Biochimie 130:91–96

    Article  CAS  PubMed  Google Scholar 

  • Trethewey RN (2004) Metabolite profiling as an aid to metabolic engineering in plants. Curr Opin Plant Biol 7:196–201

    Article  CAS  PubMed  Google Scholar 

  • Unamba CIN, Nag A, Sharma RK (2015) Next generation sequencing technologies: the doorway to the unexplored genomics of non-model plants. Front Plant Sci 6:1074

    Article  PubMed  PubMed Central  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

    Article  CAS  PubMed  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 57(6):1065–1078

    Article  CAS  PubMed  Google Scholar 

  • Van Dongen JT, Frohlich A, Ramirez-Aguilar SJ, Schauer N, Fernie AR, Erban A, Kopka J, Clark J, Langer A, Geigenberger P (2009) Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of Arabidopsis plants. Ann Bot 103:269–280

    Article  PubMed  Google Scholar 

  • Velazquez SF, Harnendez VEB (2013) Abiotic stress in plants and metabolic responses. INTECH Open 25–48

  • Wang P, Su L, Gao H, Jiang X, Wu X, Li Y, Zhang Q, Wang Y, Ren F (2018) Genome-wide characterization of bHLH genes in grape and analysis of their potential relevance to abiotic stress tolerance and secondary metabolite biosynthesis. Front Plant Sci 9:64

    Article  PubMed  PubMed Central  Google Scholar 

  • Ward JL, Beale MH (2006) NMR spectroscopy in plant metabolomics. In: Saito K, Dixon RA, Willmitzer L (eds) Biotechnology in agriculture and forestry. Plant metabolomics, vol 57. Springer, Berlin, pp 81–91

    Google Scholar 

  • Weckwerth W (2003) Metabolomics in systems biology. Ann Rev Plant Biol 54:669–689

    Article  CAS  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 Proteom 7:1725–1736

    Article  CAS  Google Scholar 

  • Wrobel K, Esperanza MG, Barrientos EY, Escobosa ARC, Wrobel K (2020) Differential approaches in metabolomics analysis of plants exposed to selenium: a comprehensive review. Acta Physiol Plant 42:125

    Article  CAS  Google Scholar 

  • Wu SH, Ramonell K, Gollub J, Somerville S (2001) Plant gene expression profiling with DNA microarrays. Plant Physiol Biochem 39:917–926

    Article  CAS  Google Scholar 

  • Wu D, Cai S, Chen M, Ye E, Chen Z, Zhang H (2013) Tissue metabolic response to salt stress in wild and cultivated barley. PLoS ONE 8:e55431

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yong B, Xie H, Li Z, Li YP, Zhang Y, Nei G, Zhang XQ, Ma X, Huang LK, Yan YH, Peng Y (2017) Exogenous application of GABA improved PEG—induced drought tolerance positively associated with GABA—shunt, polyamines and proline metabolism in white clover. Front Physiol 8:1107

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang L, Li X, Ma B, Gao Q, Du H, Han Y, Cao Y, Qi M, Zhu Y, Lu H (2017) The tartary buckwheat genome provide insight into rutin biosynthesis and abiotic stress tolerance. Mol Plant 10(9):1224–1237

    Article  CAS  PubMed  Google Scholar 

  • Zhu Z, Chen Y, Shi G, Zhang X (2017) Selenium delays tomato fruit ripening by inhibiting ethylene biosynthesis and enhancing the antioxidant defense system. Food Chem 219:79–184

    Article  Google Scholar 

  • Zhu Z, Zhang Y, Liu J, Chen Y, Zhang X (2018) Exploring the effects of selenium treatment on the nutritional quality of tomato fruit. Food Chem 252:9–15

    Article  CAS  PubMed  Google Scholar 

  • Zivy M, Wienkoop S, Renaut J, Pinheiro C, Goulas E, Carpentier S (2015) The quest for tolerant varieties: the importance of integrating “omics” techniques to phenotyping. Front Plant Sci 6:448

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We deeply acknowledge the work and contribution of biologists and chemists in making us understand the importance of metabolomic tools to comprehend plant abiotic stress responses. Our effort is aimed to curve out a general outlook of plant metabolomics for abiotic stress; possibly many essential points are missed, which is totally unintentional.

Author information

Authors and Affiliations

  1. Plant Stress Biology and Metabolomics Laboratory, Central Instrumentation Laboratory, Assam University, Silchar, 788011, India

    Shuvasish Choudhury, Debojyoti Moulick & Muhammed Khairujjaman Mazumder

  2. Department of Life Science and Bioinformatics, Assam University, Silchar, 788011, India

    Shuvasish Choudhury

  3. Don Bosco School, Silchar, 788003, India

    Parul Sharma

  4. Department of Zoology, Dhemaji College, Dhemaji, 787057, India

    Muhammed Khairujjaman Mazumder

Authors
  1. Shuvasish Choudhury
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Parul Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Debojyoti Moulick
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Muhammed Khairujjaman Mazumder
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Shuvasish Choudhury.

Ethics declarations

Conflict of interest

None.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Choudhury, S., Sharma, P., Moulick, D. et al. Unrevealing metabolomics for abiotic stress adaptation and tolerance in plants. J. Crop Sci. Biotechnol. 24, 479–493 (2021). https://doi.org/10.1007/s12892-021-00102-8

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12892-021-00102-8

Keywords

Search

Navigation