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Genomics-Based Analyses of Environmental Stresses in Crop Plants

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Approaches to Plant Stress and their Management

Abstract

The obligate sessile nature of plants imposes a considerable challenge with regard to their ability to adapt and thrive in the wake of rapid climate change disasters. This includes extremes of moisture stress – drought and flooding, temperature extremes – heat and cold, and atmospheric pollutants such as ozone. These climate change factors can significantly retard the phenology, physiology, and molecular programs of crop plants that in turn adversely impact the crop yields and hence represent a significant threat for global food security. On the brighter side, plants being resilient have evolved a gamut of adaptive mechanisms to thwart such catastrophes. In this chapter, we focus our attention on the molecular aspects of adaptive mechanisms in plants. In particular, we attempt to highlight the major findings from omics-based studies in response to climate change factors. We offer some perspectives on the need for integrated omics approaches and realistic field-level studies of stresses.

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References

  • Agrawal GK, Rakwal R, Yonekura M, Kubo A, Saji H (2002) Proteome analysis of differentially displayed proteins as a tool for investigating ozone stress in rice (Oryza sativa L.) seedlings. Proteomics 2:947–959

    Article  PubMed  CAS  Google Scholar 

  • Ahsan N, Nanjo Y, Sawada H, Kohno Y, Komatsu S (2010) Ozone stress-induced proteomic changes in leaf total soluble and chloroplast proteins of soybean reveal that carbon allocation is involved in adaptation in the early developmental stage. Proteomics 10:2605–2619

    Article  PubMed  CAS  Google Scholar 

  • Ahuja I, De Vos RC, Bones AM, Hall RD (2010) Plant molecular stress responses face climate change. Trends Plant Sci 15:664–674

    Article  PubMed  CAS  Google Scholar 

  • Alam I, Lee DG, Kim KH et al (2010) Proteome analysis of soybean roots under waterlogging stress at an early vegetative stage. J Biosci 35:49–62

    Article  PubMed  CAS  Google Scholar 

  • Araus JL, Slafer GA, Reynolds MP, Royo C (2002) Plant breeding and drought in C-3 cereals: what should we breed for? Ann Bot 89:925–940

    Article  PubMed  Google Scholar 

  • Balbuena TS, Salas JJ, Martinez-Force E, Garces R, Thelen JJ (2011) Proteome analysis of cold acclimation in sunflower. J Proteome Res 10:2330–2346

    Article  PubMed  CAS  Google Scholar 

  • Baniwal SK, Bharti K, Chan KY et al (2004) Heat stress response in plants: a complex game with chaperones and more than twenty heat stress transcription factors. J Biosci 29:471–487

    Article  PubMed  CAS  Google Scholar 

  • Barkla BJ, Vera-Estrella R, Pantoja O (2013) Progress and challenges for abiotic stress proteomics of crop plants. Proteomics. doi: 10.1002/pmic.201200401

  • Beauclair L, Yu A, Bouche N (2010) microRNA-directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis. Plant J 62:454–462

    Article  PubMed  CAS  Google Scholar 

  • Benesova M, Hola D, Fischer L et al (2012) The physiology and proteomics of drought tolerance in maize: early stomatal closure as a cause of lower tolerance to short-term dehydration? PLoS One 7:e38017

    Article  PubMed  CAS  Google Scholar 

  • Biehler K, Fock H (1996) Evidence for the contribution of the Mehler-peroxidase reaction in dissipating excess electrons in drought-stressed wheat. Plant Physiol 112:265–272

    PubMed  CAS  Google Scholar 

  • Boyer JS (1982) Plant productivity and environment. Science 218:443–448

    Article  PubMed  CAS  Google Scholar 

  • Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M et al (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 320:1185–1190

    Article  PubMed  CAS  Google Scholar 

  • Carrington JC, Ambros V (2003) Role of microRNAs in plant and animal development. Science 301:336–338

    Article  PubMed  CAS  Google Scholar 

  • Cassman KG (1999) Ecological intensification of cereal production systems: yield potential, soil quality, and precision agriculture. Proc Natl Acad Sci U S A 96:5952–5959

    Article  PubMed  CAS  Google Scholar 

  • Chen XM (2005) microRNA biogenesis and function in plants. FEBS Lett 579:5923–5931

    Article  PubMed  CAS  Google Scholar 

  • Chen L, Ren YY, Zhang YY et al (2012) Genome-wide identification and expression analysis of heat-responsive and novel microRNAs in Populus tomentosa. Gene 504:160–165

    Article  PubMed  CAS  Google Scholar 

  • Cho K, Shibato J, Kubo A et al (2013) Genome-wide mapping of the ozone-responsive transcriptomes in rice panicle and seed tissues reveals novel insight into their regulatory events. Biotechnol Lett 35:647–656

    Article  PubMed  CAS  Google Scholar 

  • Choudhary MK, Basu D, Datta A, Chakraborty N, Chakraborty S (2009) Dehydration-responsive nuclear proteome of rice (Oryza sativa L.) illustrates protein network, novel regulators of cellular adaptation, and evolutionary perspective. Mol Cell Proteomics 8:1579–1598

    Article  PubMed  CAS  Google Scholar 

  • Crifo T, Puglisi I, Petrone G, Recupero GR, Lo Piero AR (2011) Expression analysis in response to low temperature stress in blood oranges: implication of the flavonoid biosynthetic pathway. Gene 476:1–9

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • De Lima JC, Loss-Morais G, Margis R (2012) MicroRNAs play critical roles during plant development and in response to abiotic stresses. Genet Mol Biol 35:1069–1077

    Article  PubMed  Google Scholar 

  • Dhalmini Z, Spillane C, Moss JP, Ruane J, Urquia N, Sonnino A (2005) Status of research and application of crop biotechnologies in developing countries. Food and Agricultural Organization, Rome, pp 1–62. Available at http://www.fao.org/docrep/008/y5800e/Y5800E09.htm

  • Evans LT (1998) Feeding the ten billion: plants and population growth. Cambridge University Press, Cambridge

    Google Scholar 

  • Fedoroff N, Brown NM (2004) Mendel in the kitchen. Joseph Henry Press, Washington, DC

    Google Scholar 

  • Fukushima A, Kusano M, Redestig H, Arita M, Saito K (2009) Integrated OMICS approaches in plant systems biology. Curr Opin Chem Biol 13:532–538

    Article  PubMed  CAS  Google Scholar 

  • Galant A, Koester RP, Ainsworth EA, Hicks LM, Jez JM (2012) From climate change to molecular response: redox proteomics of ozone-induced responses in soybean. New Phytol 194:220–229

    Article  PubMed  CAS  Google Scholar 

  • Gorantla M, Babu PR, Lachagari VB et al (2007) Identification of stress-responsive genes in an indica rice (Oryza sativa L.) using ESTs generated from drought-stressed seedlings. J Exp Bot 58:253–265

    Article  PubMed  CAS  Google Scholar 

  • Guan Q, Lu X, Zeng H, Zhang Y, Zhu J (2013) Heat stress induction of miR398 triggers a regulatory loop that is critical for thermotolerance in Arabidopsis. Plant J 74:840–851

    Google Scholar 

  • Gulick PJ, Drouin S, Yu Z et al (2005) Transcriptome comparison of winter and spring wheat responding to low temperature. Genome 48:913–923

    Article  PubMed  CAS  Google Scholar 

  • Hajheidari M, Abdollahian-Noghabi M, Askari H et al (2005) Proteome analysis of sugar beet leaves under drought stress. Proteomics 5:950–960

    Article  PubMed  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 

  • Hashimoto M, Komatsu S (2007) Proteomic analysis of rice seedlings during cold stress. Proteomics 7:1293–1302

    Article  PubMed  CAS  Google Scholar 

  • Iyer NJ, Jia X, Sunkar R, Tang G, Mahalingam R (2012) MicroRNAs responsive to ozone-induced oxidative stress in Arabidopsis thaliana. Plant Signal Behav 7:484–491

    Article  PubMed  CAS  Google Scholar 

  • Jagadeeswaran G, Saini A, Sunkar R (2009) Biotic and abiotic stress down-regulate miR398 expression in Arabidopsis. Planta 229:1009–1014

    Article  PubMed  CAS  Google Scholar 

  • Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787–799

    Article  PubMed  CAS  Google Scholar 

  • Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Physiol Plant Mol Biol 57:19–53

    CAS  Google Scholar 

  • Kantar M, Unver T, Budak H (2010) Regulation of barley miRNAs upon dehydration stress correlated with target gene expression. Funct Integr Genomics 10:493–507

    Article  PubMed  CAS  Google Scholar 

  • Kantar M, Lucas SJ, Budak H (2011) miRNA expression patterns of Triticum dicoccoides in response to shock drought stress. Planta 233:471–484

    Article  PubMed  CAS  Google Scholar 

  • Khraiwesh B, Zhu JK, Zhu J (2012) Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim Biophys Acta 1819:137–148

    Article  PubMed  CAS  Google Scholar 

  • Kulcheski FR, De Oliveira LF, Molina LG et al (2011) Identification of novel soybean microRNAs involved in abiotic and biotic stresses. BMC Genomics 12:307

    Article  PubMed  CAS  Google Scholar 

  • Lanet E, Delannoy E, Sormani R et al (2009) Biochemical evidence for translational repression by Arabidopsis microRNAs. Plant Cell 21:1762–1768

    Article  PubMed  CAS  Google Scholar 

  • Lee S, Yun SC (2006) The ozone stress transcriptome of pepper (Capsicum annuum L.). Mol Cells 21:197–205

    PubMed  CAS  Google Scholar 

  • Lee DG, Ahsan N, Lee SH et al (2007) A proteomic approach in analyzing heat-responsive proteins in rice leaves. Proteomics 7:3369–3383

    Article  PubMed  CAS  Google Scholar 

  • Li WX, Oono Y, Zhu JH et al (2008) The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance. Plant Cell 20:2238–2251

    Article  PubMed  CAS  Google Scholar 

  • Li YF, Zheng Y, Addo-Quaye C et al (2010) Transcriptome-wide identification of microRNA targets in rice. Plant J 62:742–759

    Article  PubMed  CAS  Google Scholar 

  • Li B, Qin Y, Duan H, Yin W, Xia X (2011) Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica. J Exp Bot 62:3765–3779

    Article  PubMed  CAS  Google Scholar 

  • Liberman LM, Sozzani R, Benfey PN (2012) Integrative systems biology: an attempt to describe a simple weed. Curr Opin Plant Biol 15:162–167

    Article  PubMed  CAS  Google Scholar 

  • Liu HH, Tian X, Li YJ, Wu CA, Zheng CC (2008) Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14:836–843

    Article  PubMed  CAS  Google Scholar 

  • Lu SF, Sun YH, Shi R, Clark C, Li LG, Chiang VL (2005) Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 17:2186–2203

    Article  PubMed  CAS  Google Scholar 

  • Lu S, Sun YH, Chiang VL (2008) Stress-responsive microRNAs in Populus. Plant J 55:131–151

    Article  PubMed  CAS  Google Scholar 

  • Ludwikow A, Sadowski J (2008) Gene networks in plant ozone stress response and tolerance. J Integr Plant Biol 50:1256–1267

    Article  PubMed  CAS  Google Scholar 

  • Lv DK, Bai X, Li Y et al (2010) Profiling of cold-stress-responsive miRNAs in rice by microarrays. Gene 459:39–47

    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 

  • Malthus TR (1817) An essay on the principle of population. Murray, London

    Google Scholar 

  • Maul P, Mccollum GT, Popp M, Guy CL, Porat R (2008) Transcriptome profiling of grapefruit flavedo following exposure to low temperature and conditioning treatments uncovers principal molecular components involved in chilling tolerance and susceptibility. Plant Cell Environ 31:752–768

    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 

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

    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 Proteomics 7:88–107

    Article  PubMed  CAS  Google Scholar 

  • Puckette MC, Tang Y, Mahalingam R (2008) Transcriptomic changes induced by acute ozone in resistant and sensitive Medicago truncatula accessions. BMC Plant Biol 8:46

    Article  PubMed  Google Scholar 

  • Ramachandran V, Chen X (2008) Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science 321:1490–1492

    Article  PubMed  CAS  Google Scholar 

  • Reyes JL, Chua NH (2007) ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J 49:592–606

    Article  PubMed  CAS  Google Scholar 

  • Rinalducci S, Egidi MG, Karimzadeh G, Jazii FR, Zolla L (2011) Proteomic analysis of a spring wheat cultivar in response to prolonged cold stress. Electrophoresis 32:1807–1818

    Article  PubMed  CAS  Google Scholar 

  • Rosegrant MW, Cline SA (2003) Global food security: challenges and policies. Science 302:1917–1919

    Article  PubMed  CAS  Google Scholar 

  • Ruiz-Ferrer V, Voinnet O (2009) Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol 60:485–510

    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 

  • Sharma YK, Davis KR (1994) Ozone-induced expression of stress-related genes in Arabidopsis thaliana. Plant Physiol 105:1089–1096

    PubMed  CAS  Google Scholar 

  • Shuai P, Liang D, Zhang Z, Yin W, Xia X (2013) Identification of drought-responsive and novel Populus trichocarpa microRNAs by high-throughput sequencing and their targets using degradome analysis. BMC Genomics 14:233

    Article  PubMed  CAS  Google Scholar 

  • Sunkar R (2010) MicroRNAs with macro-effects on plant stress responses. Semin Cell Dev Biol 21:805–811

    Article  PubMed  CAS  Google Scholar 

  • Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001–2019

    Article  PubMed  CAS  Google Scholar 

  • Sunkar R, Kapoor A, Zhu JK (2006) Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell 18:2051–2065

    Article  PubMed  CAS  Google Scholar 

  • Sunkar R, Li YF, Jagadeeswaran G (2012) Functions of microRNAs in plant stress responses. Trends Plant Sci 17:196–203

    Article  PubMed  CAS  Google Scholar 

  • Svensson JT, Crosatti C, Campoli C et al (2006) Transcriptome analysis of cold acclimation in barley albina and xantha mutants. Plant Physiol 141:257–270

    Article  PubMed  CAS  Google Scholar 

  • Tang Z, Zhang L, Xu C et al (2012) Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male-sterile line by deep sequencing. Plant Physiol 159:721–738

    Article  PubMed  CAS  Google Scholar 

  • Tester M, Bacic A (2005) Abiotic stress tolerance in grasses. From model plants to crop plants. Plant Physiol 137:791–793

    Article  PubMed  CAS  Google Scholar 

  • Torres NL, Cho K, Shibato J et al (2007) Gel-based proteomics reveals potential novel protein markers of ozone stress in leaves of cultivated bean and maize species of Panama. Electrophoresis 28:4369–4381

    Article  PubMed  CAS  Google Scholar 

  • Trindade I, Capitao C, Dalmay T, Fevereiro MP, Santos DM (2010) miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula. Planta 231:705–716

    Article  PubMed  CAS  Google Scholar 

  • Van Vuuren DP, Meinshausen M, Plattner GK et al (2008) Temperature increase of 21st century mitigation scenarios. Proc Natl Acad Sci U S A 105:15258–15262

    Article  PubMed  Google Scholar 

  • Verslues PE, Agarwal M, Katiyar-Agarwal S, Zhu JH, Zhu JK (2006) Methods and concepts in quantifying resistance to drought, salt and freezing, abiotic stresses that affect plant water status. Plant J 45:523–539

    Article  PubMed  CAS  Google Scholar 

  • Vitamvas P, Prasil IT, Kosova K, Planchon S, Renaut J (2012) Analysis of proteome and frost tolerance in chromosome 5A and 5B reciprocal substitution lines between two winter wheats during long-term cold acclimation. Proteomics 12:68–85

    Article  PubMed  CAS  Google Scholar 

  • Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136:669–687

    Article  PubMed  CAS  Google Scholar 

  • Weiss J, Egea-Cortines M (2009) Transcriptomic analysis of cold response in tomato fruits identifies dehydrin as a marker of cold stress. J Appl Genet 50:311–319

    Article  PubMed  CAS  Google Scholar 

  • Xin M, Wang Y, Yao Y et al (2010) Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.). BMC Plant Biol 10:123

    Article  PubMed  Google Scholar 

  • Yu X, Wang H, Lu YZ et al (2012) Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa. J Exp Bot 63:1025–1038

    Article  PubMed  CAS  Google Scholar 

  • Zeng CY, Wang WQ, Zheng Y et al (2010) Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants. Nucleic Acids Res 38:981–995

    Article  PubMed  CAS  Google Scholar 

  • Zhang JY, Xu YY, Huan Q, Chong K (2009) Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response. BMC Genom 10:449. doi: 10.1186/1471-2164-10-449

  • Zhang T, Zhao X, Wang W et al (2012) Comparative transcriptome profiling of chilling stress responsiveness in two contrasting rice genotypes. PLoS One 7:e43274

    Article  PubMed  CAS  Google Scholar 

  • Zhao B, Liang R, Ge L et al (2007) Identification of drought-induced microRNAs in rice. Biochem Biophys Res Commun 354:585–590

    Article  PubMed  CAS  Google Scholar 

  • Zhou X, Wang G, Sutoh K, Zhu JK, Zhang W (2008) Identification of cold-inducible microRNAs in plants by transcriptome analysis. Biochim Biophys Acta 1779:780–788

    Article  PubMed  CAS  Google Scholar 

  • Zhou L, Liu Y, Liu Z, Kong D, Duan M, Luo L (2010) Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. J Exp Bot 61:4157–4168

    Article  PubMed  CAS  Google Scholar 

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Correspondence to Ramamurthy Mahalingam .

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Muthuramalingam, M., Li, YF., Mahalingam, R. (2014). Genomics-Based Analyses of Environmental Stresses in Crop Plants. In: Gaur, R., Sharma, P. (eds) Approaches to Plant Stress and their Management. Springer, New Delhi. https://doi.org/10.1007/978-81-322-1620-9_22

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