Drought stress responses in crops

Functional and Integrative Genomics

Volumn 14, Issue 1, 2014, Pages 11-22

  Shanker, Arun K ^a   Maheswari, M ^a   Yadav, S K ^a   Desai, S ^a   Bhanu, Divya ^a   Attal, Neha Bajaj ^a   Venkateswarlu, B ^a  

^a CENTRAL RESEARCH INSTITUTE FOR DRYLAND AGRICULTURE   (India)

Author keywords

Bioinformatics; Climate change; Drought tolerance; Interactome; Metabolome; Proteome; Transcriptome

Indexed keywords

ABSCISIC ACID; MICRORNA; MITOGEN ACTIVATED PROTEIN KINASE; REACTIVE OXYGEN METABOLITE; TRANSCRIPTION FACTOR; HISTONE; PROTEOME; TRANSCRIPTOME;

ARABIDOPSIS; CROP; DNA METHYLATION; DROUGHT RESISTANCE; DROUGHT STRESS; DROUGHT TOLERANCE; GENE EXPRESSION; HISTONE METHYLATION; HISTONE MODIFICATION; METABOLOMICS; NONHUMAN; PHENOTYPIC VARIATION; PLANT GENE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEOMICS; REVIEW; RNA INTERFERENCE; SIGNAL TRANSDUCTION; TRANSCRIPTOMICS; DROUGHT; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; MAIZE; METABOLISM; METABOLOME; PHYSIOLOGICAL STRESS; PHYSIOLOGY; RICE; SORGHUM;

ARABIDOPSIS; TRITICUM AESTIVUM; ZEA MAYS;

ABSCISIC ACID; ARABIDOPSIS; CROPS, AGRICULTURAL; DROUGHTS; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, PLANT; HISTONES; METABOLOME; ORYZA SATIVA; PROTEOME; RNA INTERFERENCE; SIGNAL TRANSDUCTION; SORGHUM; STRESS, PHYSIOLOGICAL; TRANSCRIPTOME; ZEA MAYS;

EID: 84898056617     PISSN: 1438793X     EISSN: 14387948     Source Type: Journal    
DOI: 10.1007/s10142-013-0356-x     Document Type: Review

References (80)

1. Alvarez S, Marsh EL, Schroeder SG, Schachtman DP (2008), Metabolomic and proteomic changes in the xylem sap of maize under drought. Plant, Cell & Environment 31: 325-340
2. Aranjuelo I, Molero G, Erice G, Avice JC, Nogués S (2011) Plant physiology and proteomics reveals the leaf response to drought in alfalfa (Medicago sativa L.). J Exp Bot 62:111-123
3. Ashoub A, Beckhaus T, Berberich T, Karas M, Brüggemann W (2013) Comparative analysis of barley leaf proteome as affected by drought stress. Planta 237:771-781
4. Babita M, Maheswari M, Rao LM, Shanker AK, Rao DG (2010) Osmotic adjustment, drought tolerance and yield in castor (Ricinus communis L.) hybrids. Environ Exp Bot 69:243-249
5. Batlang U, Baisakh N, Ambavaram MM, Pereira A (2013) Phenotypic and physiological evaluation for drought and salinity stress responses in rice. Methods Mol Biol 956:209-225
6. Benešová M, Holá D, Fischer L, Jedelský PL, Hnilička F, Wilhelmová N, Hniličková H (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
7. Bertolini E, Verelst W, Horner DS, Gianfranceschi L, Piccolo V, DInze D, Pe ME, Mica E (2013) Addressing the role of microRNAs in reprogramming leaf growth during drought stress in Brachypodium distachyon. Mol Plant 6:423-443
8. Boyko A, Kovalchuk I (2013) Epigenetic modifications in plants under adverse conditions: agricultural applications. In: Plant acclimation to environmental stress. Springer, New York, pp 233-267
9. Braun P, Carvunis AR, Charloteaux B, Dreze M, Ecker JR, Hill DE, Roth FP, Vidal M et al (2011) Evidence for network evolution in an Arabidopsis interactome map. Science 333:601-607
10. Cao M, Liu X, Zhang Y, Xue X, Zhou XE, Melcher K, Gao P, Wang F, Zeng L, Zhao Y, Zhao Y, Deng P, Zhong D, Zhu JK, Xu HE, Xu Y (2013) An ABA-mimicking ligand that reduces water loss and promotes drought resistance in plants. Cell Res 23:1043-1054
11. Chan KX, Wirtz M, Phua SY, Estavillo GM, Pogson BJ (2012) Balancing metabolites in drought: the sulfur assimilation conundrum. Trends in Plant Science 18:18-29
12. Charlton AJ, Donarski JA, Harrison M, Jones SA, Godward J, Oehlschlager S, Arques JL, Ambrose M, Chinoy C, Mullineaux PM, Domoney C (2008) Responses of the pea (Pisum sativum L.) leaf metabolome to drought stress assessed by nuclear magnetic resonance spectroscopy. Metabolomics 4:312-327
13. Chen Z, Huang J, Muttucumaru N, Powers SJ, Halford NG (2013) Expression analysis of abscisic acid (ABA) and metabolic signaling factors in developing endosperm and embryo of barley. J Cereal Sci 58:255-262
14. Colcombet J, Hirt H (2008), Arabidopsis MAPKs: a complex signalling network involved in multiple biological processes. Biochem. J 413: 217-226
15. Deeba F, Pandey AK, Ranjan S, Mishra A, Singh R, Sharma YK, Shirke PA, Pandey V (2012) Physiological and proteomic responses of cotton (Gossypium herbaceum L.) to drought stress. Plant Physiol Biochem 53:6-18
16. Duque L, Setter T (2013) Cassava response to water deficit in deep pots: root and shoot growth, ABA and carbohydrate reserves in stems, leaves and storage roots. Tropical Plant Biol 6:199-209
17. Galle A, Csiszar J, Benyo D, Laskay G, Leviczky T, Erdei L, Tari I (2013) Isohydric and anisohydric strategies of wheat genotypes under osmotic stress: biosynthesis and function of ABA in stress responses. J Plant Physiol 170:1389-1399
18. Gentile A, Ferreira TH, Mattos RS, Dias LI, Hoshino AA, Carneiro MS, Souza GM, Calsa T Jr, Nogueira RM, Endres L, Menossi M (2013) Effects of drought on the microtranscriptome of field-grown sugarcane plants. Planta 237(3):783-798
19. Ghaffari M, Mahmoud T, Valizadeh M, Komatsu S (2013) Differential response of root proteome to drought stress in drought sensitive and tolerant sunflower inbred lines. Functional Plant Biology 40, 609-617
20. González RM, Ricardi MM, Iusem ND (2013) Epigenetic marks in an adaptive water stress-responsive gene in tomato roots under normal and drought conditions. Epigenetics 8(8):864-872
21. Gupta S, Bharalee R, Bhorali P, Bandyopadhyay T, Gohain B, Agarwal N, Parveen Ahmed Saikia H, Borchetia S, Kalita MC, Handique AK, Das S (2012) Identification of drought tolerant progenies in tea by gene expression analysis. Functional & integrative genomics 12:543-563
22. Hamel LP, Nicole MC, Duplessis S, Ellis BE (2012) Mitogen-activated protein kinase signaling in plant-interacting fungi: distinct messages from conserved messengers. Plant Cell 24:1327-51
23. Houle D, Govindaraju DR, Omholt S (2010) Phenomics: the next challenge. Nature Rev Gen 11:855-866
24. Hua D, Wang C, He J, Liao H, Duan Y, Zhu Z, Guo Y, Chen Z, Gong Z (2012) A plasma membrane receptor kinase GHR1 mediates abscisic acid and hydrogen peroxide-regulated stomatal movement in Arabidopsis. Plant Cell 24:2546-2561
25. Iyer NJ, Tang Y, Mahalingam R (2013) Physiological, biochemical and molecular responses to a combination of drought and ozone in Medicago truncatula. Plant Cell Environ 36:706-720
26. Jiang Y, Liang G, Yu D (2012) Activated expression of WRKY57 confers drought tolerance in Arabidopsis. Mol Plant 5:1375-1388
27. Kadam S, Singh K, Shukla S, Goel S, Vikram P, Pawar V, Gaikwad K, Khanna-Chopra R, Singh N (2012) Genomic associations for drought tolerance on the short arm of wheat chromosome 4B. Functional & integrative genomics 12(3):447-464
28. Kakumanu A, Ambavaram MR, Klumas C, Krishnan A, Batlang U, Myers E, Grene R, Pereira A (2012) Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-seq. Plant Physiol 160:846-867
29. Kang Y, Udvardi M (2012) Global regulation of reactive oxygen species scavenging genes in alfalfa root and shoot under gradual drought stress and recovery. Plant Signaling and Behavior 7:539-543
30. Kim H, Hwang H, Hong JW, Lee YN, Ahn IP, Yoon IS, Yoo SD, Lee S, Lee SC, Kim BG (2011) A rice orthologue of the ABA receptor, OsPYL/RCAR5, is a positive regulator of the ABA signal transduction pathway in seed germination and early seedling growth. J Exp Bot 63:1013-1024
31. Kottapalli KR, Rakwal R, Shibato J, Burow G, Tissues D, Burke J, Puppala N, Burow M, Payton P (2009) Physiology and proteomics of the water-deficit stress response in three contrasting peanut genotypes. Plant Cell Environ 32:380-407
32. Krugman T, Chagué V, Peleg Z, Balzergue S, Just J, Korol AB, Nevo E, Saranga Y, Chalhoub B, Fahima T (2010) Multilevel regulation and signalling processes associated with adaptation to terminal drought in wild emmer wheat. Functional & integrative genomics 10:167-186
33. Kumari S, Roy S, Singh P, Singla-Pareek SL, Pareek A (2013) Cyclophilins: proteins in search of function. Plant Signaling Behavior 8(1):e22734
34. 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 stages under drought stress revealed by genome-wide transcriptome analysis. PLoS One 7:449522
35. Lembke CG, Nishiyama J, Sato PM, de Andrade RF, Souza GM (2012) Identification of sense and antisense transcripts regulated by drought in sugarcane. Plant Mol Biol 79:461-477
36. Lenka SK, Katiyar A, Chinnusamy V, Bansal KC (2011) Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance. Plant Biotechnol J 9:315-327
37. Liang W, Yang B, Yu BJ, Zhou Z, Li C, Jia M, Jiang YQ (2013) Identification and analysis of MKK and MPK gene families in canola (Brassica napus L.). BMC Genomics 14(1):392
38. Mandel T, Rogachev I, Venger I, Mintz-Oron S, Aharoni A, Adato A (2009) The ins and outs of tomato fruit peel metabolome. ISHS Acta Horticulturae 814:465-474
39. Mirouze M, Paszkowski J (2011) Epigenetic contribution to stress adaptation in plants. Curr Opin Plant Biol 14:267-274
40. Mirzaei M, Soltani N, Sarhadi E, Pascovici D, Keighley T, Salekdeh GH, Haynes PA, Atwell BJ (2011) Shotgun proteomic analysis of long-distance drought signaling in rice roots. J Proteome Res 11:348-358
41. Moco S, Capanoglu E, Tikunov Y, Bino RJ, Boyacioglu D, Hall RD, Vervoort J, De Vos RC (2007) Tissue specialization at the metabolite level is perceived during the development of tomato fruit. J Exp Bot 58:4131-4146
42. Mohammadi PP, Moieni A, Komatsu S (2012) Comparative proteome analysis of drought-sensitive and drought-tolerant rapeseed roots and their hybrid F1 line under drought stress. Amino Acids 43:2137-2152
43. Moumeni A, Satoh K, Kondoh H, Asano T, Hosaka A, Venuprasad R, Serraj R, Kumar A, Leung H, Kikuchi S (2011) Comparative analysis of root transcriptome profiles of two pairs of drought-tolerant and susceptible rice near-isogenic lines under different drought stress. BMC Plant Biol 11:174
44. Muller T, Ensminger I, Schmid KJ (2012) A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings. BMC Genomics 13:673
45. Niu Y, Wang Y, Li P, Zhang F, Liu H, Zheng G (2012) Drought stress induces oxidative stress and the antioxidant defense system in ascorbate-deficient vtc1 mutants of Arabidopsis thaliana. Acta Physiologiae Plantarum 35:1189-1200
46. Ozfidan C, Turkan I, Sekmen AH, Seckin B (2013) Time course analysis of ABA and non-ionic osmotic stress-induced changes in water status, chlorophyll fluorescence and osmotic adjustment in Arabidopsis thaliana wild-type (Columbia) and ABA-deficient mutant (aba2). Environ Exp Bot 86:44-51
47. Peng S, Jiang H, Zhang S, Chen L, Li X, Korpelainen H, Li C (2012) Transcriptional profiling reveals sexual differences of the leaf transcriptomes in response to drought stress in Populus yunnanensis. Tree Physiol 32:1541-1555
48. Perrone I, Pagliarani C, Lovisolo C, Chitarra W, Roman F, Schubert A (2012) Recovery from water stress affects grape leaf petiole transcriptome. Planta 235:1383-1396
49. Pizzio GA, Lesia R, Regina A, Miguel GG, Cristina Y, Ebe M, Hannes K, Armando A, Pedro LR (2013) The PYL4 A194T Mutant Uncovers a Key Role of PYR1-LIKE4/PROTEIN PHOSPHATASE 2CA Interaction for Abscisic Acid Signaling and Plant Drought Resistance. Plant Physiol 163: 441-455
50. Popescu SC, Popescu GV, Bachan S, Zhang Z, Gerstein M, Snyder M, Dinesh Kumar SP (2009), MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Gene Dev 23:80-92
51. Qi X, Xie S, Liu Y, Yi F, Yu J (2013) Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing. Plant Mol Biol 83:459-473
52. Ranjan A, Pandey N, Lakhwani D, Dubey NK, Pathre UV, Sawant SV (2012) Comparative transcriptomic analysis of roots of contrasting Gossypium herbaceum genotypes revealing adaptation to drought. BMC Genomics 13:680
53. Rao KP, Richa T, Kumar K, Raghuram B, Sinha AK (2010) In silico analysis reveals 75 members of mitogen-activated protein kinase kinase kinase gene family in rice. DNA Res 17:139-153
54. Ray S, Dansana PK, Giri J, Deveshwar P, Arora R, Agarwal P, Khurana JP, Kapoor S, Tyagi AK (2011) Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice. Functional & integrative genomics 11:157-178
55. Ren Y, Chen L, Zhang Y, Kang X, Zhang Z, Wang Y (2012) Identification of novel and conserved Populus tomentosa microRNA as components of a response to water stress. Functional & integrative genomics 12:327-339
56. Rico L, Ogaya R, Barbeta R, Penuelas J (2013) Changes in DNA methylation fingerprint of Quercus ilex trees in response to experimental field drought simulating projected climate change. Plant Biol. doi: 10.1111/plb.12049
57. Rivas-Ubach A, Sardans J, Pérez-Trujillo M, Estiarte M, Peñuelas J (2012) Strong relationship between elemental stoichiometry and metabolome in plants. Proc Natl Acad Sci U S A 109:4181-4186
58. Saad AS, Li X, Li HP, Huang T, Gao CS, Guo MW, Cheng W, Zhao GY, Liao YC (2013) A rice stress-responsive NAC gene enhances tolerance of transgenic wheat to drought and salt stresses. Plant Sci 203-204:33-40
59. Sanchez DH, Schwabe F, Erban A, Udvardi MK, Kopka J (2012) Comparative metabolomics of drought acclimation in model and forage legumes. Plant Cell Environ 35:136-149
60. Seo YS, Chern M, Bartley LE, Han M, Jung KH, Lee I, Ronald PC (2011) Towards establishment of a rice stress response interactome. PLoS Genet 7:e1002020
61. Shaik R, Ramakrishna W (2012) Bioinformatic analysis of epigenetic and microRNA mediated regulation of drought responsive genes in rice. PLoS One 7(11):e49331
62. Shanker AK, Djanaguiraman M, Venkateswarlu B (2009) Chromium interactions in plants: current status and future strategies. Metallomics 1:375-383
63. Shanker AK, Maddaala A, Anil Kumar M, Yadav SK, Maheshwari M, Venkateswarlu B (2012) In silico targeted genome mining and comparative modelling reveals a putative protein similar to an Arabidopsis drought tolerance DNA binding transcription factor in chromosome 6 of Sorghum bicolor genome. Interdiscip Sci: Comput Life Sci 4:133-141
64. Singh R, Jwa NS (2013) The rice MAPKK-MAPK interactome: the biological significance of MAPK components in hormone signal transduction. Plant Cell Rep 32:923-931
65. Sinha AK, Jaggi M, Raghuram B, Tuteja N (2011) Mitogen-activated protein kinase signaling in plants under abiotic stress. Plant Signal Behav 6:196-203
66. Soding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960
67. Soon FF, Ng LM, Zhou XE, West GM, Kovach A, Tan MHE, Suino-Powell KM, He Y, Xu Y, Chalmers MJ, Brunzelle JS, Zhang H, Yang H, Jiang H, Li J, Yong EL, Cutler S, Zhu JK, Griffin PR, Melcher K, Xu HE (2012) Molecular mimicry regulates ABA signaling by SnRK2 kinases and PP2C phosphatases. Science 335:85-88
68. 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 506:265-273
69. Su Z, Ma X, Guo H, Sukiran NL, Guo B, Assmann SM, Ma H (2013) Flower development under drought stress: morphological and transcriptomic analyses reveal acute responses and long-term acclimation in Arabidopsis. Plant Cell 25:3785-3807
70. Taj G, Agarwal P, Grant M, & Kumar A (2010), MAPK machinery in plants: recognition and response to different stresses through multiple signal transduction pathways. Plant Signal Behav 5(11):1370-1378
71. Tanaka H, Osakabe Y, Katsura S, Mizuno S, Maruyama K, Kusakabe K, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2012) Abiotic stress-inducible receptor-like kinases negatively control ABA signaling in Arabidopsis. The Plant J 70:599-613
72. Utsumi Y, Tanaka M, Morosawa T, Kurotani A, Yoshida T, Mochida K, Matsui A, Umemura Y, Ishitani M, Shinozaki K, Sakurai T, Seki M (2012) Transcriptome analysis using a high-density oligomicroarray under drought stress in various genotypes of cassava: an important tropical crop. DNA Res 19:335-345
73. Venkateswarlu B, Shanker AK (2012) Dryland agriculture: bringing resilience to crop production under changing climate. In: Venkateswarlu B, Shanker AK, Shanker C, Maheswari M (eds) Crop stress and its management: perspectives and strategies. Springer, the Netherlands, pp 19-44
74. Wang WS, Pan YJ, Zhao XQ, Dwivedi D, Zhu LH, Ali J, Li ZK (2011) Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.). J Exp Bot 62(6):1951-1960
75. Warren CR, Aranda I, Cano FJ (2012) Metabolomics demonstrates divergent responses of two Eucalyptus species to water stress. Metabolomics 8:186-200
76. Xu C, Huang B (2010) Differential proteomic responses to water stress induced by PEG in two creeping bentgrass cultivars differing in stress tolerance. J Plant Physiol 167:1477-1485
77. Ye N, Jia L, Zhang J (2012) ABA signal in rice under stress conditions. Rice 5:1-9
78. Yu S, Zhang F, Yu Y, Zhang D, Zhao X, Wang W (2012) Transcriptome profiling of dehydration stress in the Chinese cabbage (Brassica rapa L. ssp. Pekinensis) by tag sequencing. Plant Mol Biol Reporter 30:17-28
79. Zhang S, Chen L, Duan B, Korpelainen H, Li C (2012) Populus cathayana males exhibit more efficient protective mechanisms than females under drought stress. Forest Ecology Management 275:68-78
80. Zong W, Zhong X, You J, Xiong L (2013) Genome-wide profiling of histone H3K4-tri-methylation and gene expression in rice under drought stress. Plant Mol Biol 81(1-2):175-188