بازسازی شبکه‌های ژنی و برهم کنش پروتئینی دخیل در پاسخ به تنش خشکی در برنج

REFERENCES

Ahmed HU, Henry A, Mauleon R, Dixit S, Vikram P, Tilatto R, Verulkar SB, Perraju P, Mandal NPVariar M (2013) Genetic, physiological, and gene expression analyses reveal that multiple QTL enhance yield of rice mega-variety IR64 under drought. PLoS One(5): e62795.

Cao M, Liu X, Zhang Y, Xue X, Zhou XE, Melcher K, Gao P, Wang F, Zeng LZhao Y (2013) An ABA-mimicking ligand that reduces water loss and promotes drought resistance in plants. Cell Research. 23 (8): 1043-1054.

Carrera EPrat S (1998) Expression of the Arabidopsisabi1–1mutant allele inhibits proteinase inhibitor wound‐induction in tomato. The Plant Journal. 15 (6): 765-771.

Chin C-H, Chen S-H, Wu H-H, Ho C-W, Ko M-TLin C-Y (2014) cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Systems Biology. 8 (4): 1.

Correia M, Pereira J, Chaves M, Rodrigues MPacheco C (1995) ABA xylem concentrations determine maximum daily leaf conductance of field‐grown Vitis vinifera L. plants. Plant, Cell & Environment. 18 (5): 511-521.

Cutler SR, Rodriguez PL, Finkelstein RRAbrams SR (2010) Abscisic acid: emergence of a core signaling network. Annual Reviews Plant Biology. 61: 651-679.

Danquah A, de Zelicourt A, Colcombet JHirt H (2014) The role of ABA and MAPK signaling pathways in plant abiotic stress responses. Biotechnology advances. 32 (1): 40-52.

Daszkowska-Golec ASzarejko I (2013) Open or close the gate–stomata action under the control of phytohormones in drought stress conditions. Frontiers in plant science. 4 138.

Degenkolbe T, Do PT, Zuther E, Repsilber D, Walther D, Hincha DKKöhl KI (2009) Expression profiling of rice cultivars differing in their tolerance to long-term drought stress. Plant molecular biology. 69 (1-2): 133-153.

Dóczi R, Brader G, Pettkó-Szandtner A, Rajh I, Djamei A, Pitzschke A, Teige MHirt H (2007) The Arabidopsis mitogen-activated protein kinase kinase MKK3 is upstream of group C mitogen-activated protein kinases and participates in pathogen signaling. The Plant Cell Online. 19 (10): 3266-3279.

Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano MYoshimura A (2004) Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes & Development. 18 (8): 926-936.

Fell DAWagner A (2000) The small world of metabolism. Nature Biotechnology. 18 (11): 1121-1122.

Fitzgerald HA, Chern M-S, Navarre RRonald PC (2004) Overexpression of (At) NPR1 in rice leads to a BTH-and environment-induced lesion-mimic/cell death phenotype. Molecular Plant-Microbe Interactions. 17 (2): 140-151.

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

Fujii HZhu J-K (2009) Arabidopsis mutant deficient in 3 abscisic acid-activated protein kinases reveals critical roles in growth, reproduction, and stress. Proceedings of the National Academy of Sciences. 106 (20): 8380-8385.

Fujita Y, Fujita M, Satoh R, Maruyama K, Parvez MM, Seki M, Hiratsu K, Ohme-Takagi M, Shinozaki KYamaguchi-Shinozaki K (2005) AREB1 is a transcription activator of novel ABRE-dependent ABA signaling that enhances drought stress tolerance in Arabidopsis. The Plant Cell. 17 (12): 3470-3488.

Fukushima A, Kusano M, Nakamichi N, Kobayashi M, Hayashi N, Sakakibara H, Mizuno TSaito K (2009) Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination. Proceedings of the National Academy of Sciences. 106(17): 7251-7256.

Gao H, Jin M, Zheng X-M, Chen J, Yuan D, Xin Y, Wang M, Huang D, Zhang ZZhou K (2014) Days to heading 7, a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice. Proceedings of the National Academy of Sciences. 111 (46): 16337-16342.

Gendron JM, Pruneda-Paz JL, Doherty CJ, Gross AM, Kang SEKay SA (2012) Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor. Proceedings of the National Academy of Sciences. 109(8): 3167-3172.

Gonzalez-Guzman M, Rodriguez L, Lorenzo-Orts L, Pons C, Sarrion-Perdigones A, Fernandez MA, Peirats-Llobet M, Forment J, Moreno-Alvero MCutler SR (2014) Tomato PYR/PYL/RCAR abscisic acid receptors show high expression in root, differential sensitivity to the abscisic acid agonist quinabactin, and the capability to enhance plant drought resistance. Journal of experimental botany. 65 (15): 4451-4464.

Hayama R, Yokoi S, Tamaki S, Yano MShimamoto K (2003) Adaptation of photoperiodic control pathways produces short-day flowering in rice. Nature. 422 (6933): 719-722.

Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem WZimmermann P (2008) Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Advances in bioinformatics. 2008

Hu HXiong L (2014) Genetic engineering and breeding of drought-resistant crops. Annual review of plant biology. 65 715-741.

Huang W, Pérez-García P, Pokhilko A, Millar A, Antoshechkin I, Riechmann JLMas P (2012) Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator. Science. 336 (6077): 75-79.

Ishikawa R, Aoki M, Kurotani K-i, Yokoi S, Shinomura T, Takano MShimamoto K (2011) Phytochrome B regulates Heading date 1 (Hd1)-mediated expression of rice florigen Hd3a and critical day length in rice. Molecular Genetics and Genomics. 285(6): 461-470.

Jin X-F, Xiong A-S, Peng R-H, Liu J-G, Gao F, Chen J-MYao Q-H (2010) OsAREB1, an ABRE-binding protein responding to ABA and glucose, has multiple functions in Arabidopsis. BMB reports. 43 34-39.

Kepes F, Guelzim N, Bottani SBourgine P (2002) Topological and causal structure of the yeast transcriptional regulatory network. Nature Genetics. 31 (1): 60-63.

Kim H, Lee K, Hwang H, Bhatnagar N, Kim D-Y, Yoon IS, Byun M-O, Kim ST, Jung K-HKim B-G (2014) Overexpression of PYL5 in rice enhances drought tolerance, inhibits growth, and modulates gene expression. Journal of experimental botany. 65 (2): 453-464.

Komiya R, Ikegami A, Tamaki S, Yokoi SShimamoto K (2008) Hd3a and RFT1 are essential for flowering in rice. Development. 135 (4): 767-774.

Komiya R, Yokoi SShimamoto K (2009) A gene network for long-day flowering activates RFT1 encoding a mobile flowering signal in rice. Development. 136 (20): 3443-3450.

Kwon C-T, Koo B-H, Kim D, Yoo S-CPaek N-C (2015) Casein kinases I and 2α phosphorylate Oryza sativa pseudo-response regulator 37 (OsPRR37) in photoperiodic flowering in rice. Mol Cells. 38 (1): 81-88.

Laby RJ, Kincaid MS, Kim DGibson SI (2000) The Arabidopsis sugar‐insensitive mutants sis4 and sis5 are defective in abscisic acid synthesis and response. The Plant Journal. 23 (5): 587-596.

Lara‐nuñez A, Romero‐romero T, Ventura JL, Blancas V, Anaya Alcruz‐ortega R (2006) Allelochemical stress causes inhibition of growth and oxidative damage in Lycopersicon esculentum Mill. Plant, Cell & Environment. 29 (11): 2009-2016.

Lee HG, Mas PSeo PJ (2016) MYB96 shapes the circadian gating of ABA signaling in Arabidopsis. Scientific reports. 6

Legnaioli T, Cuevas JMas P (2009) TOC1 functions as a molecular switch connecting the circadian clock with plant responses to drought. The EMBO Journal. 28 (23): 3745-3757.

Liu T, Carlsson J, Takeuchi T, Newton LFarre EM (2013) Direct regulation of abiotic responses by the Arabidopsis circadian clock component PRR7. The Plant Journal. 76 (1): 101-114.

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

Maclean JL, Dawe DCHettel GP (2002). Rice almanac: Source book for the most important economic activity on earth, CABI Publishing.

Makumburage GB, Richbourg HL, LaTorre KD, Capps A, Chen CStapleton AE (2013) Genotype to phenotype maps: multiple input abiotic signals combine to produce growth effects via attenuating signaling interactions in maize. G3: Genes| Genomes| Genetics. 3 (12): 2195-2204.

Manning G, Whyte DB, Martinez R, Hunter Tsudarsanam S (2002) The protein kinase complement of the human genome. Science. 298 (5600): 1912-1934.

Mickelbart MV, Hasegawa PMBailey-Serres J (2015) Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability. Nature Reviews Genetics. 16 (4): 237-251.

Miyakawa T, Fujita Y, Yamaguchi-Shinozaki KTanokura M (2013) Structure and function of abscisic acid receptors. Trends in plant science. 18 (5): 259-266.

Nikitin A, Egorov S, Daraselia NMazo I (2003) Pathway studio the analysis and navigation of molecular networks. Bioinformatics. 19: 2155-2157.

Obayashi TKinoshita K (2009) Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression. DNA Research. 16 (5): 249-260.

Okamoto M, Peterson FC, Defries A, Park S-Y, Endo A, Nambara E, Volkman BFCutler SR (2013) Activation of dimeric ABA receptors elicits guard cell closure, ABA-regulated gene expression, and drought tolerance. Proceedings of the National Academy of Sciences. 110 (29): 12132-12137.

Osuna D, Usadel B, Morcuende R, Gibon Y, Bläsing OE, Höhne M, Günter M, Kamlage B, Trethewey RScheible WR (2007) Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon‐deprived Arabidopsis seedlings. The Plant Journal. 49 (3): 463-491.

Ouzounis CAKarp PD (2000) Global properties of the metabolic map of Escherichia coli. Genome Research. 10 (4): 568-576.

Pandey GK, Cheong YH, Kim K-N, Grant JJ, Li L, Hung W, D'Angelo C, Weinl S, Kudla JLuan S (2004) The calcium sensor calcineurin B-like 9 modulates abscisic acid sensitivity and biosynthesis in Arabidopsis. The Plant Cell Online. 16 (7): 1912-1924.

Park JM, Park C-J, Lee S-B, Ham B-K, Shin RPaek K-H (2001) Overexpression of the tobacco Tsi1 gene encoding an EREBP/AP2–type transcription factor enhances resistance against pathogen attack and osmotic stress in tobacco. The Plant Cell Online. 13 (5): 1035-1046.

Park S-Y, Fung P, Nishimura N, Jensen DR, Fujii H, Zhao Y, Lumba S, Santiago J, Rodrigues ATsz-fung FC (2009) Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. science. 324 (5930): 1068-1071.

Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki KYamaguchi-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 physiology. 133 (4): 1755-1767.

Rabello A, Guimarães C, Rangel P, da Silva F, Seixas D, de Souza E, Brasileiro A, Spehar C, Ferreira MMehta  (2008) Identification of drought-responsive genes in roots of upland rice (Oryza sativa L). BMC genomics. 9 (1): 485.

Ravi K, Vadez V, Isobe S, Mir R, Guo Y, Nigam S, Gowda M, Radhakrishnan T, Bertioli DKnapp S (2011) Identification of several small main-effect QTLs and a large number of epistatic QTLs for drought tolerance related traits in groundnut (Arachis hypogaea L.). Theoretical and Applied Genetics. 122 (6): 1119-1132.

Robertson FC, Skeffington AW, Gardner MJWebb AA (2009) Interactions between circadian and hormonal signalling in plants. Plant Molecular Biology. 69 (4): 419-427.

Rohila JSYang Y (2007) Rice Mitogen‐activated Protein Kinase Gene Family and Its Role in Biotic and Abiotic Stress Response. Journal of Integrative Plant Biology. 49 (6): 751-759.

Sandhu N, Singh A, Dixit S, Cruz MTS, Maturan PC, Jain RKKumar A (2014) Identification and mapping of stable QTL with main and epistasis effect on rice grain yield under upland drought stress. BMC Genetics. 15 (1): 1.

Schaffer R, Ramsay N, Samach A, Corden S, Putterill J, Carré IACoupland G (1998) The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell. 93 (7): 1219-1229.

Schallau A, Kakhovskaya I, Tewes A, Czihal A, Tiedemann J, Mohr M, Grosse I, Manteuffel RBäumlein H (2008) Phylogenetic footprints in fern spore‐and seed‐specific gene promoters. The Plant Journal. 53 (3): 414-424.

Semagn K, Beyene Y, Warburton ML, Tarekegne A, Mugo S, Meisel B, Sehabiague PPrasanna BM (2013) Meta-analyses of QTL for grain yield and anthesis silking interval in 18 maize populations evaluated under water-stressed and well-watered environments. BMC genomics. 14 (1): 1.

Shinozaki KYamaguchi-Shinozaki K (2007) Gene networks involved in drought stress response and tolerance. Journal of experimental botany. 58 (2): 221-227.

Smoot ME, Ono K, Ruscheinski J, Wang P-LIdeker T (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 27 (3): 431-432.

Strayer C, Oyama T, Schultz TF, Raman R, Somers DE, Más P, Panda S, Kreps JAKay SA (2000) Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog. Science. 289 (5480): 768-771.

Sugano S, Jiang C-J, Miyazawa S-I, Masumoto C, Yazawa K, Hayashi N, Shimono M, Nakayama A, Miyao MTakatsuji H (2010) Role of OsNPR1 in rice defense program as revealed by genome-wide expression analysis. Plant Molecular Biology. 74 (6): 549-562.

Sun C, Chen D, Fang J, Wang P, Deng XChu C (2014) Understanding the genetic and epigenetic architecture in complex network of rice flowering pathways. Protein & Cell. 5 (12): 889-898.

Takahashi F, Ichimura K, Shinozaki KShirasu K (2009). Plant mitogen-activated protein kinase cascades in signaling crosstalk. Signal cross talk in plant stress responses. K. Yoshioka and K. Shinozaki. England, Wiley-Blackwell, Oxford. 136: 23-42.

Tamaki S, Matsuo S, Wong HL, Yokoi SShimamoto K (2007) Hd3a protein is a mobile flowering signal in rice. Science. 316 (5827): 1033-1036.

Tardieu F (2011) Any trait or trait-related allele can confer drought tolerance: just design the right drought scenario. Journal of Experimental Botany. 269.

Thieffry D, Huerta AM, Perez-Rueda ECollado-Vides J (1998) From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. Bioessays. 20 (5): 433-440.

Tran L-SPMochida K (2010) Functional genomics of soybean for improvement of productivity in adverse conditions. Functional & integrative genomics. 10 (4): 447-462.

Tsuji H, Taoka K-iShimamoto K (2013) Florigen in rice: complex gene network for florigen transcription, florigen activation complex, and multiple functions. Current Opinion In Plant Biology. 16 (2): 228-235.

Wang Z-YTobin EM (1998) Constitutive expression of the Circadian Clock Associated 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell. 93(7): 1207-1217.

Weber VS, Melchinger AE, Magorokosho C, Makumbi D, Bänziger MAtlin GN (2012) Efficiency of managed-stress screening of elite maize hybrids under drought and low nitrogen for yield under rainfed conditions in Southern Africa. Crop Science. 52 (3): 1011-1020.

Wu W, Zheng X-M, Lu G, Zhong Z, Gao H, Chen L, Wu C, Wang H-J, Wang QZhou K (2013) Association of functional nucleotide polymorphisms at DTH2 with the northward expansion of rice cultivation in Asia. Proceedings of the National Academy of Sciences. 110 (8): 2775-2780.

Xu J, Yuan Y, Xu Y, Zhang G, Guo X, Wu F, Wang Q, Rong T, Pan GCao M (2014) Identification of candidate genes for drought tolerance by whole-genome resequencing in maize. BMC Plant Biology. 14 (1): 1.

Yan W, Liu H, Zhou X, Li Q, Zhang J, Lu L, Liu T, Liu H, Zhang CZhang Z (2014) Natural variation in Ghd7. 1 plays an important role in grain yield and adaptation in rice. Cell Research. 23 (7): 2969-2971.

Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, Pinter RY, Alon UMargalit H (2004) Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc. Natl. Acad Sci. USA. 101(16): 5934-5939.

Yoshida R, Umezawa T, Mizoguchi T, Takahashi S, Takahashi FShinozaki K (2006) The regulatory domain of SRK2E/OST1/SnRK2. 6 interacts with ABI1 and integrates abscisic acid (ABA) and osmotic stress signals controlling stomatal closure in Arabidopsis. Journal of Biological Chemistry. 281 (8): 5310-5318.

Zhang C, Liu J, Zhao T, Gomez A, Li C, Yu C, Li H, Lin J, Yang Y, Liu BLin C (2016) A Drought-Inducible transcription factor delays reproductive timing in rice. Plant Physiol. 171 (1): 334-343.

Zhang Q (2007) Strategies for developing green super rice. Proceedings of the national Academy of Sciences. 104 (42): 16402-16409.

Zheng J, Fu J, Gou M, Huai J, Liu Y, Jian M, Huang Q, Guo X, Dong ZWang H (2010) Genome-wide transcriptome analysis of two maize inbred lines under drought stress. Plant Molecular Biology. 72 (4-5): 407-421.