Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64

Molecular Genetics and Genomics

Volumn 287, Issue 1, 2012, Pages 1-19

  Sharoni, Akhter Most ^a,b   Nuruzzaman, Mohammed ^a   Satoh, Kouji ^a   Moumeni, Ali ^a   Attia, Kotb ^c,d   Venuprasad, Ramiah ^e   Serraj, Rachid ^f   Kumar, Arvind ^g   Leung, Hei ^g   Islam, A K M Rafiul ^b   Kikuchi, Shoshi ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^b UNIVERSITY OF RAJSHAHI   (Bangladesh)

^c NIIGATA UNIVERSITY   (Japan)

^d KING SAUD UNIVERSITY   (Saudi Arabia)

^e AFRICA RICE CENTER AFRICARICE   (Côte d’Ivoire)

^f INTERNATIONAL CENTER FOR AGRICULTURAL RESEARCH IN THE DRY AREAS ICARDA   (Syrian Arab Republic)

^g INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

Author keywords

AP2 EREBP; Expression profile; Hormone; Microarray; NILs; Stress

Indexed keywords

PHYTOHORMONE; SOIL WATER; TRANSCRIPTION FACTOR AP 2; TRANSCRIPTOME; DNA BINDING PROTEIN; ETHYLENE RESPONSIVE ELEMENT BINDING PROTEIN; ETHYLENE-RESPONSIVE ELEMENT BINDING PROTEIN; VEGETABLE PROTEIN;

AP2 GENE; ARTICLE; CONTROLLED STUDY; DOWN REGULATION; DROUGHT STRESS; DROUGHT TOLERANCE; EVAPOTRANSPIRATION; FLOWERING; GENE ACTIVATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC SELECTION; GENOTYPE; GROWTH CURVE; MICROARRAY ANALYSIS; MOLECULAR CLONING; MULTIGENE FAMILY; NEAR ISOGENIC LINE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENE; PLANT GROWTH; PLANT LEAF; PLANT REPRODUCTION; PLANT ROOT; PRIORITY JOURNAL; RICE; VEGETATIVE GROWTH; COMPARATIVE STUDY; DROUGHT; DRUG EFFECT; FLOWER; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PHYSIOLOGICAL STRESS; PHYSIOLOGY; QUANTITATIVE TRAIT LOCUS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SPECIES DIFFERENCE;

DNA-BINDING PROTEINS; DROUGHTS; FLOWERS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENOTYPE; MICROARRAY ANALYSIS; MULTIGENE FAMILY; ORYZA SATIVA; PLANT GROWTH REGULATORS; PLANT LEAVES; PLANT PROTEINS; PLANT ROOTS; QUANTITATIVE TRAIT LOCI; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SPECIES SPECIFICITY; STRESS, PHYSIOLOGICAL;

EID: 84857006809     PISSN: 16174615     EISSN: 16174623     Source Type: Journal    
DOI: 10.1007/s00438-011-0659-3     Document Type: Article

References (68)

1. Agarwal PK, Agarwal P, Reddy MK, Sopory SK (2006) Roles of DREB transcription factors in biotic and abiotic stress tolerance in plants. Plant Cell Rep 25:1263-1274 (Pubitemid 44786606)
2. Agarwal P, Agarwal PK, Joshi AJ, Sopory SK, Reddy MK (2010) Overexpression of PgDREB2A transcription factor enhances abiotic stress tolerance and activates downstream stress-responsive genes. Mol Biol Rep 37:1125-1135
3. Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R et al (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301:653-657 (Pubitemid 36927950)
4. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R (2007) NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acids Res 35:D760-D765 (Pubitemid 46056306)
5. Becker JD, Boavida LC, Carneiro J, Haury M, Feijo JA (2003) Transcriptional profiling of Arabidopsis tissues reveals the unique characteristics of the pollen transcriptome. Plant Physiol 133:713-725 (Pubitemid 37325681)
6. Bernier J, Kumar A, Ramaiah V, Spaner D, Atlin G (2007) A large-effect QTL for grain yield under reproductive-stage drought stress in upland rice. Crop Sci 47:505-516
7. Bobb AJ, Eiben HG, Bustos MM (1995) PvAlf, an embryo-specific acidic transcriptional activator enhances gene expression from phaseolin and phytohemagglutinin promoters. Plant J 8:331-343
8. Chae MJ, Lee JS, Nam MH, Cho K, Hong JY, Yi SA, Suh SC, Yoon IS (2007) A rice dehydration-inducible SNF1 related protein kinase 2 phosphorylates an abscisic acid responsive element binding factor and associates with ABA signaling. Plant Mol Biol 63:151-169 (Pubitemid 46058721)
9. Cooper B, Clarke JD, Budworth P, Kreps J, Hutchison D, Park S, Guimil S, Dunn M, Luginbühl P, Ellero C, GoV SA, Glazebrook J (2003) A network of rice genes associated with stress response and seed development. Proc Natl Acad Sci USA 100:4945-4950 (Pubitemid 36457833)
10. Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible WR (2005) Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol 139:5-17 (Pubitemid 43951587)
11. Degenkolbe T, Do PT, Zuther E, Repsilber D, Walther D, Hincha DK, Köhl KI (2009) Expression profiling of rice cultivars differing in their tolerance to long-term drought stress. Plant Mol Biol 69:133-153
12. Doi K, Hosaka A, Nagata T, Satoh K, Suzuki K, Mauleon R, Mendoza MJ, Bruskiewich R, Kikuchi S (2008) Development of a novel data mining tool to Wnd cis-elements in rice gene promoter regions. BMC Plant Biol 8:20
13. Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38:W64-W70
14. Dubouzet JG, Sakuma Y, Ito Y, Kasuga M, Dubouzet EG, Miura S, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought, high-salt- and cold-responsive gene expression. Plant J 33:751-763 (Pubitemid 36325917)
15. Elliott RC, Betzner AS, Huttner E, Oakes MP, Tucker WQ, Gerentes D, Perez P, Smyth DR (1996) AINTEGUMENTA, an APET-ALA2- like gene of Arabidopsis with pleiotropic roles in ovule development and Xoral organ growth. Plant Cell 8:155-168
16. Fowler S, Thomashow F (2002) Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14:1675-1690 (Pubitemid 35002928)
17. Fujimoto SY, Ohta M, Usui A, Shinshi H, Ohme-Takagi M (2000) Arabidopsis ethylene-responsive element binding factors act as transcriptional activators and repressors of GCC box-mediated gene expression. Plant Cell 12:393-404 (Pubitemid 30186308)
18. Gao S, Zhang H, Tian Y, Li F, Zhang Z, Lu X et al (2008) Expression of TERF1 in rice regulates expression of stress-responsive genes and enhances tolerance to drought and high-salinity. Plant Cell Rep 27:1787-1795
19. Guan YS, Serraj R, Liu SH, Xu JL, Ali J, Wang WS, Venus E, Zhu LH, Li ZK (2010) Simultaneously improving yield under drought stress and non-stress conditions: a case study of rice (Oryza sativa L.). J Exp Bot 61(15):4145-4156. doi:10.1093/jxb/erq212
20. Gutterson N, Reuber TL (2004) Regulation of disease resistance pathways by AP2/ERF transcription factors. Curr Opin Plant Biol 7:465-471 (Pubitemid 38871622)
21. Hao DY, Ohme-Takagi M, Sarai A (1998) Unique mode of GCC box recognition by the DNA-binding domain of ethylene-responsive element-binding factor (ERF domain) in plant. J Biol Chem 273:26857-26861 (Pubitemid 28471704)
22. Hazen SP, Pathan MS, Sanchez A, Baxter I, Dunn M, Estes B, Chang HS, Zhu T, Kreps JA, Nguyen HT (2005) Expression profiling of rice segregating for drought tolerance QTLs using a rice genome array. Funct Integr Genomics 5:104-116 (Pubitemid 40425091)
23. Hu YX, Wang YX, Liu XF, Li JY (2004) Arabidopsis RAVI is down-regulated by brassinosteroid and may act as a negative regulator during plant development. Cell Res 14:8-15
24. Jofuku KD, den Boer BGW, Van Montagu M, Okamuro JK (1994) Control of Arabidopsis Xower and seed development by the homeotic gene APETALA2. Plant Cell 6:1211-1225
25. Kagaya Y, Ohmiya K, Hattori T (1999) RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Nucleic Acids Res 27:470-478 (Pubitemid 29210010)
26. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480-D484 (Pubitemid 351149770)
27. Khush GS, Angeles E, Virk PS, Brar DS (2004) Breeding rice for resistance to tungro virus at IRRI. SABRAO J Breed Genet 36:101-106 (Pubitemid 40077286)
28. Kitomi Y, Ito H, Hobo T, Aya K, Kitano H, Inukai Y (2011) The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type-A response regulator of cytokinin signaling. Plant J 67:472-484
29. Kizis D, Pages M (2002) Maize DRE-binding proteins DBF1 and DBF2 are involved in rab17 regulation through the drought-responsive element in an ABA-dependent pathway. Plant J 30:679-689 (Pubitemid 34696060)
30. Lafitte HR, Li ZK, Vijayakumar CHM, Gao YM, Shi Y, Xu JL, Fu BY, Yu SB, Ali AJ, Domingo J, Maghirang R, Torres R, Mackill D (2006) Improvement of rice drought tolerance through backcross breeding: evaluation of donors and selection in drought nurseries. Field Crops Res 97:77-86
31. Lan L, Li M, Lai Y, Xu W, Kong Z, Ying K, Han B, Xue Y (2005) Microarray analysis reveals similarities and variations in genetic programs controlling pollination/fertilization and stress responses in rice (Oryza sativa L.). Plant Mol Biol 59:151-164 (Pubitemid 41429426)
32. Lee JH, Hong JP, Oh SK, Lee S, Choi D, Kim WT (2004) The ethylene responsive factor like protein 1 (CaERFLP1) of hot pepper (Capsicum annuum L.) interacts in vitro with both GCC and DRE/CRT sequences with different binding affinities: possible biological roles of CaERFLP1 in response to pathogen infection and high salinity conditions in transgenic tobacco plants. Plant Mol Biol 55:61-81
33. McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR et al (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci USA 106:12273-12278
34. Moumeni A, Satoh K, Kondoh H, Asano T, Hosaka A, Venuprasa 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 (accepted)
35. Nuruzzaman M, Gupta M, Zhang C, Wang L, Xie W, Xiong L, Zhang Q, Lian X (2008) Sequence and expression analysis of the thioredoxin protein gene family in rice. Mol Genet Genomics 280:139-151
36. Nuruzzaman M, Manimekalai R, Sharoni AM, Satoh K, Kondoh H, Ooka H, Kikuchi S (2010) Genome-wide analysis of NAC transcription factor family in rice. Gene 465:30-44
37. Oh SJ, Kim SY, Kwon CW, Park HK, Jeong JS, Kim JK (2009) Overexpression of the transcription factor ap37 in rice improves grain yield under drought conditions. Plant Physiol 150:1368-1379
38. Ohme-Takagi M, Shinshi H (1995) Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 7:173-182
39. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35:D883-D887 (Pubitemid 46056327)
40. Parent B, Suard B, Serraj R, Tardieu F (2010) Rice leaf growth and water potential are resilient to evaporative demand and soil water deficit once the effects of root system are neutralized. Plant Cell Environ 33:1256-1267
41. Park JM, Park CJ, Lee SB, Ham BK, Shin R, Paek KH (2001) Overexpression of the tobacco Tsi1 gene encoding an EREBP/AP2-type transcription factor enhances resistance against pathogen attack and osmotic stress in tobacco. Plant Cell 13:1035-1046 (Pubitemid 32480640)
42. Qin QL, Liu JG, Zhang Z, Peng RH, Xiong AS (2007a) Isolation, optimization, and functional analysis of the cDNA encoding transcription factor RdreB1 in Oryza Sativa L. Mol Breed 19:329-340 (Pubitemid 46440194)
43. Qin F, Kakimoto M, Sakuma Y, Maruyama K, Osakabe Y, Tran LS, Shinozaki K, Yamaguchi-Shinozaki K (2007b) Regulation and functional analysis of ZmDREB2A in response to drought and heat stresses in Zea mays L. Plant J 50:54-69 (Pubitemid 46493397)
44. Quan R, Hu S, Zhang Z, Zhang H, Zhang Z, Huang R (2010) Overexpression of an ERF transcription factor TSRF1 improves rice drought tolerance. Plant Biotechnol J 8:1-13
45. Riechmann JL, Meyerowitz EM (1998) The AP2/EREBP family of plant transcription factors. Biol Chem 379:633-646 (Pubitemid 28327562)
46. Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A et al (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34:374-378 (Pubitemid 36184095)
47. Sakuma Y, Liu Q, Dubouzet JG, Abe H, Shinozaki K, Yamaguchi- Shinozaki K (2002) DNA-binding specificity of the AP2/ERF domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression. Biochem Biophys Res Commun 290:998-1009 (Pubitemid 34687462)
48. Sakuma Y, Maruyama K, Osakabe Y, Qin F, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2006) Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. Plant Cell 18:1292-1309 (Pubitemid 43956132)
49. Serraj R, Kumar A, McNally KL, Slamet-Loedin I, Bruskiewich R, Mauleon R, Cairns J, Hijimans RJ (2009) Improvement of drought resistance in rice. Adv Agron 103:41-99
50. Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, Sharan R, Shiloh Y, Elkon R (2005) EXPANDER-an integrative program suite for microarray data analysis. BMC Bioinformatics 6:232
51. Sharoni AM, Nuruzzaman M, Satoh K, Shimizu T, Kondoh H, Sasaya T, Choi IR, Omura T, Kikuchi S (2011) Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice. Plant Cell Physiol 52:344-360
52. Shen S, Sharma A, Komatsu S (2002) Characterization of proteins responsive of gibberellin in the leaf-sheath of rice (Oryza sativa L.) seedling using proteome analysis. Biol Pharm Bull 26:129-136 (Pubitemid 41699654)
53. Shen YG, Zhang WK, He SJ, Zhang JS, Liu Q, Chen SY (2003) An EREBP/AP2-type protein in Triticum aestivum was a DRE-binding transcription factor induced by cold, dehydration and ABA stress. Theor Appl Genet 106:923-930 (Pubitemid 36599656)
54. Shinozaki K, Yamaguchi-Shinozaki K, Seki M (2003) Regulatory network of gene expression in the drought and cold stress responses. Curr Opin Plant Biol 6:410-417 (Pubitemid 37195741)
55. Sinclair TR, Ludlow M (1986) Influence of soil water supply on the plant water balance of four tropical grain legumes. Aust J Plant Physiol 13:329-341
56. Sohn KH, Lee SC, Jung HW, Hong JK, Hwang BK (2006) Expression and functional roles of the pepper pathogen-induced transcription factor RAV1 in bacterial disease resistance, and drought and salt stress tolerance. Plant Mol Biol 61:897-915 (Pubitemid 44268254)
57. Spollen WG, Sharp RE, Saab IN, Wu Y (1993) Regulation of cell expansion in roots and shoots at low water potentials. In: Smith JAC, Griffiths H (eds) Water deficits: plant responses from cell to community. BIOS Scientific Publishers, Oxford, pp 37-52
58. Udupa SM, Robertson LD, Weigand F, Baum M, Kahl G (1999) Allelic variation at (TAA)n microsatellite loci in a world collection of chickpea (Cicer arietinum L.) germplasm. Mol Gen Genet 261:354-363 (Pubitemid 29140050)
59. Venuprasad R, Zenna N, Choi IR, Amante M, Virk PS, Kumar A (2007) Identification of marker loci associated with tungro and drought tolerance in near-isogenic rice lines derived from IR64/ Aday Sel. IRRN 32:27-29
60. Venuprasad R, Dalid CO, Del-Valle M, Ma-Emeru B, Zhao L, Espiritu M, Sta Cruz MT, Amante M, Atlin G, Kumar A (2009) Identification and characterization of large-effect quantitative trait loci (QTL) for grain yield under lowland drought stress and aerobic conditions in rice using bulk-segregant analysis (BSA). Theor Appl Genet 120:177-190
61. Venuprasad R, Impa S, Veeresh-Gowda RP, Atlin GN, Serraj R (2011) Rice near-isogenic-lines (NILs) contrasting for grain yield under lowland drought stress. Field Crops Res 123:38-46
62. Yaish MW, El-Kereamy A, Zhu T, Beatty PH, Good AG, Bi YM, Rothstein SJ (2010) The APETALA-2-like transcription factor OsAP2-39 controls key interactions between abscisic acid and gibberellin in rice. PLoS Genet 6:9
63. Yang HJ, Shen H, Chen L, Xing YY, Wang ZY, Zhang JL, Hong MM (2002) The OsEBP-89 gene of rice encodes a putative EREBP transcription factor and is temporally expressed in developing endosperm and intercalary meristem. Plant Mol Biol 50:379-391
64. Yazaki J, Kishimoto N, Nagata Y, Ishikawa M, Fujii F et al (2003) Genomics approach to abscisic acid- and gibberellin-responsive genes in rice. DNA Res 10:249-261 (Pubitemid 38249932)
65. Ye S, Wang L, Xie W, Wan B, Li X, Lin Y (2009) Expression profile of calcium-dependent protein kinase (CDPKs) genes during the whole lifespan and under phytohormone treatment conditions in rice (Oryza sativa L.). Plant Mol Biol 70:311-325
66. Zhou J, Wang X, Jiao Y, Qin Y, Liu X, He K, Chen C, Ma L, Wang J, Xiong L, Zhang Q, Fan L, Deng XW (2007) Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, Xag leaf, and panicle. Plant Mol Biol 63:591-608
67. Zhu Y, Cai XL, Wang ZY, Hong MM (2003) An interaction between a MYC protein and an EREBP protein is involved in transcriptional regulation of the rice Wx gene. J Biol Chem 278:47803-47811 (Pubitemid 37523227)
68. Zhu Q, Zhang J, Gao X, Tong J, Xiao L, Li W et al (2010) The Arabidopsis AP2/ERF transcription factor RAP2.6 participates in ABA, salt and osmotic stress responses. Gene 457:1-12