Genome-Wide Identification of Genes Responsive to ABA and Cold/Salt Stresses in Gossypium hirsutum by Data-Mining and Expression Pattern Analysis

Agricultural Sciences in China

Volumn 10, Issue 4, 2011, Pages 499-508

  Zhu, Long fu ^a   He, Xin ^a   Yuan, Dao jun ^a   Xu, Lian ^a   Xu, Li ^a   Tu, Li li ^a   Shen, Guo xin ^b   Zhang, Hong ^b   Zhang, Xian long ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b TEXAS TECH UNIVERSITY   (United States)

Author keywords

Cold stress; Data mining; Gene; Gossypium hirsutum; Salt stress

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA; GOSSYPIUM HIRSUTUM;

EID: 79955002321     PISSN: 16712927     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1671-2927(11)60030-8     Document Type: Article

References (47)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ Basic local alignment search tool. Journal of Molecular Biology 1990, 215:403-410.
2. Apse MP, Aharon GS, Snedden WA, Blumwald E Salt tolerance conferred by overexpression of a vacuolar Na+/H+ antiport in Arabidopsis. Science 1999, 285:1256-1258.
3. Boyer JS Plant productivity and environment. Science 1982, 218:443-448.
4. Bressan RA, Zhang C, Zhang H, Hasegawa PM, Bohnert HJ, Zhu JK Learning from the Arabidopsis experience. The next gene search paradigm. Plant Physiology 2001, 127:1354-1360.
5. Cheong YH, Kim KN, Pandey GK, Gupta R, Grant JJ, Luan S CBL1, a calcium sensor that differentially regulates salt, drought, and cold responses in Arabidopsis. The Plant Cell 2003, 15:1833-1845.
6. Czernic P, Visser B, Sun W, Savoure A, Deslandes L, Marco Y, van Montagu M, Verbruggen N Characterization of an Arabidopsis thaliana receptor-like protein kinase gene activated by oxidative stress and pathogen attack. The Plant Journal 1999, 18:321-327.
7. Dai X, Xu Y, Ma Q, Xu W, Wang T, Xue Y, Chong K Overexpression of an R1R2R3 MYB gene, OsMYB3R-2, increases tolerance to freezing, drought, and salt stress in transgenic Arabidopsis. Plant Physiology 2007, 143:1739-1751.
8. Gomez-Porras JL, Riano-Pachon DM, Dreyer I, Mayer JE, Mueller-Roeber B Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC Genomics 2007, 8:260.
9. Hu H, Dai M, Yao J, Xiao B, Li X, Zhang Q, Xiong L Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proceedings of the National Academy of Sciences of the USA 2006, 103:12987-12992.
10. Huang D, Wu W, Abrams SR, Cutler AJ The relationship of drought-related gene expression in Arabidopsis thaliana to hormonal and environmental factors. Journal of Experimental Botany 2008, 59:2991-3007.
11. Jain M, Tyagi AK, Khurana JP Overexpression of putative topoisomerase 6 genes from rice confers stress tolerance in transgenic Arabidopsis plants. FEBS Letters 2006, 273:5245-5260.
12. Jiang Y, Deyholos MK Functional characterization of Arabidopsis NaCl-inducible WRKY25 and WRKY33 transcription factors in abiotic stresses. Plant Molecular Biology 2009, 69:91-105.
13. Karaba A, Dixit S, Greco R, Aharoni A, Trijatmiko KR, Marsch-Martinez N, Krishnan A, Nataraja KN, Udayakumar M, Pereira A Improvement of water use efficiency in rice by expression of HARDY, an Arabidopsis drought and salt tolerance gene. Proceedings of the National Academy of Sciences of the USA 2007, 104:15270-15275.
14. Kreps JA, Wu Y, Chang HS, Zhu T, Wang X, Harper JF Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiology 2002, 130:2129-2141.
15. Laule O, Hirsch-Hoffmann M, Hruz T, Gruissem W, Zimmermann P Web-based analysis of the mouse transcriptome using Genevestigator. BMC Bioinformatics 2006, 7:311.
16. Leung J, Merlot S, Giraudat J The Arabidopsis ABSCISIC ACID-INSENSITIVE2 (ABI2) and ABI1 genes encode homologous protein phosphatases 2C involved in abscisic acid signal transduction. The Plant Cell 1997, 9:759-771.
17. Liu C, Wang T, Zhang W, Li X Computational identification and analysis of immune-associated nucleotide gene family in Arabidopsis thaliana. Journal of Plant Physiology 2008, 165:777-787.
18. Menges M, Hennig L, Gruissem W, Murray JA Genome-wide gene expression in an Arabidopsis cell suspension. Plant Molecular Biology 2003, 53:423-442.
19. Misson J, Raghothama KG, Jain A, Jouhet J, Block MA, Bligny R, Ortet P, Creff A, Somerville S, Rolland N, et al. A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation. Proceedings of the National Academy of Sciences of the USA 2005, 102:11934-11939.
20. Mizoguchi T, Irie K, Hirayama T, Hayashida N, Yamaguchi-Shinozaki K, Matsumoto K, Shinozaki K A gene encoding a mitogen-activated protein kinase kinase kinase is induced simultaneously with genes for a mitogen-activated protein kinase and an S6 ribosomal protein kinase by touch, cold, and water stress in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the USA 1996, 93:765-769.
21. Mullan DJ, Colmer TD, Francki MG Arabidopsis-rice-wheat gene orthologues for Na+ transport and transcript analysis in wheat-L. elongatum aneuploids under salt stress. Molecular Genetics and Genomics 2007, 277:199-212.
22. Nelson DE, Repetti PP, Adams TR, Creelman RA, Wu J, Warner DC, Anstrom DC, Bensen RJ, Castiglioni PP, Donnarummo MG, et al. Plant nuclear factor Y (NF-Y) B subunits confer drought tolerance and lead to improved corn yields on water-limited acres. Proceedings of the National Academy of Sciences of the USA 2007, 104:16450-16455.
23. Noutoshi Y, Kuromori T, Wada T, Hirayama T, Kamiya A, Imura Y, Yasuda M, Nakashita H, Shirasu K, Shinozaki K Loss of necrotic spotted lesions 1 associates with cell death and defense responses in Arabidopsis thaliana. Plant Molecular Biology 2006, 62:29-42.
24. Novillo F, Medina J, Salinas J Arabidopsis CBF1 and CBF3 have a different function than CBF2 in cold acclimation and define different gene classes in the CBF regulon. Proceedings of the National Academy of Sciences of the USA 2007, 104:21002-21007.
25. Oh SJ, Song SI, Kim YS, Jang HJ, Kim SY, Kim M, Kim YK, Nahm BH, Kim JK Arabidopsis CBF3/DREB1A and ABF3 in transgenic rice increased tolerance to abiotic stress without stunting growth. Plant Physiology 2005, 138:341-351.
26. Peng M, Bi YM, Zhu T, Rothstein SJ Genome-wide analysis of Arabidopsis responsive transcriptome to nitrogen limitation and its regulation by the ubiquitin ligase gene NLA. Plant Molecular Biology 2007, 65:775-797.
27. Perruc E, Charpenteau M, Ramirez BC, Jauneau A, Galaud JP, Ranjeva R, Ranty B A novel calmodulin-binding protein functions as a negative regulator of osmotic stress tolerance in Arabidopsis thaliana seedlings. The Plant Journal 2004, 38:410-420.
28. Provart NJ, Gil P, Chen W, Han B, Chang HS, Wang X, Zhu T Gene expression phenotypes of Arabidopsis associated with sensitivity to low temperatures. Plant Physiology 2003, 132:893-906.
29. Safrany J, Haasz V, Mate Z, Ciolfi A, Feher B, Oravecz A, Stec A, Dallmann G, Morelli G, Ulm R, Nagy F Identification of a novel cis-regulatory element for UV-B-induced transcription in Arabidopsis. The Plant Journal 2008, 54:402-414.
30. Sakuma Y, Maruyama K, Qin F, Osakabe Y, Shinozaki K, Yamaguchi-Shinozaki K Dual function of an Arabidopsis transcription factor DREB2A in water-stress-responsive and heat-stress-responsive gene expression. Proceedings of the National Academy of Sciences of the USA 2006, 103:18822-18827.
31. Salse J, Bolot S, Throude M, Jouffe V, Piegu B, Quraishi UM, Calcagno T, Cooke R, Delseny M, Feuillet C Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. The Plant Cell 2008, 20:11-24.
32. Shameer K, Ambika S, Varghese SM, Karaba N, Udayakumar M, Sowdhamini R STIFDB - Arabidopsis stress responsive transcription factor data base. International Journal of Plant Genomics 2009, 2009:1-8.
33. Shi H, Zhu JK Regulation of expression of the vacuolar Na+/H+ antiporter gene AtNHX1 by salt stress and abscisic acid. Plant Molecular Biology 2002, 50:543-550.
34. Sun J, Jiang H, Xu Y, Li H, Wu X, Xie Q, Li C The CCCH-type zinc finger proteins AtSZF1 and AtSZF2 regulate salt stress responses in Arabidopsis. Plant Cell Physiology 2007, 48:1148-1158.
35. Takahashi S, Katagiri T, Yamaguchi-Shinozaki, Shinozaki K An Arabidopsis gene encoding a Ca2+-binding protein is induced by abscisic acid during dehydration. Plant Cell Physiology 2000, 41:898-903.
36. Tripathi V, Parasuraman B, Laxmi A, Chattopadhyay D CIPK6, a CBL-interacting protein kinase is required for development and salt tolerance in plants. The Plant Journal 2009, 58:778-790.
37. Tu LL, Zhang XL, Liu DQ, Jin SX, Cao JL, Zhu LF, Deng FL, Tan JF, Zhang C Suitable internal control genes for qRT-PCR normalization in cotton fiber development and somatic embryogenesis. Chinese Science Bulletin 2007, 52:3110-3117.
38. Urao T, Noji M, Yamaguchi-Shinozaki K, Shinozaki K A transcriptional activation domain of ATMYB2, a drought-inducible Arabidopsis Myb-related protein. The Plant Journal 1996, 10:1145-1148.
39. Xue T, Wang D, Zhang S, Ehlting J, Ni F, Jakab S, Zheng C, Zhong Y Genome-wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis. BMC Genomics 2008, 9:550.
40. Yamaguchi-Shinozaki K, Shinozaki K The plant hormone abscisic acid mediates the drought-induced expression but not the seed-specific expression of rd22, a gene responsive to dehydration stress in Arabidopsis thaliana. Molecular and General Genetics 1993, 238:17-25.
41. Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, et al. Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1. The Plant Cell 2004, 16:3448-3459.
42. Yoo JH, Park CY, Kim JC, Heo WD, Cheong MS, Park HC, Kim MC, Moon BC, Choi MS, Kang YH, et al. Direct interaction of a divergent CaM isoform and the transcription factor, MYB2, enhances salt tolerance in Arabidopsis. Journal of Biological Chemistry 2005, 280:3697-3706.
43. Zhang MQ Computational prediction of eukaryotic protein-coding genes. Nature Reviews Genetics 2002, 3:698-709.
44. Zhao J, Barkla BJ, Marshall J, Pittman JK, Hirschi KD The Arabidopsis cax3 mutants display altered salt tolerance, pH sensitivity and reduced plasma membrane H+-ATPase activity. Planta 2008, 227:659-669.
45. Zhu LF, Tu LL, Zeng FC, Liu DQ, Zhang XL An improved simple protocol for isolation of high quality RNA from Gossypium spp. suitable for cDNA library construction. Acta Agronomica Sinica 2005, 31:1657-1659. (in Chinese).
46. Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiology 2004, 136:2621-2632.
47. Zimmermann P, Laule O, Schmitz J, Hruz T, Bleuler S, Gruissem W Genevestigator transcriptome meta-analysis and biomarker search using rice and barley gene expression databases. Molecular Plant 2008, 1:851-857.