Analysis of gene expression in response to water deficit of chickpea (Cicer arietinum L.) varieties differing in drought tolerance

BMC Plant Biology

Volumn 10, Issue , 2010, Pages

  Jain, Deepti ^a   Chattopadhyay, Debasis ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CICER ARIETINUM;

PLANT DNA; WATER;

ARTICLE; CHICKPEA; CLUSTER ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; COMPARATIVE STUDY; DNA MICROARRAY; DNA SEQUENCE; DROUGHT; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; METABOLISM; SEEDLING;

CICER; CLUSTER ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; DNA, PLANT; DROUGHTS; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEEDLING; SEQUENCE ANALYSIS, DNA; WATER;

EID: 77950934817     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-10-24     Document Type: Article

References (59)

1. Graham PH, Vance CP. Legumes: importance and constraints to greater use. Plant Physiol 2003, 131(3):872-877. 10.1104/pp.017004, 1540286, 12644639.
2. Udupa SM, Robertson LD, Weigand F, Baum M, Kahl G. Allelic variation at (TAA)n microsatellite loci in a world collection of chickpea (Cicer arietinum L.) germplasm. Mol Gen Genet 1999, 261(2):354-363. 10.1007/s004380050976, 10102371.
3. Ingram J, Bartels D. The Molecular Basis of Dehydration Tolerance in Plants. Annu Rev Plant Physiol Plant Mol Biol 1996, 47:377-403. 10.1146/annurev.arplant.47.1.377, 15012294.
4. Cushman JC, Bohnert HJ. Genomic approaches to plant stress tolerance. Curr Opin Plant Biol 2000, 3(2):117-124. 10.1016/S1369-5266(99)00052-7, 10712956.
5. Seki M, Narusaka M, Abe H, Kasuga M, Yamaguchi-Shinozaki K, Carninci P, Hayashizaki Y, Shinozaki K. Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 2001, 13(1):61-72. 10.1105/tpc.13.1.61, 102214, 11158529.
6. Thomashow MF. PLANT COLD ACCLIMATION: Freezing Tolerance Genes and Regulatory Mechanisms. Annu Rev Plant Physiol Plant Mol Biol 1999, 50:571-599. 10.1146/annurev.arplant.50.1.571, 15012220.
7. Cheong YH, Chang HS, Gupta R, Wang X, Zhu T, Luan S. Transcriptional profiling reveals novel interactions between wounding, pathogen, abiotic stress, and hormonal responses in Arabidopsis. Plant Physiol 2002, 129(2):661-677. 10.1104/pp.002857, 161692, 12068110.
8. Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, Kawai K, Galbraith D, Bohnert HJ. Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 2001, 13(4):889-905. 10.1105/tpc.13.4.889, 135538, 11283343.
9. Ueda A, Shi W, Nakamura T, Takabe T. Analysis of salt-inducible genes in barley roots by differential display. J Plant Res 2002, 115(1118):119-130. 10.1007/s102650200017, 12884135.
10. Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K, Yamaguchi-Shinozaki K. 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 Physiol 2003, 133(4):1755-1767. 10.1104/pp.103.025742, 300730, 14645724.
11. Shiozaki N, Yamada M, Yoshiba Y. Analysis of salt-stress-inducible ESTs isolated by PCR-subtraction in salt-tolerant rice. Theor Appl Genet 2005, 110(7):1177-1186. 10.1007/s00122-005-1931-x, 15791452.
12. Sahi C, Agarwal M, Reddy MK, Sopory SK, Grover A. Isolation and expression analysis of salt stress-associated ESTs from contrasting rice cultivars using a PCR-based subtraction method. Theor Appl Genet 2003, 106(4):620-628.
13. Chao DY, Luo YH, Shi M, Luo D, Lin HX. Salt-responsive genes in rice revealed by cDNA microarray analysis. Cell Res 2005, 15(10):796-810. 10.1038/sj.cr.7290349, 16246269.
14. Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng L, Wanamaker SI, Mandal J, Xu J, Cui X, et al. Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage. Plant Physiol 2005, 139(2):822-835. 10.1104/pp.105.065961, 1255998, 16183841.
15. Walia H, Wilson C, Zeng L, Ismail AM, Condamine P, Close TJ. Genome-wide transcriptional analysis of salinity stressed japonica and indica rice genotypes during panicle initiation stage. Plant Mol Biol 2007, 63(5):609-623. 10.1007/s11103-006-9112-0, 1805040, 17160619.
16. Zhou J, Wang X, Jiao Y, Qin Y, Liu X, He K, Chen C, Ma L, Wang J, Xiong L, et al. Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle. Plant Mol Biol 2007, 63(5):591-608. 10.1007/s11103-006-9111-1, 1805039, 17225073.
17. Kumari S, Panjabi Nee Sabharwal V, Kushwaha HR, Sopory SK, Singla-Pareek SL, Pareek A. Transcriptome map for seedling stage specific salinity stress response indicates a specific set of genes as candidate for saline tolerance in Oryza sativa L. Funct Integr Genomics 2009, 9(1):109-123. 10.1007/s10142-008-0088-5, 18594887.
18. Yamane K, Kawasaki M, Taniguchi M, Miyake H. Differential effect of NaCl and polyethylene glycol on the ultrastructure of chloroplasts in rice seedlings. J Plant Physiol 2003, 160(5):573-575. 10.1078/0176-1617-00948, 12806788.
19. Yu LX, Setter TL. Comparative transcriptional profiling of placenta and endosperm in developing maize kernels in response to water deficit. Plant Physiol 2003, 131(2):568-582. 10.1104/pp.014365, 166833, 12586881.
20. Boominathan P, Shukla R, Kumar A, Manna D, Negi D, Verma PK, Chattopadhyay D. Long term transcript accumulation during the development of dehydration adaptation in Cicer arietinum. Plant Physiol 2004, 135(3):1608-1620. 10.1104/pp.104.043141, 519075, 15247380.
21. Ma Q, Behboudian MH, Turner NC, Palta JA. Gas exchange by pods and subtending leaves and internal recycling of CO(2) by pods of chickpea (Cicer arietinum L.) subjected to water deficits. J Exp Bot 2001, 52(354):123-131. 10.1093/jexbot/52.354.123, 11181721.
22. Ahmad F, Gaur P, Crosser J. Chickpea (Cicer arietinum L.). Genetic Resources, Chromosome Engineering and Crop Improvement - Grain Legumes 2005, 1:185-214.
23. Mantri NL, Ford R, Coram TE, Pang EC. Transcriptional profiling of chickpea genes differentially regulated in response to high-salinity, cold and drought. BMC Genomics 2007, 8:303. 10.1186/1471-2164-8-303, 2025592, 17764573.
24. Jayashree B. A legume genomics resource: The Chickpea Root Expressed Sequence Tag Database. Electronic Journal of Biotechnology 2005, 8.
25. Pandey A, Chakraborty S, Datta A, Chakraborty N. Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.). Mol Cell Proteomics 2008, 7(1):88-107.
26. Bhushan D, Pandey A, Choudhary MK, Datta A, Chakraborty S, Chakraborty N. Comparative proteomics analysis of differentially expressed proteins in chickpea extracellular matrix during dehydration stress. Mol Cell Proteomics 2007, 6(11):1868-1884. 10.1074/mcp.M700015-MCP200, 17686759.
27. Molina C, Rotter B, Horres R, Udupa SM, Besser B, Bellarmino L, Baum M, Matsumura H, Terauchi R, Kahl G, et al. SuperSAGE: the drought stress-responsive transcriptome of chickpea roots. BMC Genomics 2008, 9:553. 10.1186/1471-2164-9-553, 2628679, 19025623.
28. Delauney AJ, Hu CA, Kishor PB, Verma DP. Cloning of ornithine delta-aminotransferase cDNA from Vigna aconitifolia by trans-complementation in Escherichia coli and regulation of proline biosynthesis. J Biol Chem 1993, 268(25):18673-18678.
29. Yoshiba Y, Kiyosue T, Nakashima K, Yamaguchi-Shinozaki K, Shinozaki K. Regulation of levels of proline as an osmolyte in plants under water stress. Plant Cell Physiol 1997, 38(10):1095-1102.
30. Skriver K, Mundy J. Gene expression in response to abscisic acid and osmotic stress. Plant Cell 1990, 2(6):503-512. 10.1105/tpc.2.6.503, 159906, 2152172.
31. Shinozaki K, Yamaguchi-Shinozaki K. Molecular responses to drought and cold stress. Curr Opin Biotechnol 1996, 7(2):161-167. 10.1016/S0958-1669(96)80007-3, 8791336.
32. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95(25):14863-14868. 10.1073/pnas.95.25.14863, 24541, 9843981.
33. Mehta PA, Sivaprakash K, Parani M, Venkataraman G, Parida AK. Generation and analysis of expressed sequence tags from the salt-tolerant mangrove species Avicennia marina (Forsk) Vierh. Theor Appl Genet 2005, 110(3):416-424. 10.1007/s00122-004-1801-y, 15609053.
34. Qiu QS, Guo Y, Quintero FJ, Pardo JM, Schumaker KS, Zhu JK. Regulation of vacuolar Na+/H+ exchange in Arabidopsis thaliana by the salt-overly-sensitive (SOS) pathway. J Biol Chem 2004, 279(1):207-215. 10.1074/jbc.M307982200, 14570921.
35. Gong Z, Koiwa H, Cushman MA, Ray A, Bufford D, Kore-eda S, Matsumoto TK, Zhu J, Cushman JC, Bressan RA, et al. Genes that are uniquely stress regulated in salt overly sensitive (sos) mutants. Plant Physiol 2001, 126(1):363-375. 10.1104/pp.126.1.363, 102310, 11351099.
36. Batelli G, Verslues PE, Agius F, Qiu Q, Fujii H, Pan S, Schumaker KS, Grillo S, Zhu JK. SOS2 promotes salt tolerance in part by interacting with the vacuolar H+-ATPase and upregulating its transport activity. Mol Cell Biol 2007, 27(22):7781-7790. 10.1128/MCB.00430-07, 2169139, 17875927.
37. Gosti F, Beaudoin N, Serizet C, Webb AA, Vartanian N, Giraudat J. ABI1 protein phosphatase 2C is a negative regulator of abscisic acid signaling. Plant Cell 1999, 11(10):1897-1910. 10.1105/tpc.11.10.1897, 144098, 10521520.
38. Yamaguchi-Shinozaki K, Shinozaki K. A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell 1994, 6(2):251-264. 10.1105/tpc.6.2.251, 160431, 8148648.
39. Liu Q, Kasuga M, Sakuma Y, Abe H, Miura S, Yamaguchi-Shinozaki K, Shinozaki K. Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell 1998, 10(8):1391-1406. 10.1105/tpc.10.8.1391, 144379, 9707537.
40. Kikuchi K, Ueguchi-Tanaka M, Yoshida KT, Nagato Y, Matsusoka M, Hirano HY. Molecular analysis of the NAC gene family in rice. Mol Gen Genet 2000, 262(6):1047-1051. 10.1007/PL00008647, 10660065.
41. Xie Q, Frugis G, Colgan D, Chua NH. Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development. Genes Dev 2000, 14(23):3024-3036. 10.1101/gad.852200, 317103, 11114891.
42. Tran LS, Nakashima K, Sakuma Y, Simpson SD, Fujita Y, Maruyama K, Fujita M, Seki M, Shinozaki K, Yamaguchi-Shinozaki K. Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter. Plant Cell 2004, 16(9):2481-2498. 10.1105/tpc.104.022699, 520947, 15319476.
43. Davletova S, Schlauch K, Coutu J, Mittler R. The Zinc-Finger Protein Zat12 Plays a Central Role in Reactive Oxygen and Abiotic Stress Signaling in Arabidopsis. Plant Physiol 2005, 139(2):847-856. 10.1104/pp.105.068254, 1256000, 16183833.
44. Mukhopadhyay A, Vij S, Tyagi AK. Overexpression of a zinc-finger protein gene from rice confers tolerance to cold, dehydration, and salt stress in transgenic tobacco. Proc Natl Acad Sci USA 2004, 101(16):6309-6314. 10.1073/pnas.0401572101, 395965, 15079051.
45. Cellier F, Conejero G, Breitler J-C, Casse F. Molecular and Physiological Responses to Water Deficit in Drought-Tolerant and Drought-Sensitive Lines of Sunflower. Accumulation of Dehydrin Transcripts Correlates with Tolerance. Plant Physiol 1998, 116(1):319-328. 10.1104/pp.116.1.319, 35172, 9499218.
46. Yan L, Guizhu C. Physiological adaptability of three mangrove species to salt stress. Acta Ecologica Sinica 2007, 27(6):2208-2214.
47. Srivastava S, Fristensky B, Kav NN. Constitutive expression of a PR10 protein enhances the germination of Brassica napus under saline conditions. Plant Cell Physiol 2004, 45(9):1320-1324. 10.1093/pcp/pch137, 15509856.
48. Chakraborty N, Ohta M, Zhu JK. Recognition of a PP2C interaction motif in several plant protein kinases. Methods Mol Biol 2007, 365:287-298.
49. Kim JS, Jung HJ, Lee HJ, Kim KA, Goh CH, Woo Y, Oh SH, Han YS, Kang H. Glycine-rich RNA-binding protein 7 affects abiotic stress responses by regulating stomata opening and closing in Arabidopsis thaliana. Plant J 2008, 55(3):455-466. 10.1111/j.1365-313X.2008.03518.x, 18410480.
50. Tripathi V, Parasuraman B, Laxmi A, Chattopadhyay D. CIPK6, a CBL-interacting protein kinase is required for development and salt tolerance in plant. Plant J 2009, 58(5):778-90. 10.1111/j.1365-313X.2009.03812.x, 19187042.
51. Jain D, Roy N, Chattopadhyay D. CaZF, a plant transcription factor functions through and parallel to HOG and calcineurin pathways in Saccharomyces cerevisiae to provide osmotolerance. PLoS ONE 2009, 4(4):e5154. 10.1371/journal.pone.0005154, 2664467, 19365545.
52. Kathiresana A, Lafittea HR, Chena J, Mansuetoa L, Bruskiewich R, Bennett J. Gene expression microarrays and their application in drought stress research. Field Crops Research 2006, 97(1):101-110.
53. VandenBosch K, Stacey G. Advances in Legume Biology. Plant Physiol 2003, 131(3):839.
54. Sambrook J, Russell D, Sambrook J. Molecular Cloning: A Laboratory Manual (3-Volume Set). 2001, Cold Spring Harbor Laboratory Press.
55. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8(3):186-194.
56. de Silva M, Purcell LC, King CA. Soybean Petiole Ureide Response to Water Deficits and Decreased Transpiration. Crop Sci 1996, 36(3):611-616.
57. Setter TL, Flannigan BA. Water deficit inhibits cell division and expression of transcripts involved in cell proliferation and endoreduplication in maize endosperm. J Exp Bot 2001, 52(360):1401-1408. 10.1093/jexbot/52.360.1401, 11457899.
58. Bates LS, Waldren RP, Teare ID. Rapid determination of free proline for water-stress studies. Plant and Soil 1973, 39(1):205-207.
59. Lichtenthaler HKBC. Current Protocols in Food Analytical Chemistry 2001, F4.2.1-F4.2.6. John Wiley & Sons: New York.