Sorghum bicolor's transcriptome response to dehydration, high salinity and ABA

Plant Molecular Biology

Volumn 58, Issue 5, 2005, Pages 699-720

  Buchanan, Christina D ^a   Lim, Sanghyun ^a   Salzman, Ron A ^a   Kagiampakis, Ioannis ^a   Morishige, Daryl T ^a   Weers, Brock D ^a   Klein, Robert R ^b   Pratt, Lee H ^c   Cordonnier Pratt, Marie Michèle ^c   Klein, Patricia E ^a   Mullet, John E ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b SOUTHERN PLAINS AGRICULTURAL RESEARCH CENTER   (United States)

^c UNIVERSITY OF GEORGIA   (United States)

Author keywords

ABA; Dehydrin; Drought; Gene regulation; Microarray; Sorghum

Indexed keywords

BIOSYNTHESIS; DEHYDRATION; DEPOLYMERIZATION; DNA; ENZYMES; METABOLISM; OSMOSIS; SALINITY MEASUREMENT; SEED;

DEHYDRIN; DROUGHTS; GENE REGULATION; MICROARRAY;

GENES;

ABSCISIC ACID; MACROGOL DERIVATIVE; PHYTOHORMONE; SODIUM CHLORIDE; WATER;

ARTICLE; CLUSTER ANALYSIS; DNA MICROARRAY; DRUG EFFECT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METHODOLOGY; REPRODUCIBILITY; SORGHUM;

ABSCISIC ACID; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT GROWTH REGULATORS; POLYETHYLENE GLYCOLS; REPRODUCIBILITY OF RESULTS; SODIUM CHLORIDE; SORGHUM; TRANSCRIPTION, GENETIC; WATER;

DEPOLYMERIZATION; GENES; LOPHIRA; METABOLISM; NUCLEIC ACIDS; SALINITY; SORGHUM;

LILIOPSIDA; SORGHUM BICOLOR;

EID: 24744450935     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-005-7876-2     Document Type: Article

References (97)

1. S. An S. Park D. Jeong D. Lee H. Kang J. Yu J. Hur S. Kim Y. Kim M. Lee 2003 Generation and analysis of end sequence database for T-DNA tagging lines in rice Plant Physiol. 133 2040 2047
2. I. Bieche I. Laurendeau S. Tozlu M. Olivi D. Vidaud R. Lidereau M. Vidaud 1999 Quantitation of MYC gene expression in sporadic breast tumors with a real-time reverse transcription-PCR assay Cancer Res. 59 2759 2765
3. A. Blum 1996 Crop responses to drought and the interpretation of adaptation Plant Growth Regulat. 20 135 148
4. J. Boyer 1982 Plant productivity and the environment Science 218 444 448
5. E. Bray 1997 Plant responses to water deficit Trends Plant Sci. 2 48 54
6. E. Bray 2002 Classification of genes differentially expressed during water-deficit stress in Arabidopsis thaliana: an analysis using microarray and differential expression data Ann. Bot. 89 803 811
7. A. Brazma P. Hingamp J. Quackenbush G. Sherlock P. Spellman C. Stoeckert J. Aach W. Ansorge C. Ball H. Causton 2001 Minimum information about a microarray experiment. MIAME - toward standards for microarray data Nat. Genet. 29 365 371
8. S. Briggs 1998 Plant genomics: more than food for thought Proc. Natl. Acad. Sci. USA 95 1986 1988
9. C. Buchanan P. Klein J. Mullet 2004 Phylogenetic analysis of 5'-non-coding regions from the ABA-responsive rab16/17 gene family of sorghum, maize and rice provides insight into the composition, organization and function of cis-regulatory modules Genetics 168 1639 1654
10. W. Chi J. Yang N. Wu F. Zhang 2004 Four rice genes encoding NADP malic enzyme exhibit distinct expression profiles Biosci. Biotechnol. Biochem. 68 1865 1874
11. T. Close 1996 Dehydrins: emergence of a biochemical role of a family of plant dehydration proteins Physiol. Plant 97 795 803
12. T. Close 1997 Dehydrins: a commonality in the response of plants to dehydration and low temperature Physiol. Plant 100 291 296
13. M.-M. Cordonnier-Pratt C. Liang H. Wang D. Kolychev F. Sun R. Freeman R. Sullivan L. Pratt 2004 MAGIC database and interfaces: an integrated package for gene discovery and expression Comp. Funct. Genom. 3 268 275
14. O. Crasta W. Xu D. Rosenow J. Mullet H. Nguyen 1999 Mapping of post-flowering drought resistance traits in grain sorghum: association between QTLs influencing premature senescence and maturity Mol. Gen. Genet. 262 579 588
15. R. Creelman H. Mason R. Bensen J. Boyer J. Mullet 1990 Water deficit and abscisic acid cause differential inhibition of shoot versus root growth in soybean seedlings. Analysis of growth, sugar accumulation, and gene expression Plant Physiol. 92 205 214
16. R. Creelman J. Mullet 1991 Water deficit modulates gene expression in growing zones of soybean seedlings. Analysis of differentially expressed cDNAs, a new beta-tubulin gene, and expression of genes encoding cell wall proteins Plant Mol. Biol. 17 591 608
17. A. Delauney D. Verma 1993 Proline biosynthesis and osmoregulation in plants Plant J. 4 215 223
18. H. Doggett 1988 Sorghum John Wiley New York, NY
19. R. Dolferus E. Dennis W. Peacock 1994 Regulation of the Arabidopsis Adh gene by anaerobic and other environmental stresses Ann. Bot. 74 301 308
20. X. Draye Y. Lin X. Qian J. Bowers G. Burow P. Morrell D. Peterson G. Presting S. Ren R. Wing 2001 Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation Plant Physiol. 125 1325 1341
21. M. Drincovich P. Casati C. Andreo 2001 NADP-malic enzyme from plants: a ubiquitous enzyme involved in different metabolic pathways FEBS Lett. 490 1 6
22. L. Dure 1993 A repeating 11-mer amino acid motif and plant desiccation Plant J. 3 363 369
23. R. Finkelstein S. Gampala C. Rock 2002 Abscisic acid signaling in seeds and seedlings Plant Cell 14 S15 S45
24. A. Garg J. Kim T. Owens A. Ranwala Y. Choi L. Kochian R. Wu 2002 Trehalose accumulation in rice plants confers high tolerance levels to different abiotic stresses Proc. Natl. Acad. Sci. USA 99 15898 15903
25. P. Gleick 2003 Global freshwater resources: soft-path solutions for the 21st century Science 302 1524 1528
26. S. Goff D. Ricke T.-H. Lan G. Presting R. Wang M. Dunn J. Glazebrook A. Sessions P. Oeller H. Varma 2002 A draft sequence of the rice genome Oryza sativa L. ssp. japonica Science 296 92 100
27. C. Grieve E. Maas 1984 Betaine accumulation in salt-stressed sorghum Physiol. Plant 61 167 171
28. F. Guerrero J. Jones J. Mullet 1990 Turgor-responsive gene transcription and RNA levels increase rapidly when pea shoots are wilted. Sequence and expression of three inducible genes Plant Mol. Biol. 15 11 26
29. P. Hasegawa R. Bressan J.-K. Zhu H. Bohnert 2000 Plant cellular and molecular responses to high salinity Annu. Rev. Plant Physiol. Plant Mol. Biol. 51 463 499
30. A. Himmelbach Y. Yang E. Grill 2003 Relay and control of abscisic acid signaling Curr. Opin. Plant Biol. 6 470 479
31. S. Holzberg P. Brosio C. Gross G. Pogue 2002 Barley stripe mosaic virus-induced gene silencing in a monocot plant Plant J. 30 315 327
32. S. Hoth M. Morgante J. Sanchez M. Hanafey S. Tingey N. Chua 2002 Genome-wide gene expression profiling in Arabidopsis thaliana reveals new targets of abscisic acid and largely impaired gene regulation in the abi1-1 mutant J. Cell Sci. 115 4891 4900
33. T. Hsiao 1973 Plant responses to water stress Annu. Rev. Plant Physiol. 24 519 570
34. M. Ishitani A. Majumder A. Bornhouser C. Michalowski R. Jensen H. Bohnert 1996 Coordinate transcriptional induction of myo-inositol metabolism during environmental stress Plant J. 9 537 548
35. Ismail, A., Hall, A. and Close, T., 1999. Allelic variation of a dehydrin gene cosegregates with chilling tolerance during seedling emergence. Proc. Natl. Acad. Sci. USA 96: 9
36. M. Jeanneau D. Gerentes X. Foueillassar M. Zivy J. Vidal A. Toppan P. Perez 2002 Improvement of drought tolerance in maize: towards the functional validation of the Zm-Asr1 gene and increase of water use efficiency by over-expressing C4-PEPC Biochimie 84 1127 1135
37. N. Johnson C. Revenga J. Echeverria 2001 Managing water for people and nature Science 292 1071 1072
38. L. Jones S. McQueen-Mason 2004 A role for expansins in dehydration and rehydration of the resurrection plant Craterostigma plantagineum FEBS Lett. 559 61 65
39. S. Kawasaki C. Borchert M. Deyholos H. Wang S. Brazille K. Kawai D. Galbraith H. Bohnert 2001 Gene expression profiles during the initial phase of salt stress in rice Plant Cell 13 889 905
40. E. Keller D. Cosgrove 1995 Expansins in growing tomato leaves Plant J. 8 795 802
41. G. Khush 1999 Green revolution: preparing for the 21st century Genome 42 646 655
42. P. Klein R. Klein S. Cartinhour P. Ulanch J. Dong J. Obert D. Morishige S. Schlueter K. Childs M. Ale 2000 A high-throughput AFLP-based method for constructing integrated genetic and physical maps: progress toward a sorghum genome map Genome Res. 10 789 807
43. P. Klein R. Klein J. Vrebalov J. Mullet 2003 Sequence-based alignment of sorghum chromosome 3 and rice chromosome 1 reveals extensive conservation of gene order and one major chromosomal rearrangement Plant J. 34 605 621
44. K. Koster A. Leopold 1988 Sugars and desiccation tolerance in seeds Plant Physiol. 88 829 832
45. J. Kreps Y. Wu H. Chang T. Zhu X. Wang J. Harper 2002 Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress Plant Physiol. 130 2129 2141
46. M. Lee 1998 Genome projects and gene pools: new germplasm for plant breeding? Proc. Natl. Acad. Sci. USA 95 2001 2004
47. N. Leonhardt J. Kwak N. Robert D. Waner G. Leonhardt J. Schroeder 2004 Microarray expression analyses of Arabidopsis guard cells and isolation of a recessive abscisic acid hypersensitive protein phosphatase 2C mutant Plant Cell 16 596 615
48. F. Lin S. Xu W. Ni Z. Chu Z. Xu H. Xue 2003 Identification of ABA-responsive genes in rice shoots via cDNA macroarray Cell Res. 13 59 68
49. F. Loewus P. Murthy 2000 myo-Inositol metabolism in plants Plant Sci. 150 1 19
50. E. Lopez Becerra P. Puigdomenech V. Stiefel 1998 A gene coding for a malic enzyme expressed in the embryo root epidermis from Zea mays Accession No. AJ224847. PGR 98-081 Plant Physiol. 117 332
51. M. Ludlow R. Muchow 1990 A critical evaluation of traits for improving crop yields in water-limited environments Adv. Agron. 43 107 153
52. M. Ludlow J. Santamaria S. Fukai 1990 Contribution of osmotic adjustment to grain yield in Sorghum bicolor L. Moench under water-limited conditions. II. Water stress after anthesis Aust. J. Agric. Res. 41 67 78
53. S. McNeil M. Nuccio A. Hanson 1999 Betaines and related osmoprotectants. Targets for metabolic engineering of stress resistance Plant Physiol. 120 945 949
54. M. Menz R. Klein J. Mullet J. Obert N. Unruh P. Klein 2002 A high-density genetic map of Sorghum bicolor L. Moench based on 2926 AFLP-R, RFLP and SSR markers Plant Mol. Biol. 48 483 499
55. R. Ming S. Liu Y. Lin J. da Silva W. Wilson D. Braga A. van Deynze T. Wenslaff K. Wu P. Moore 1998 Detailed alignment of Saccharum and Sorghum chromosomes: Comparative organization of closely related diploid and polyploid genomes Genetics 150 1663 1682
56. P. Morgan S. Finlayson K. Childs J. Mullet W. Rooney 2002 Opportunities to improve adaptability and yield in grasses: lessons from sorghum Crop Sci. 42 1791 1799
57. J. Mullet R. Klein P. Klein 2001 Sorghum bicolor - an important species for comparative grass genomics and a source of beneficial genes for agriculture Curr. Opin. Plant Biol. 5 118 121
58. H. Nonami J. Boyer 1989 Turgor and growth at low water potentials Plant Physiol. 89 798 804
59. H. Nonami J. Boyer 1990 Primary events regulating stem growth at low water potentials Plant Physiol. 93 1601 1609
60. Y. Oono M. Seki T. Nanjo M. Narusaka M. Fujita R. Satoh M. Satou T. Sakurai J. Ishida K. Akiyama 2003 Monitoring expression profiles of Arabidopsis gene expression during rehydration process after dehydration using ca. 7000 full-length cDNA microarray Plant J. 34 868 887
61. F. Ouellet E. Carpentier M. Cope A. Monroy F. Sarhan 2001 Regulation of a wheat actin-depolymerizing factor during cold acclimation Plant Physiol. 125 360 368
62. Z. Ozturk V. Talame M. Deyholos C. Michalowski D. Galbraith N. Gozukirmizi R. Tuberosa H. Bohnert 2002 Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barley Plant Mol. Biol. 48 551 573
63. Pratt, L.H., Liang, C., Shah, M., Sun, F., Wang, H., Reid, St-P., Gingle, A.R., Paterson, A.H., Wing, R., Dean, R., Klein, R.R., Nguyen, H.T., Ma, H-M., Zhao, X., Morishige, D.T., Mullet, J.E. and Cordonnier-Pratt, M-M. 2005. Sorghum Expressed Sequence Tags Identify Signature Genes for Drought, Pathogenesis and Skotomorphogenesis from a Milestone Set of 16,801 Unique Transcripts. Plant Physiol. (In press)
64. A. Price J. Cairns P. Horton H. Jones H. Griffiths 2002 Linking drought-resistance mechanisms to drought avoidance in upland rice using a QTL approach: progress and new opportunities to integrate stomatal and mesophyll responses J. Exp. Bot. 53 989 1004
65. J. Quackenbush 2002 Microarray data normalization and transformation Nat. Genet. 32 496 501
66. M. Rabbani K. Maruyama H. Abe M. Khan K. Katsura Y. Ito K. Yoshiwara M. Seki K. Shinozaki K. Yamaguchi-Shinozaki 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 Physiol. 133 1755 1767
67. M. Rajeevan D. Ranamukhaarachchi S. Vernon E. Unger 2001 Use of real-time quantitative PCR to validate the results of cDNA array and differential display PCR technologies Methods 25 443 451
68. D. Rontein G. Basset A. Hanson 2002 Metabolic engineering of osmoprotectant accumulation in plants Metab. Eng. 4 49 56
69. D. Rosenow G. Ejeta L. Clark M. Gilbert R. Henzell A. Borell R. Muchow 1996 Breeding for pre- and post-flowering drought stress resistance in sorghum D.T. Rosenow J.M. Yohe Proceeding of the International Conference on Genetic Improvement in Sorghum and Pearl Millet Lubbock TX 400 411
70. D. Rosenow J. Quisenberry C. Wendt L. Clark 1983 Drought tolerant sorghum and cotton germplasm Agric. Water Manage. 7 207 222
71. Salzman, R.A., Brady, J.A., Finlayson S.A., Buchanan, C.D., Sun, F. Klein, P.E., Klein, R.R., Pratt, L.M., Cordonnier-Pratt, M.M. and Mullet, J.E. 2005. Transcriptional profiling of sorghum induced by methyl jasmonate, salicyclic acid, and aminocyclopropene carboxylic acid reveals cooperative regulation and novel gene responses. Plant Physiol, 138: 352-368
72. M. Schein Z. Yang T. Mitchell-Olds K. Schmid 2004 Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thaliana and closely related species Mol. Biol. Evol. 21 659 669
73. S. Schwartz X. Qin J. Zeevaart 2003 Elucidation of the indirect pathway of abscisic acid biosynthesis by mutants, genes, and enzymes Plant Physiol. 131 1591 1601
74. M. Seki J. Ishida M. Narusaka M. Fujita T. Nanjo T. Umezawa A. Kamiya M. Nakajima A. Enju T. Sakurai 2002a Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatment using a full-length cDNA microarray Funct. Integrat. Genom. 2 282 291
75. M. Seki M. Narusaka H. Abe M. Kasuga K. Yamaguchi-Shinozaki P. Carninci Y. Hayashizaki K. Shinozaki 2001a Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray Plant Cell 13 61 72
76. M. Seki M. Narusaka J. Ishida T. Nanjo M. Fujita Y. Oono A. Kamiya M. Nakajima A. Enju T. Sakurai 2002b Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray Plant J. 31 279 292
77. R. Sharp W. Silk T. Hsiao 1988 Growth of the maize primary root at low water potentials Plant Physiol. 87 50 57
78. K. Shinozaki E. Dennis M. Seki 2003 Regulatory network of gene expression in the drought and cold stress responses Curr. Opin. Plant Biol. 6 410 417
79. P. Spellman G. Sherlock M. Zhang V. Iyer K. Anders M. Eisen P. Brown D. Botstein B. Futcher 1998 Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarry hybridization Mol. Biol. Cell 9 3273 3297
80. W.-K. Tang C. Cheng W.-P. Fong 2002 First purification of the antiquitin protein and demonstration of its enzymatic activity FEBS Lett. 516 183 186
81. S. Tausta H. Coyle B. Rothermel V. Stiefel T. Nelson 2002 Maize C4 and non-C4 NADP-dependent malic enzymes are encoded by distinct genes derived from a plastid-localized ancestor Plant Mol. Biol. 50 635 652
82. R. Tuberosa S. Salvi M. Sanguineti P. Landi M. Maccaferri S. Conti 2002 Mapping QTLs regulating morpho-physiological traits and yield: case studies, shortcomings and perspectives in drought-stressed maize Ann. Bot. 89 941 963
83. M. Tuinstra E. Grote P. Goldsbrough G. Ejeta 1997 Genetic analysis of post-flowering drought tolerance and components of grain development of Sorghum bicolor. L. Moench Mol. Breed. 3 439 448
84. A. Van Dijken H. Schluepmann S. Smeekens 2004 Arabidopsis trehalose-6-phosphate synthase 1 is essential for normal vegetative growth and transition to flowering Plant Physiol. 135 1 9
85. P. Verslues E. Ober R. Sharp 1998 Root growth and oxygen relations at low water potentials. Impact of oxygen availability in polyethylene glycol solutions Plant Physiol. 116 1403 1412
86. H. Wang S. Miyazaki K. Kawai M. Deyholos D. Galbraith H. Bohnert 2003 Temporal progression of gene expression responses to salt shock in maize roots Plant Mol. Biol. 52 873 891
87. R. Weinburg H. Lerner A. Poljakoff-Mayber 1982 A relationship between potassium and proline accumulation in salt-stressed Sorghum bicolor Physiol. Plant 55 5 10
88. A. Wood H. Saneoka D. Rhodes R. Joly P. Goldsbrough 1996 Betaine aldehyde dehydrogenase in sorghum. Molecular cloning and expression of two related genes Plant Physiol. 110 1301 1308
89. Y. Wu E. Thorne R. Sharp D. Cosgrove 2001 Modification of expansin transcript levels in the maize primary root at low water potentials Plant Physiol. 126 1471 1479
90. L. Xiong K. Schumaker J.-K. Zhu 2002 Cell signaling during cold, drought, and salt stress Plant Cell 14 S165 S183
91. W. Xu P. Subudhi O. Crasta D. Rosenow J. Mullet H. Nguyen 2000 Molecular mapping of QTLs conferring stay-green in grain sorghum Sorghum bicolor L. Moench Genome 43 461 469
92. J. Yazaki Z. Shimatani A. Hashimoto Y. Nagata F. Fujii K. Kojima K. Suzuki T. Taya M. Tonouchi C. Nelson 2004 Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis Physiol. Genom. 17 87 100
93. Y. Yoshiba T. Kiyosue T. Katagiri H. Ueda T. Mizoguchi K. Yamaguchi-Shinozaki K. Wada Y. Harada K. Shinozaki 1995 Correlation between the induction of a gene for delta 1-pyrroline-5-carboxylate synthetase and the accumulation of proline in Arabidopsis thaliana under osmotic stress Plant J. 7 751 760
94. J. Yu S. Hu J. Wang G.K.-S. Wong S. Li B. Liu Y. Deng L. Dai Y. Zhou X. Zhang 2002 A draft sequence of the rice genome Oryza sativa L. ssp. indica Science 296 79 92
95. J. Zhang R. Creelman J. Zhu 2004 From laboratory to field. Using information from Arabidopsis to engineer salt, cold and drought tolerance in crops Plant Physiol. 135 615 621
96. J.-K. Zhu 2001a Cell signaling under salt, water and cold stresses Curr. Opin. Plant Biol. 4 401 406
97. J.-K. Zhu 2001b Plant salt tolerance Trends Plant Sci. 6 66 71