Characterization of an 18,166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes

Plant Cell Reports

Volumn 26, Issue 9, 2007, Pages 1605-1618

  Lokko, Y ^a,e   Anderson, J V ^b   Rudd, S ^c   Raji, A ^a   Horvath, D ^b   Mikel, M A ^d   Kim, R ^d   Liu, L ^d   Hernandez, A ^d   Dixon, A G O ^a   Ingelbrecht, I L ^a  

^a INTERNATIONAL INSTITUTE OF TROPICAL AGRICULTURE   (Nigeria)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

^c TURKU CENTRE FOR BIOTECHNOLOGY   (Finland)

^d UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^e INTERNATIONAL ATOMIC ENERGY AGENCY   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

PLANTS (BOTANY); STARCH;

EXPRESSED SEQUENCE TAGS (EST); STARCH PRODUCTION;

CROPS;

MICROSATELLITE DNA;

ARTICLE; BIOLOGY; CASSAVA; DISASTER; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE; GENE DOSAGE; GENE LIBRARY; GENETICS; NORTHERN BLOTTING; NUCLEIC ACID DATABASE; VARIABLE NUMBER OF TANDEM REPEAT;

BLOTTING, NORTHERN; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; EXPRESSED SEQUENCE TAGS; GENE DOSAGE; GENE LIBRARY; GENES, PLANT; MANIHOT; MICROSATELLITE REPEATS; MINISATELLITE REPEATS; NATURAL DISASTERS; SEQUENCE ANALYSIS, DNA;

MANIHOT ESCULENTA;

EID: 34548025846     PISSN: 07217714     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00299-007-0378-8     Document Type: Article

References (68)

1. Alba R, Fei Z, Payton P, Liu Y, Moore SL, Debbie P, Cohn J, D'Ascenzo M, Gordon JS, Rose JKC, Martin G, Tanksley SD, Bouzayen M, Jahn MM, Giovannoni J (2004) ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development. Plant J 39:697-714
2. Ali S, Holloway B, Taylor WC (2000) Normalization of cereal endosperm EST libraries for structural and functional genomic analysis. Plant Mol Biol Rep 18:123-132
3. Alves AA, Setter TL (2004a) Abscisic acid accumulation and osmotic adjustment in cassava under water deficit. Environ Exp Bot 51:259-271
4. Alves AA, Setter TL (2004b) Response of cassava leaf area expansion to water deficit: cell proliferation, cell expansion and delayed development. Ann Bot (Lond) 94:605-613
5. Anderson JV, Delseny M, Fregene MA, Jorge V, Mba C, Lopez C, Restrepo S, Soto M, Piegu B, Verdier V, Cooke R, Tohme J, Horvath DP (2004) An EST resource for cassava and other species of Euphorbiaceae. Plant Mol Biol 56:527-539
6. Anderson JV, Horvath DP (2001) Random sequencing of cDNAs and identification of mRNAs. Weed Sci 49:581-589
7. Asamizu E, Nakamura Y, Sato S, Tabata S (2000a) A large scale analysis of cDNA in Arabidopsis thaliana: generation of 12,028 non-redundant expressed sequence tags from normalized and size-selected cDNA libraries. DNA Res 7:175-180
8. Asamizu E, Nakamura Y, Sato S, Tabata S (2000b) Generation of 7,137 non-redundant expressed sequence tags from a legume, Lotus japonicus. DNA Res 7:127-130
9. Balagopalan C (2002) Cassava Utilization in Food, Feed and Industry. In: Hillocks RI, Thresh JM (eds) Cassava Biology, Production and Utilization. CAB Intl, Wallingford, UK, pp 301-318
10. Blum A (1998) Plant breeding for stress environments. CRC, Boca Raton, FL, pp 43-76
11. Bonaldo MF, Lennon G, Soares MB (1996) Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res 6:791-806
12. Cattivelli L, Baldi P, Crosatti C, Di Fonzo N, Faccioli P, Grossi M, Mastrangelo AM, Pecchioni N, Stanca AM (2002) Chromosome regions and stress-related sequences involved in resistance to abiotic stress in Triticeae. Plant Mol Biol 6:649-665
13. Chaves MM, Oliveira MM (2004) Mechanisms underlying plant resilience to water deficits: prospects for water-saving agriculture. J Exp Bot 55:2365-2384
14. Chini A, Grant JJ, Seki M, Shinozaki K, Loake G (2004) Drought tolerance established by enhanced expression of the CC-NB-LRR gene, ADR1, requires salicylic acid, EDS1 and ABI1. Plant J 38:810-822
15. Cheong YH, Kim K-N, Pandey GK, Gupta R, Grant JJ, Luan S (2003) CBL1, a calcium sensor that differentially regulates salt, drought, and cold responses in Arabidopsis. Plant Cell 15:1833-1845
16. Cho S, Ok S, Jeung J, Shim K, Jung K, You M, Kang K, Chung Y, Choi H, Moon H, Shin J (2004) Comparative analysis of 5,211 leaf ESTs of wild rice (Oryza minuta). Plant Cell Rep 22:839-847
17. Cordeiro GM, Casu R, McIntyre CL, Manners JM, Henry RJ (2001) Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant Sci 160:1115-1123
18. El Sharkawy MA (2004) Cassava biology and physiology. Plant Mol Biol 56:481-501
19. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175-185
20. Fregene M, Puonti-Kaerlas J (2002) Cassava Biotechnology. In: Hillocks RI, Thresh JM (eds) Cassava Biology, Production and Utilization. CAB Intl, Wallingford, UK, pp 179-207
21. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92-100
22. Gorantla M, Babu PR, Reddy Lachagari VB, Reddy AMM, Wusirika R, Bennetzen JL, Reddy AR (2007) Identification of stress-responsive genes in indica rice (Oryza sativa L.) using ESTs generated from drought-stressed seedlings. J Exp Bot 58:253-265
23. Gosti F, Bertauche N, Vartanian N, Giraudat J (1995) Abscisic acid-dependent and -independent regulation of gene expression by progressive drought in Arabidopsis thaliana. Mol Gen Genet 246:10-18
24. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la CN, Tonellato P, Jaiswal P, Seigfried T, White R (2004) The gene ontology (GO) database and informatics resource. Nucleic Acids Res 32:D258-D261
25. Hirayama T, Ohto C, Mizoguchi T, Shinozaki K (1995) A gene encoding a phosphatidylinositol-specific phospholipase C is induced by dehydration and salt stress in Arabidopsis thaliana. Proc Natl Acad Sci USA 92:3903-3907
26. Hsieh HM, Liu WK, Huang PC (1995) A novel stress-inducible metallothionein-like gene from rice. Plant Mol Biol 28:381-389
27. Ingram J, Bartels D (1996) The molecular basis of dehydration tolerance in plants. Annu Rev Plant Physiol Plant Mol Biol 47:377-403
28. Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 138-148
29. Kader J-C (1997) Lipid-transfer proteins: a puzzling family of plant proteins. Trends Plant Sci 2:66-70
30. Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, Kawai K, Galbraith D, Bohnert HJ (2001) Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13:889-906
31. Kiyosue T, Yamaguchi-Shinozaki K, Shinozaki K (1994) Cloning of cDNA for genes that are early-responsive to dehydration-stress (ERDs) in Arabidopsis thaliana L.: identification of three ERDs as HSP cognate genes. Plant Mol Biol 25:791-798
32. Knight H, Knight MR (2001) Abiotic stress signalling pathways: specificity and cross-talk. Trends Plant Sci 6:262-267
33. Kota R, Rudd S, Facius A, Kolesov G, Thiel T, Zhang H, Stein N, Mayer K, Graner A (2003) Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.). Mol Genet Genomics 270:24-33
34. Kudla J, Xu Q, Harter K, Gruissem W, Luan S (1999) Genes for calcineurin B-like proteins in Arabidopsis are differentially regulated by stress. Proc Natl Acad Sci 96:4718-4723
35. Larosa PC, Hasegawa PM, Rhodes D, Clithero JM, Watad AE, Bressan RA (1987) Abscisic acid stimulated osmotic adjustment and its involvement in adaptation of tobacco cells to NaCl. Plant Physiol 85:174-181
36. Lecoeur J, Wery J, Turc O, Tardieu F (1995) Expansion of pea leaves subjected to short water deficit: cell number and cell size are sensitive to stress at different periods of leaf development. J Exp Bot 46:1093-1101
37. Lindorff-Larsen K, Lerche HM, Poulsen FM, Roepstorff P, Winther JR (2001) Barley lipid transfer protein, LTP1, contains a new type of lipid-like post-translational modification. J Biol Chem 36:33547-33553
38. Machuka J, Bashiardes S, Ruben E, Spooner K, Cuming A, Knight C, Cove D (1999) Sequence analysis of expressed sequence tags from an ABA-treated cDNA library identifies stress response genes in the moss Physcomitrella patens. Plant Cell Physiol 40:378-387
39. Meijer HJ, Munnik T (2003) Phospholipid-based signaling in plants. Annu Rev Plant Biol 54:265-306
40. Mewes HW, Frishman D, Guldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B, Munsterkotter M, Rudd S, Weil B (2002) MIPS: a database for genomes and protein sequences. Nucleic Acids Res 30:31-34
41. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJ, Vaughan R, Zdobnov EM (2003) The InterPro database, 2003 brings increased coverage and new features. Nucleic Acids Res 31:315-318
42. Netzer WJ, Hartl FU (1998) Protein folding in the cytosol: chaperonin-dependent and -independent mechanisms. Trends Biochem Sci 23:68-73
43. Okogbenin E, Ekanayake IJ, Porto MCM (2003) Genotypic variability in adaptation responses of selected clones of cassava to drought stress in the Sudan Savanna Zone of Nigeria. J Agric Crop Sci 189:376-389
44. Okogbenin E, Marin J, Fregene M (2006) An SSR-based molecular genetic map for cassava. Euphytica 147:433-440
45. Olsson AS, Engström P, Söderman E (2004) The homeobox genes ATHB12 and ATHB7 encode potential regulators of growth in response to water deficit in Arabidopsis. Plant Mol Biol 55:663-677
46. Palmiter RD (1998) The elusive function of metallothioneins. Proc Natl Acad Sci USA 95:8428-8430
47. Ramírez M, Graham MA, Blanco-López L, Silvente S, Medrano-Soto A, Blair MW, Hernández G, Vance CP, Lara M (2005) Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiol 137:1211-1227
48. Reddy AR, Ramakrishna W, Chandra Sekhar A, Ithal N, Ravindra Babu P, Bonaldo MF, Soares MB, Bennetzen JL (2002) Novel genes are enriched in normalized cDNA libraries from drought-stressed seedlings of rice (Oryza sativa L. subsp. indica cv. Nagina 22). Genome 45:204-211
49. Richmond T, Somerville S (2000) Chasing the dream: plant EST microarrays. Curr Opin Plant Biol 3:108-116
50. Rodriguez Milla MA, Butler E, Rodriguez Huete A, Wilson CF, Anderson O, Gustafson JP (2002) Expressed sequence tag-based gene expression analysis under Aluminum stress in Rye. Plant Physiol 130:1706-1716
51. Rohila JS, Jain RK, Wu R (2002) Genetic improvement of Basmati rice for salt and drought tolerance by regulated expression of a barley Hva1 cDNA. Plant Sci 163:525-532
52. Rudd S (2005) openSputnik-a database to ESTablish comparative plant genomics using unsaturated sequence collections. Nucleic Acids Res 33:D622-D627
53. Rudd S, Schoof H, Mayer K (2005) PlantMarkers-a database of predicted molecular markers from plants. Nucleic Acids Res 33:D628-D632
54. Sakai T, Nakagawa Y, Uritani I, Data ES (1994) Occurence and characterization of stress metabolites in cassava roots. In: Uritani I, Garcia VV, Mendoza EMT (eds) Postharvest biochemistry of plant food-materials in the tropics. Japan Scientific Society Press, Tokyo, pp 95-110
55. Satou Y, Kawashima T, Kohara Y, Satoh N (2003) Large scale EST analyses in Ciona intestinalis: its application as Northern blot analyses. Dev Genes Evol 213:314-318
56. Scott KD, Eggler P, Seaton G, Rosetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723-726
57. Sharp RE, Wu Y, Voetberg GS, Saab IN, LeNoble ME (1994) Confirmation that abscisic acid accumulation is required for maize primary root elongation at low water potentials. J Exp Bot 45:1743-1751
58. Sivamani E, Bahieldin A, Wraith JM, Al-Niemi T, Dyer WE, Ho THD, Qu R (2000) Improved biomass productivity and water use efficiency under water deficit conditions in transgenic wheat constitutively expressing the barley HVA1 gene. Plant Sci 155:1-9
59. Taylor N, Chavarriaga P, Raemakers K, Siritunga D, Zhang P (2004) Development and application of transgenic technologies in cassava. Plant Mol Biol 56:671-688
60. Tobias CM, Twigg P, Hayden DM, Vogel KP, Mitchell RM, Lazo GR, Chow EK, Sarath G (2005) Analysis of expressed sequence tags and the identification of associated short tandem repeats in switchgrass. Theor Appl Genet 111:956-964
61. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411-422
62. Treviño MB, O'Connell MA (1998) Three drought-responsive members of the nonspecific lipid-transfer protein gene family in Lycopersicon pennellii show different developmental patterns of expression. Plant Physiol 116:1461-1468
63. Umezawa T, Fujita M, Fujita Y, Yamaguchi-Shinozaki K, Shinozaki K (2006) Engineering drought tolerance in plants: discovering and tailoring genes to unlock the future. Curr Opin Biot 17:113-122
64. Vierling E (1991) The role of heat-shock proteins in plants. Annu Rev Plant Physiol Plant Mol Biol 42:579-620
65. Wood AJ, Duff RJ, Oliver MJ (1999) Expressed sequence tags (ESTs) from desiccated Tortula ruralis identify a large number of novel plant genes. Plant Cell Physiol 40:361-368
66. Yamagushi-Shinozaki K, Shinozaki K (1993) 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. Mol Gen Genet 238:17-25
67. Zhang JZ, Creelman RA, Zhu J-K (2004) From laboratory to field. Using information from Arabidopsis to engineer salt, cold and drought tolerance in crops. Plant Physiol 135:615-621
68. Zimmerman G, Bäumlein H, Mock H-P, Himmelbach A, Schweizer P (2006) The multigene family encoding germin-like proteins of barley. Regulation and function in basal host resistance. Plant Physiol 142:181-192