Skip to main content
SpringerLink
Log in

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

  • Genetics and Genomics
  • Published:
Plant Cell Reports Aims and scope Submit manuscript

Abstract

Cassava (Manihot esculenta Crantz) is a staple food for over 600 million people in the tropics and subtropics and is increasingly used as an industrial crop for starch production. Cassava has a high growth rate under optimal conditions but also performs well in drought-prone areas and on marginal soils. To increase the tools for understanding and manipulating drought tolerance in cassava, we generated expressed sequence tags (ESTs) from normalized cDNA libraries prepared from dehydration-stressed and control well-watered tissues. Analysis of a total of 18,166 ESTs resulted in the identification of 8,577 unique gene clusters (5,383 singletons and 3,194 clusters). Functional categories could be assigned to 63% of the unigenes, while another ∼11% were homologous to hypothetical genes with unclear functions. The remaining ∼26% were not significantly homologous to sequences in public databases suggesting that some may be novel and putatively specific to cassava. The dehydration-stressed library uncovered numerous ESTs with recognized roles in drought-responses, including those that encode late-embryogenesis-abundant proteins thought to confer osmoprotective functions during water stress, transcription factors, heat-shock proteins as well as proteins involved in signal transduction and oxidative stress. The unigene clusters were screened for short tandem repeats for further development as microsatellite markers. A total of 592 clusters contained 646 repeats, representing 3.3% of the ESTs queried. The ESTs presented here are the first dehydration stress transcriptome of cassava and can be utilized for the development of microarrays and gene-derived molecular markers to further dissect the molecular basis of drought tolerance in cassava.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Alves AA, Setter TL (2004a) Abscisic acid accumulation and osmotic adjustment in cassava under water deficit. Environ Exp Bot 51:259–271

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Anderson JV, Horvath DP (2001) Random sequencing of cDNAs and identification of mRNAs. Weed Sci 49:581–589

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • Blum A (1998) Plant breeding for stress environments. CRC, Boca Raton, FL, pp 43–76

    Google Scholar 

  • Bonaldo MF, Lennon G, Soares MB (1996) Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res 6:791–806

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • Chaves MM, Oliveira MM (2004) Mechanisms underlying plant resilience to water deficits: prospects for water-saving agriculture. J Exp Bot 55:2365–2384

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • El Sharkawy MA (2004) Cassava biology and physiology. Plant Mol Biol 56:481–501

    Article  PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Hsieh HM, Liu WK, Huang PC (1995) A novel stress-inducible metallothionein-like gene from rice. Plant Mol Biol 28:381–389

    Article  PubMed  CAS  Google Scholar 

  • Ingram J, Bartels D (1996) The molecular basis of dehydration tolerance in plants. Annu Rev Plant Physiol Plant Mol Biol 47:377–403

    Article  PubMed  CAS  Google Scholar 

  • 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

  • Kader J-C (1997) Lipid-transfer proteins: a puzzling family of plant proteins. Trends Plant Sci 2:66–70

    Article  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Knight H, Knight MR (2001) Abiotic stress signalling pathways: specificity and cross-talk. Trends Plant Sci 6:262–267

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Meijer HJ, Munnik T (2003) Phospholipid-based signaling in plants. Annu Rev Plant Biol 54:265–306

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Netzer WJ, Hartl FU (1998) Protein folding in the cytosol: chaperonin-dependent and -independent mechanisms. Trends Biochem Sci 23:68–73

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • Okogbenin E, Marin J, Fregene M (2006) An SSR-based molecular genetic map for cassava. Euphytica 147:433–440

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Palmiter RD (1998) The elusive function of metallothioneins. Proc Natl Acad Sci USA 95:8428–8430

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Richmond T, Somerville S (2000) Chasing the dream: plant EST microarrays. Curr Opin Plant Biol 3:108–116

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Rudd S (2005) openSputnik—a database to ESTablish comparative plant genomics using unsaturated sequence collections. Nucleic Acids Res 33:D622–D627

    Article  PubMed  CAS  Google Scholar 

  • Rudd S, Schoof H, Mayer K (2005) PlantMarkers—a database of predicted molecular markers from plants. Nucleic Acids Res 33:D628–D632

    Article  PubMed  CAS  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Vierling E (1991) The role of heat-shock proteins in plants. Annu Rev Plant Physiol Plant Mol Biol 42:579–620

    Article  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The authors thank Dr. R. Okechukwu for help with statistical analysis, Mrs. J. Plancarte for preparing figures and bibliography, Mrs. F. Kolade for technical assistance, and Mrs. R. Umelo for critical reading of the manuscript. This research was partially supported by the US Agency for International Development (USAID). The opinions expressed herein are those of the authors and do not necessarily reflect the views of the USAID.

Author information

Author notes

  1. Y. Lokko

    Present address: Plant Breeding and Genetics Section, International Atomic Energy Agency, Wagramer Strasse 5, PO Box 200, 1400, Vienna, Austria

Authors and Affiliations

  1. Central Biotechnology Laboratory, International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria

    Y. Lokko, A. Raji, A. G. O. Dixon & I. L. Ingelbrecht

  2. Biosciences Research Laboratory, USDA-Agricultural Research Service, 1605 Albrecht Blvd., Fargo, ND, 58105-5674, USA

    J. V. Anderson & D. Horvath

  3. Centre for Biotechnology, Tykistökatu 6, 20521, Turku, Finland

    S. Rudd

  4. Department of Crop Sciences and Roy J. Carver Biotechnology Center, 2610 Institute for Genomic Biology, University of Illinois, 1206 W. Gregory Drive, Urbana, IL, 61801, USA

    M. A. Mikel

  5. W.M. Keck Center for Comparative and Functional Genomics, Edward R. Madigan Laboratory, University of Illinois, 1201 W. Gregory Drive, Urbana, IL, 61801, USA

    R. Kim, L. Liu & A. Hernandez

Authors
  1. Y. Lokko
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. J. V. Anderson
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. S. Rudd
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. A. Raji
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. D. Horvath
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. M. A. Mikel
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. R. Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. L. Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. A. Hernandez
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. A. G. O. Dixon
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. I. L. Ingelbrecht
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to I. L. Ingelbrecht.

Additional information

Communicated by R. Reski.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Lokko, Y., Anderson, J.V., Rudd, S. et al. Characterization of an 18,166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes. Plant Cell Rep 26, 1605–1618 (2007). https://doi.org/10.1007/s00299-007-0378-8

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00299-007-0378-8

Keywords

Search

Navigation