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An EST resource for cassava and other species of Euphorbiaceae

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Abstract

Cassava (Manihot esculenta) is a major food staple for nearly 600 million people in Africa, Asia, and Latin America. Major losses in yield result from biotic and abiotic stresses that include diseases such as Cassava Mosaic Disease (CMD) and Cassava Bacterial Blight (CBB), drought, and acid soils. Additional losses also occur from deterioration during the post-harvest storage of roots. To help cassava breeders overcome these obstacles, the scientific community has turned to modern genomics approaches to identify key genetic characteristics associated with resistance to these yield-limiting factors. One approach for developing a genomics program requires the development of ESTs (expressed sequence tags). To date, nearly 23000 ESTs have been developed from various cassava tissues, and genotypes. Preliminary analysis indicates existing EST resources contain at least 6000–7000 unigenes. Data presented in this report indicate that the cassava ESTs will be a valuable resource for the study of genetic diversity, stress resistance, and growth and development, not only in cassava, but also other members of the Euphorbiaceae family.

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Abbreviations

BAC:

bacterial amplified chromosome

bp:

base pair

CAPS:

cleaved amplicon polymorphisms

CBB:

cassava bacterial blight

CMD:

cassava mosaic disease

EST:

expressed sequence tag

PCR:

polymerase chain reaction

QTLs:

quantitative trait loci

RFLP:

restriction fragment length polymorphism

SAGE:

serial analysis of gene expression

SNP:

single nucleotide polymorphisms

References

  • A. Aharoni L.C.P. Keizer H.J. Bouwmeester Z. Sun M. Alvarez-Huerta H.A. Verhoeven J. Blaas A.M.M.L. Houwelingen Particlevan R.C.H. De Vos H. Voet Particlevan der R.C. Jansen M. Guis J. Mol R.W. Davis M. Schena A.J. Tunen Particlevan A.P. O’Connell (2000) ArticleTitleIdentification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays Plant Cell 12 647–661 Occurrence Handle10810141

    PubMed  Google Scholar 

  • O. Akano A. Dixon C. Mba E. Barrera M. Fregene (2002) ArticleTitleGenetic mapping of a dominant gene conferring resistance to Cassava mosaic disease Theor. Appl. Genet. 105 521–525 Occurrence Handle10.1007/s00122-002-0891-7 Occurrence Handle12582500

    Article  PubMed  Google Scholar 

  • S.F. Altschul T.L. Madden A.A. Shaffer J. Zhang Z. Zhang W. Miller D.J. Lipman (1997) ArticleTitle‘Gapped BLAST and PSI-BLAST: a new generation of protein database search programs’ Nucleic Acids Res. 25 3389–3402 Occurrence Handle10.1093/nar/25.17.3389 Occurrence Handle9254694

    Article  PubMed  Google Scholar 

  • Anderson, J.V., Gedil, M., Horvath, D.P. and Dixon, A. 2001. Preliminary studies directed towards the development of Euphorbiaceae-specific microarrays. In: N.J. Taylor, F. Ogbe and C.M. Fauquet (Eds.), 5th International Scientific Meeting of the Cassava Biotechnology Network: Abstract Book Donald Danforth Plant Science Center, St. Louis, Missouri, pp. S5-02.

  • J.V. Anderson D.P. Horvath (2001) ArticleTitleRandom sequencing of cDNAs and identification of mRNAs Weed Sci. 49 581–589

    Google Scholar 

  • G. Blanc K. Hokamp K.H. Wolfe (2003) ArticleTitleA recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome Genome Res. 13 137–144 Occurrence Handle12566392

    PubMed  Google Scholar 

  • M.S. Boguski T.M. Lowe C.M. Tolstoshev (1993) ArticleTitleDbEST-database for “expressed sequence tags” Nat. Genet. 4 IssueID4 332–333 Occurrence Handle8401577

    PubMed  Google Scholar 

  • J.E. Bowers B.A. Chapman J. Rong A. Paterson (2003) ArticleTitleUnravelling angiosperm genome evolution by phylogenetic analysis of chromosome duplication events Nature 422 433–438 Occurrence Handle10.1038/nature01521 Occurrence Handle12660784

    Article  PubMed  Google Scholar 

  • S. Chang J. Puryer J. Cairney (1993) ArticleTitleA simple and efficient method for isolating RNA from pine trees Plant Mol. Biol. Rep. 11 113–116

    Google Scholar 

  • R. Cooke M. Raynal M. Laudier F. Grellet M. Delseny P.C. Morris D. Guerrier J. Giraudat F. Quigley G. Clabault Y.F. Li R. Mache M. Krivitzky I.J.J. Gy M. Kreis A. Lecharny Y. Parmentier J. Marbach J. Fleck B. Clement G. Phillips C. Herve C. Bardet D. Tremousaygue B. Lescure C. Lacomme D. Roby M.F. Jourjon P. Chabrier J.L. Charpenteau T. Desprez J. Amselem H. Chiapello H. Hofte (1996) ArticleTitleFurther progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs Plant J. 9 101–124 Occurrence Handle10.1046/j.1365-313X.1996.09010101.x Occurrence Handle8580968

    Article  PubMed  Google Scholar 

  • M. Delseny (2003) ArticleTitleTowards an accurate sequence of the rice genome Curr. Opin. Plant Biol. 6 101–105 Occurrence Handle10.1016/S1369-5266(03)00010-4 Occurrence Handle12667864

    Article  PubMed  Google Scholar 

  • I. Dominguez E. Graziano C. Gebhardt A. Barakat S. Berry P. Arus M. Delseny S. Barnes (2003) ArticleTitlePlant genome archeology: evidence for conserved ancestral chromosome segments in dicotyledonous species Plant Biotechnol. J. 1 91–99

    Google Scholar 

  • D.J. Duggan M. Bittner Y. Chen P. Meltzer J.M. Trent (1999) ArticleTitleExpression profiling using cDNA microarrays Nat. Genet. Supplement 21 10–14

    Google Scholar 

  • M.A. Fregene F. Angel R. Gomez F. Rodriguez P. Chavarriaga W. Roca J. Tohme M.W. Bonierbale (1997) ArticleTitleA molecular genetic map of cassava (Manihot esculenta Crantz) Theor. Appl. Genet. 95 431–441 Occurrence Handle10.1007/s001220050580

    Article  Google Scholar 

  • Fregene, M.A., Matsumura, H., Akano, A., and Dixon, A. and Terauchi, R. 2003. Serial analysis of gene expression (SAGE) of host plant resistance to the cassava mosaic disease (CMD). Plant Mol. Biol. (in press)

  • T.M. Fulton R. Hoeven ParticleVan der N.T. Eannetta S.D. Tanksley (2002) ArticleTitleIdentification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants Plant Cell 14 1457–1467 Occurrence Handle12119367

    PubMed  Google Scholar 

  • C. Gebhardt B. Walkemeier H. Henselewski A. Barakat M. Delseny K. Stuber (2003) ArticleTitleComparative mapping between potato (Solanum tuberosum) and Arabidopsis thaliana reveals structurally conserved domains and ancient duplications in the potato genome Plant J. 34 529–541 Occurrence Handle12753591

    PubMed  Google Scholar 

  • S.A. Goff D. Rick e T.-H. Lan G. Presting R. Wang M. Dunn J. Glazebrook A. Sessions P. Oeller H. Varma D. Hadley D. Hutchison C. Martin F. Katagiri B.M. Lange T. Moughamer Y. Xia P. Budworth J. Zhong T. Miguel U. Paszkowski S. Zhang M. Colbert W.-L. Sun L. Chen B. Cooper S. Park T.C. Wood L. Mao P. Quai l R. Wing R. Dean Y. Yu A. Zharkikh R. Shen S. Sahasrabudhe A. Thomas R. Cannings A. Gutin D. Pruss J. Reid S. Tavtigian J. Mitchell G. Eldredge T. Scholl R.M. Miller S. Bhatnagar N. Adey T. Rubano N. Tusneem R. Robinson J. Feldhaus T. Macalma A. Oliphant S. Briggs (2002) ArticleTitleA draft sequence of the rice genome (Oryza sativa L. ssp. japonica) Science 296 92–100 Occurrence Handle10.1126/science.1068275 Occurrence Handle11935018

    Article  PubMed  Google Scholar 

  • R.A. Gutierrez R.M. Ewing J.M. Cherry P.J. Green (2002) ArticleTitleIdentification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch and specific clock-controlled genes Proc. Natl. Acad. Sci. USA. 99 IssueID17 11513–11518 Occurrence Handle12167669

    PubMed  Google Scholar 

  • D.P. Horvath R. Schaffer M. West E. Wisman (2003) ArticleTitleArabidopsis microarrays identify conserved and differentially-expressed genes involved in shoot growth and development from distantly related plant species Plant J. 34 125–134 Occurrence Handle12662315

    PubMed  Google Scholar 

  • V. Jorge M.A. Fregene M.C. Duque M.W. Bonierbale J. Tohme V. Verdier (2000) ArticleTitleGenetic mapping of resistance to bacterial blight disease in cassava (Manihot esculenta Crantz) Theor. Appl. Genet. 101 865–872 Occurrence Handle10.1007/s001220051554

    Article  Google Scholar 

  • V. Jorge M.A. Fregene C.M. Velez M.C. Duque J. Tohme V. Verdier (2001) ArticleTitleQTL analysis of field resistance to Xanthomonas axonopodis pv. manihotis in cassava Theor. Appl. Genet. 102 564–571

    Google Scholar 

  • A. Kohler C. Delaruelle D. Martin N. Encelot F. Martin (2003) ArticleTitleThe poplar root transcriptome: analysis of 7000 expressed sequence tags FEBS Lett. 542 IssueID(1–3) 37–41 Occurrence Handle12729894

    PubMed  Google Scholar 

  • J.M. Lee M.E. Williams S.V. Tingey J.A. Rafalski (2002) ArticleTitleDNA array profiling of gene expression changes during maize embryo development Funct. Integr. Genomics 2 IssueID1–2 13–27 Occurrence Handle12021847

    PubMed  Google Scholar 

  • D. Lespinasse M. Rodier-Gout L. Grivet A. Leconte H. Legnaté M. Seguin (2002) ArticleTitleA saturated genetic linkage map pf rubber tree (Hevea ssp.) based on RFLP, AFLP, microsatellite and isozyme markers Theor. Appl. Genet. 100 975–984

    Google Scholar 

  • J.C. Lozano (1986) ArticleTitleCassava bacterial blight: a manageable disease Plant. Dis. 70 1089–1093

    Google Scholar 

  • R.E.C. Mba P. Stephenson K. Edwards S. Melzer J. Mkumbira U. Gullberg K. Appel M. Gale J. Tohme M.A. Fregene (2001) ArticleTitleSimple sequence repeat (SSR) markers survey of the cassava (Manihot esculenta Crantz) genome: towards an SSR-based molecular genetic map of cassava Theor. Appl. Genet. 101 21–31

    Google Scholar 

  • T.R.I. Munyikwa S. Langeveld S.N.I.M. Salehuzzaman E. Jacobsen R.G.F. Visser (1997) ArticleTitleCassava starch biosynthesis: new avenues for modifying starch quantity and quality Euphytica 96 65–75

    Google Scholar 

  • J. Ohlrogge C. Benning (2000) ArticleTitleUnravelling plant metabolism by EST analysis Curr. Opin. Plant Biol. 3 224–228 Occurrence Handle10837264

    PubMed  Google Scholar 

  • E. Okogbenin M. Fregene (2002) ArticleTitleGenetic analysis and QTL mapping of early root bulking in an F1 population from non-inbred parents in cassava (Manihot esculenta Crantz) Theor. Appl. Genet. 106 58–66 Occurrence Handle12582871

    PubMed  Google Scholar 

  • K.M. Olsen B.A. Schaal (1999) ArticleTitleEvidence on the origin of Cassava: phylogeography of Manihot esculenta Proc. Natl. Acad. Sci. 96 5586–5591 Occurrence Handle10318928

    PubMed  Google Scholar 

  • Z.N. Oztur V. Talame M. Deyholos C.B. Michalowski D.W. Galbraith N. Gozukirmizi R. Tuberosa H.J. Bohnert (2002) ArticleTitleMonitoring large-scale changes in transcript abundance in drought- and salt-stressed barley Plant Mol. Biol. 48 IssueID5–6 551–573 Occurrence Handle11999834

    PubMed  Google Scholar 

  • A.H. Paterson T.H. Lan K.P. Reischmann (1996) ArticleTitleTowards a unified genetic map of higher plants transcending the monocot-dicot divergence Nat. Genet. 14 380–382 Occurrence Handle8944014

    PubMed  Google Scholar 

  • E. Potokina N. Sreenivasulu L. Altschmied W. Michalek A. Graner (2002) ArticleTitleDifferential gene expression during seed germination in barley (Hordeum vulgare L.) Funct. Integr. Genomics 2 IssueID1–2 28–39 Occurrence Handle12021848

    PubMed  Google Scholar 

  • R.C. Quackenbush J. Cho D. Lee F. Liang I. Holt S. Karamycheva B. Parvisi G. Pertea R. Sultana J. White (2001) ArticleTitleThe TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species Nucleic Acids Res. 29 159–164 Occurrence Handle11125077

    PubMed  Google Scholar 

  • S. Restrepo M.C. Duque V. Verdier (2000) ArticleTitleCharacterization of pathotypes among isolates of Xanthomonas axonopodis pv manihotis in Colombia. Plant Pathol. 49 680–687

    Google Scholar 

  • P. Reymond H. Weber M. Damond E.E. Farmer (2000) ArticleTitleDifferential gene expression in response to mechanical wounding and insect feeding in Arabidopsis Plant Cell 12 707–719 Occurrence Handle10810145

    PubMed  Google Scholar 

  • T. Richmond S. Somerville (2000) ArticleTitleChasing the dream: plant EST microarrays Curr. Opin. Plant Biol. 3 108–116 Occurrence Handle10712953

    PubMed  Google Scholar 

  • J. Salse B. Piegu R. Cooke M. Delseny (2002) ArticleTitleSynteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequence project Nucleic Acids Res. 30 2316–2328 Occurrence Handle12034818

    PubMed  Google Scholar 

  • J. Sambrook E.F. Fritsch T. Maniatis (1989) Molecular Cloning–A Laboratory Manual 2nd edn. Cold Spring Harbor Laboratory Press New York, USA

    Google Scholar 

  • M. Schena D. Shalon R.W. Davis P.O. Brown (1995) ArticleTitleQuantitative monitoring of gene expression patterns with a complementary DNA microarray Science 270 467–470 Occurrence Handle7569999

    PubMed  Google Scholar 

  • C. Schöpke N. Taylor R. Carcamo K.K. N’Da P. Marmey G.G. Henshaw R.N. Beachy C.M. Fauquet (1996) ArticleTitleRegeneration of transgenic cassava plants (Manihot esculenta Crantz) from microbombarded embryogenic suspension cultures Nat. Biotechnol. 14 731–735

    Google Scholar 

  • M. Seki M. Narusaka A. Kamiya J. Ishida M. Satou T. Sakurai M. Nakajima A. Enju K. Akiyama Y. Oono M. Muramatsu Y. Hayashizaki J. Kawai P. Carninci M. Itoh Y. Ishii T. Arakawa K. Shibata A. Shinagawa K. Shinozaki (2002) ArticleTitleFunctional annotation of a full-length Arabidopsis cDNA collection Science 296 141–145 Occurrence Handle11910074

    PubMed  Google Scholar 

  • C. Simillion K. Vandepoele M.C. Montagu ParticleVan M. Zabeau Y. Peer ParticleVan de (2002) ArticleTitleThe hidden duplication past of Arabidopsis thaliana Proc. Natl. Acad. Sci. 15 13627–13632

    Google Scholar 

  • The Arabidopsis Genome Initiative (2000) ArticleTitleAnalysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 408 796–815 Occurrence Handle11130711

    PubMed  Google Scholar 

  • C. Uhde-Stone K.E. Zinn M. Ramirez-Yanez A. Li C.P. Vance D.L. Allan (2003) ArticleTitleNylon filter arrays reveal differential gene expression in proteoid roots of white lupin in response to phosphorus deficiency Plant Physiol. 131 1064–1079 Occurrence Handle12644659

    PubMed  Google Scholar 

  • F.J. Loo ParticleVan de S. Turner C. Somerville (1995) ArticleTitleExpressed sequence tags from developing castor seed Plant Physiol. 108 1141–1150 Occurrence Handle12228533

    PubMed  Google Scholar 

  • N.L.W. Hal ParticleVan O. Vorst A.M.M.L. Houwelingen Particlevan E.J. Kok A. Peijnenburg A. Aharoni A.J. Tunen Particlevan J. Keijer (2000) ArticleTitleThe application of microarrays in gene expression analysis J. Biotech. 78 271–280

    Google Scholar 

  • K.H. Wolfe (2001) ArticleTitleYesterday’s polyploids and the mystery of diploidization Nature Rev. Genet. 2 333–341

    Google Scholar 

  • T. Zhu P. Budworth W. Chen N. Provart H.S. Chang S. Guimil W. Su B. Ester G.Z. Zou X. Wang (2003) ArticleTitleTranscriptional control of nutrient partitioning during rice grain filling Plant Biotechnol. J. 1 59–70

    Google Scholar 

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Authors and Affiliations

  1. USDA/ARS, Biosciences Research Laboratory, 1605 Albrecht Blvd., P.O. Box 5674, State University Station, Fargo, ND, 58105, USA

    James V. Anderson & David P. Horvath

  2. University of Perpignan, Genome and Plant Development Laboratory, UMR 5096 CNRS-IRD-UP, 52, Avenue Paul Alduy, 66860, Perpignan, France

    Michel Delseny, Veronique Jorge, Camilo Lopez, Benoit Piegu, Valerie Verdier & Richard Cooke

  3. International Center for Tropical Agriculture (CIAT), AA6713, Cali, Colombia

    Martin A. Fregene, Chikelu Mba, Silvia Restrepo, Mauricio Soto & Joe Tohme

  4. INRA, Unite Amelioration Genetique et Physiologie Forestieres, Av de la pomme de pin, BP 20619, ARDON, OLIVET Cedex, 45166, France

    Veronique Jorge

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  1. James V. Anderson
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  2. Michel Delseny
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  3. Martin A. Fregene
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  5. Chikelu Mba
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  9. Benoit Piegu
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  10. Valerie Verdier
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  12. Joe Tohme
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  13. David P. Horvath
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Correspondence to James V. Anderson.

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Anderson, J.V., Delseny, M., Fregene, M.A. et al. An EST resource for cassava and other species of Euphorbiaceae. Plant Mol Biol 56, 527–539 (2004). https://doi.org/10.1007/s11103-004-5046-6

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