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Transcriptome Analysis of The Sugarcane Genome For Crop Improvement

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Genomics-Assisted Crop Improvement

Abstract

Sugarcane is being considered one the most important crops to meet the demand of the world bionergy needs. However the productivity in commercial plantations around the world is far way from its potential of about 300 tons/ha. Sugarcane breeding did not take advantage yet of the best plant breeding technologies, mainly because constrains imposed by the high polyploid nature of its genome. Even transgenic technologies would face difficulties because of the complex behaviour of introduced genes regarding the chromosome where the gene is inserted. One important resource to overcome at least part of these difficulties is the availability of a large collection of sugarcane Expressed Sequence Tags. The transcriptome information has allowed the identification of genes involved in biotic and abiotic stress response, disease resistance and sucrose accumulation. In additioncomparative mapping has allowed the identification in sugarcane disease resistance genes already mapped in sorghum and maize. In this chapter we discuss the use of transcriptome resources for sugarcane improvement.

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References

  • Alexander AG (1985) The energy cane alternative. Elsevier, New York

    Google Scholar 

  • Araujo PG, Rossi M, de Jesus EM, Saccaro NL Jr, Kajihara D, Massa R, de Felix JM, Drummond RD, Falco MC, Chabregas SM, Ulian EC, Menossi M, Van Sluys MA (2005) Transcriptionally active transposable elements in recent hybrid sugarcane. Plant J 44:707–717

    Article  PubMed  CAS  Google Scholar 

  • Arruda P (2001) Sugarcane transcriptome: a landmark in plant genomics in the tropics. Genet Mol Biol 24:1–296

    Article  Google Scholar 

  • Asnaghi C, Paulete F, Kaye C, Grivet L, Deu M, Glaszmann J-C, D’Hont A (2000) Application of synteny across Poaceae to determine the map location of a sugarcane rust resistance gene. Theor Appl Genet 101:962–969

    Article  CAS  Google Scholar 

  • Asnaghi C, Roques D, Ruffel S, Kaye C, Hoarau JY, Telismart H, Girard JC, Raboin LM, Risterucci AM, Grivet L, D’Hont A (2004) Targeted mapping of a sugarcane rust resistance gene (Bru1) using bulked segregant analysis and AFLP markers. Theor Appl Genet 108:759–64

    Article  PubMed  CAS  Google Scholar 

  • Bennetzen JL, Freeling M (1993) Grasses as a single genetic system: genome composition, collinearity and compatibility. Trends Genet 9:259–261

    Article  PubMed  CAS  Google Scholar 

  • Bennetzen JL, Freeling M (1997) The unified grass genome: synergy in synteny. Genome Res 7:301–306

    PubMed  CAS  Google Scholar 

  • Berding N, Roach BT (1987) Germplasm collection, maintenance, and use. In: Heinz DJ (ed) Sugarcane improvement through breeding. Elsevier, New York, pp 143–210

    Google Scholar 

  • Borecký J, Nogueira FTS, de Oliveira KAP, Maia IG, Vercesi AE, Arruda P (2006) The plant energy-dissipating mitochondrial systems: depicting the genomic structure and the expression profiles of the gene families of uncoupling protein and alternative oxidase in monocots and dicots. J Exp Bot 57:849–864

    Article  PubMed  Google Scholar 

  • Botha FC, Black KG (2000) Sucrose phosphate synthase and sucrose synthase activity during maturation of internodal tissue in sugarcane. Aust J Plant Physiol 27:81–85

    CAS  Google Scholar 

  • Bower NI, Casu RE, Maclean DJ, Reverter A, Chapmann SC, Manners JM (2005) Transcriptional response of sugarcane roots to methyl jasmonate. Plant Sci 168:761–772

    Article  CAS  Google Scholar 

  • Bull TA, Glasziou KT (1963) The evolutionary significance of sugar accumulation in Saccharum. Aust J Biol Sci 16:737–742

    Google Scholar 

  • Butterfield MK, D’Hont A, Berding N (2001) The sugarcane genome: a synthesis of current understanding, and lessons for breeding and biotechnology. Proc S Afr Sug Technol Ass 75:1–5

    Google Scholar 

  • Carson DL, Botha FC (2000) Preliminary analysis of expressed sequence tags for sugarcane. Crop Sci 40:1769–1779

    Article  CAS  Google Scholar 

  • Casu RE, Grof CPL, Rae AL, McIntyre CL, Dimmock CM, Manners JM (2003) Identification of a novel sugar transporter homologue strongly expressed in maturing stem vascular tissues of sugarcane by expressed sequence tag and microarray analysis. Plant Mol Biol 52:371–386

    Article  PubMed  CAS  Google Scholar 

  • Casu RE, Dimmock CM, Chapman SC, Grof CPL, McIntyre CL, Bonnett GD, Manners JM (2004) Identification of differentially expressed transcripts from maturing stem of sugarcane by in silico analysis of stem expressed sequence tags and gene expression profiling. Plant Mol Biol 54:503–517

    Article  PubMed  Google Scholar 

  • Casu RE, Manners JM, Bonnett GD, Jackson PA, McIntyre CL, Dunne R, Chapman SC, Rae AL, Grof CPL (2005) Genomics approaches for the identification of genes determining important traits in sugarcane. Field Crop Res 92:137–147

    Article  Google Scholar 

  • Cordeiro GM, Eliott F, McIntyre CL, Casu RE, Henry RJ (2006) Characterisation of single nucleotide polymorphisms in sugarcane ESTs. Theor Appl Genet 113:331–343

    Article  PubMed  CAS  Google Scholar 

  • Da Silva JA, Bressiani JA (2005) Sucrose synthase molecular marker associated with sugar content in elite sugarcane progeny. Genet Mol Biol 28:294–298

    Google Scholar 

  • de Rosa VE Jr, Nogueira FTS, Menossi M, Ulian EC, Arruda P (2005) Identification of methyl jasmonate-responsive genes in sugarcane using cDNA arrays. Braz J Plant Physiol 17:173–180

    Article  Google Scholar 

  • D’Hont A (2005) Unravelling the genome structure of polyploids using FISH and GISH; examples of sugarcane and banana. Cytogent Genomics Res 109:27–33

    Article  CAS  Google Scholar 

  • D’Hont A, Glaszmann JC (2001) Sugarcane genome analysis with molecular markers, a first decade of research. Proc Int Soc Sugarcane Technol 24:556–559

    Google Scholar 

  • Dufour P, Deu M, Grivet L, D’Hont A, Paulet F, Bouet A, Lanaud C, Glaszmann JC, Hamon P (1997) Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid. Theor Appl Genet 94:409–418

    Article  CAS  Google Scholar 

  • Gianotti A, Rios WM, Soares-Costa A, Nogaroto V, Carmona AK, Oliva ML, Andrade SS, Henrique-Silva F (2006) Recombinant expression, purification, and functional analysis of two novel cystatins from sugarcane (Saccharum officinarum). Protein Expr Purif 47:483–489

    Article  PubMed  CAS  Google Scholar 

  • Glaszmann JC, Dufour P, Grivet L, D’Hont A, Deu M, Paulet F, Hamon P (1997) Comparative genome analysis between several tropical grasses. Euphytica 96:13–21

    Article  CAS  Google Scholar 

  • Graham MA, Marek LF, Lohnes D, Cregan P, Schoemaker RC (2000) Expression and genome organization of resistance gene analogs in soybean. Genome 43:86–93

    Article  PubMed  CAS  Google Scholar 

  • Grivet L, Arruda P (2002) Sugarcane genomics: depicting the complex genome of an important tropical crop. Curr Opin Plant Biol 5:122–127

    Article  PubMed  CAS  Google Scholar 

  • Grivet L, Glaszmann JC, Vincentz M, da Silva FR, Arruda P (2003) ESTs as a source for sequence polymorphism discovery in sugarcane: example of the Adh genes. Theor Appl Genet 106:190–197

    PubMed  CAS  Google Scholar 

  • Guimarães CT, Sills GR, Sobral BWS (1997) Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize. Proc Natl Acad Sci USA 94:14261–14266

    Article  PubMed  Google Scholar 

  • Huang, X, Madan, A (1999). CAP3: a DNA sequence assembly program. Genome Res 9:868–877

    Google Scholar 

  • Jannoo N, Grivet L, D’Hont A, Arruda P (2003) Genomic sequencing in sugarcane: first insight into the physical organization of the genome and microsynteny with other grasses. Abstracts of PAG XI Conference, San Diego, Abstract W182. URL: http://www.intl-pag.org// 11/abstracts/ W26_W182_XI.html

    Google Scholar 

  • Ma HM, Schulze S, Lee S, Yang M, Mirkov E, Irvine J, Moore P, Paterson A (2004) An EST survey of the sugarcane transcriptome. Theor Appl Genet 108:851–63

    Article  PubMed  Google Scholar 

  • McIntyre CL (2004) Homologues of the maize rust resistance gene Rp1-D are genetically associated with a major rust resistance QTL in sorghum. Theor Appl Genet 109:875–883

    Article  PubMed  CAS  Google Scholar 

  • McIntyre CL, Casu RE, Drenth J, Knight D, Whan VA, Croft BJ, Jordan DR, Manners JM (2005) Resistance gene analogues in sugarcane and sorghum and their association with quantitative trait loci for rust resistance. Genome 48:391–400

    Article  PubMed  CAS  Google Scholar 

  • Michelmore RW, Meyers BC (1998) Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res 8:1113–1130

    PubMed  CAS  Google Scholar 

  • Ming R et al (1998) Alignment of the Sorghum and Saccharum chromosomes: comparative genome organization and evolution of a polysomic polyploid genus and its diploid cousin. Genetics 150:1663–1682

    PubMed  CAS  Google Scholar 

  • Moore P (1995) Temporal and spatial regulation of sucrose accumulation in the sugarcane stem. Aust J Plant Physiol 22:661–679

    Article  CAS  Google Scholar 

  • Nogueira FTS, de Rosa VE, Menossi M, Ulian EC, Arruda P (2003) RNA expression profiles and data mining of sugarcane response to low temperature. Plant Physiol 132:1811–1824

    Article  PubMed  CAS  Google Scholar 

  • Nogueira FTS, Schlogl PS, Camargo SR, Fernandez JH, de Rosa VE, Pompermayer P, Arruda P (2005) SsNAC23, a member of the NAC domain protein family, is associated with cold, herbivory and water stress in sugarcane. Plant Sci 169:93–106

    Article  CAS  Google Scholar 

  • Papini-Terzi FS, Rocha FR, Vêncio RZN, Oliveira KC, Felix JM, Vicentini R, Rocha CS, Simões ACQ, Ulian EC, di Mauro SMZ, da Silva AM, Pereira CAB, Menossi M, Souza GM (2005) Transcription profiling of signal transduction-related genes in sugarcane tissues. DNA Res 12:27–38

    Article  PubMed  CAS  Google Scholar 

  • Pinto LR, Oliveira KM, Ulian EC, Garcia AAF, de Souza AP (2004) Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats. Genome 47:795–804

    Article  PubMed  CAS  Google Scholar 

  • Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR et al (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290:2105–2110

    Article  PubMed  CAS  Google Scholar 

  • Rossi M, Araujo PG, Paulet F, Garsmeur O, Dias VM, Chen H, Van Sluys MA, D’Hont A (2004b) Genomic distribution and characterization of EST-derived resistance gene analogs (RGAs) in sugarcane. Mol Genet Genomics 269:406–419

    Article  CAS  Google Scholar 

  • Rossi M, Araujo PG, de Jesus EM, Varani AM, Van Sluys MA (2004a) Comparative analysis of Mutator-like transposases in sugarcane. Mol Genet Genomics 272:194–203

    Article  CAS  Google Scholar 

  • Rossi M, Araujo PG, Paulet F, Garsmeur O, Dias V, Hui C, Van Sluys MA, D’Hont A (2003) Genome distribution and characterization of EST derived sugarcane resistance gene analogs. Mol Genet Genomics 269:406–419

    Article  PubMed  CAS  Google Scholar 

  • Souza GM et al (2001) The sugarcane signal transduction (SUCAST) catalogue: prospecting signal transduction in sugarcane. Genet Mol Biol 24:25–34

    Article  CAS  Google Scholar 

  • Sreenivasan TV, Ahloowalia BS, Heinz DJ (1987) Cytogenetics. In: Heinz DJ (ed) Sugarcane improvement through breeding. Elsevier, New York, pp 211–253

    Google Scholar 

  • Telles GP, da Silva FR (2001) Trimming and clustering sugarcane ESTs. Genet Mol Biol 24:17–23

    CAS  Google Scholar 

  • Vercesi AE, Borecký J, Maia IG, Arruda P, Cuccovia IM, Chaimovich H (2006) Plant uncoupling mitochondrial proteins. Annu Rev Plant Biol 57:383–404

    Article  PubMed  CAS  Google Scholar 

  • Vettore AL, da Silva FR, Kemper EL, Arruda P (2001) The libraries that made SUCEST. Genet Mol Biol 24:1–7

    Article  CAS  Google Scholar 

  • Vettore AL et al (2003) Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane. Genome Res 13:2725–2735

    Article  PubMed  Google Scholar 

  • Vincentz M et al (2004) Evaluation of monocot and eudicot divergence using the sugarcane transcriptome. Plant Physiol 134:951–959

    Article  PubMed  CAS  Google Scholar 

  • Walsh KB, Sky RB, Brown SM (2005) The anatomy of the pathway of sucrose unloading within the sugarcane stem. Funct Plant Biol 32:367–374

    Article  CAS  Google Scholar 

  • Wang M-B, Wesley SV, Finnegan EJ, Smith NA, Waterhouse PM (2001) Replicating satellite RNA induces sequence-specific DNA methylation and truncated transcripts in plants. RNA 7:16–28

    Article  PubMed  CAS  Google Scholar 

  • Whittaker A, Botha FC (1997) Carbon partitioning during sucrose accumulation in sugarcane internodal tissue. Plant Physiol 115:1651–1659

    PubMed  CAS  Google Scholar 

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Arruda, P., Silva, T.R. (2007). Transcriptome Analysis of The Sugarcane Genome For Crop Improvement. In: Varshney, R.K., Tuberosa, R. (eds) Genomics-Assisted Crop Improvement. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-6297-1_18

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