Skip to main content

Advertisement

SpringerLink
Log in

Transcriptome Analysis and Functional Genomics of Sugarcane

  • Published:
Tropical Plant Biology Aims and scope Submit manuscript

Abstract

Sugarcane is a genetically complex polyploid with increasing economic importance as a feedstock for biofuel production. The characterization of sugarcane genes and their association with biological traits such as sugar accumulation, biomass yield and stress tolerance has so far primarily relied on studies of the sugarcane transcriptome. Associations of gene expression with biological traits have been based on alterations in the timing and intensity of gene expression with various treatments and developmental stages, and in some instances, by genotypic correlations using segregating populations or genotypes contrasting for traits. The transcriptome of sugarcane is complex and includes transcripts of homo(eo)logues reflecting the highly polyploid genome of commercial sugarcane hybrids derived recently from two Saccharum species. The impact of this genomic complexity on transcription will be greatly informed by data emerging from the International Sugarcane Genome Sequencing Project. Increasingly, expressed gene sequences are exploited as genetic markers for traits in genome mapping and association studies. Reverse genetics approaches are possible in sugarcane but only very few sugarcane genes have had their specific functions examined in transgenic sugarcane plants. An integration of genome, transcriptome and metabolome data is emerging that will inform the molecular breeding of this important sugar and energy crop.

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

Similar content being viewed by others

References

  • Aitken KS, Hermann S, Karno K, Bonnett GD, McIntyre LC, Jackson PA (2008) Genetic control of yield related stalk traits in sugarcane. Theor Appl Genet 117:1191–1203

    Article  CAS  PubMed  Google Scholar 

  • Arencibia AD, Carmona ER, Tellez P, Chan MT, Yu SM, Trujillo LE, Oramos P (1998) An efficient protocol for sugarcane (Saccharum spp. L) transformation mediated by Agrobacterium tumefaciens. Transgenic Res 7:213–222

    Article  CAS  Google Scholar 

  • Basnayake SWV, Moyle R, Birch RG (2010) Embryogenic callus proliferation and regeneration conditions for genetic transformation of diverse sugarcane cultivars. Plant Cell Rep in press. doi:10.1007/s00299-010-0927-4

  • Beyene G, Buenrostro-Nava MT, Damaj MB, Gao S-J, Molina J, Mirkov TE (2010) Unprecedented enhancement of transient gene expression from minimal cassettes using a double terminator. Plant Cell Rep, in press. doi:10.1007/s00299-010-0936-3

  • Birch RG, Bower RS, Elliott AR (2010) Highly efficient, 5′-sequence-specific transgene silencing in a complex polyploidy. Trop Plant Biol 3:88–97

    Article  CAS  Google Scholar 

  • Borecky 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  CAS  PubMed  Google Scholar 

  • Borras-Hidalgo O, Thomma BPHJ, Carmona E, Borroto CJ, Pujol M, Arencibia A, Lopez J (2005) Identification of genes induced in disease-resistant somaclones upon inoculation with Ustilago scitaminea or Bipolaris sacchari. Plant Physiol Biochem 43:1115–1121

    Article  CAS  PubMed  Google Scholar 

  • Botha FC (2009) Energy yield and cost in a sugarcane biomass system. Proc Aust Soc Sugar Cane Technol 31:1–10

    Google Scholar 

  • Botha F, Sawyer B, Birch R (2001) Sucrose metabolism in the culm of transgenic sugarcane with reduced soluble acid invertase activity. Proc International Soc Sugarcane Technologists XXIV Congress ASSCT, Mackay, pp 588–591

    Google Scholar 

  • Bower R, Birch RG (1992) Transgenic sugarcane plants via microprojectile bombardment. Plant J 2:409–416

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Broderson P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, Voinnet O (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 320:1185–1190

    Article  Google Scholar 

  • Bundock PC, Elliot FG, Ablett G, Benson AD, Casu RE, Aitken KS, Henry RJ (2009) Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploidy plant species using 454 sequencing. Plant Biotechnol J 7:347–354

    Article  CAS  PubMed  Google Scholar 

  • Calsa T Jr, Figueira A (2007) Serial analysis of gene expression in sugarcane (Saccharum spp.) leaves revealed alternative C4 metabolism and putative antisense transcripts. Plant Mol Biol 63:745–762

    Article  CAS  PubMed  Google Scholar 

  • Calvino M, Bruggmann R, Messing J (2008) Screen of genes linked to high-sugar content in stems by comparative genomics. Rice 1:166–176

    Article  Google Scholar 

  • Camargo SR, Cancado GMA, Ulian EC, Menossi M (2007) Identification of genes responsive to the application of ethanol on sugarcane leaves. Plant Cell Rep 26:2119–2128

    Article  CAS  PubMed  Google Scholar 

  • Carmona E, Vargas D, Borroto CJ, Lopez J, Fernandez AI, Arencibia A, Borras-Hidalgo O (2004) cDNA-AFLP analysis of differential gene expression during the interaction between sugarcane and Puccinia melanocephala. Plant Breed 123:499–501

    Article  CAS  Google Scholar 

  • Carson D, Huckett B, Botha F (2002) Differential gene expression in sugarcane leaf and intermodal tissues of varying maturity. S Afr J Bot 68:434–442

    CAS  Google Scholar 

  • Casu RE (2010) Role of bioinfomatics as a tool for sugarcane research. In: Henry R, Kole C (eds) Genetics, genomics and breeding of sugarcane. CRC Press, Science Publishers, Enfield, pp 229–248

    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  CAS  PubMed  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 Crops Res 92:137–147

    Article  Google Scholar 

  • Casu RE, Jarmey JM, Bonnett GD, Manners JM (2007) Identification of transcripts associated with cell wall metabolism and development in the stem of sugarcane by Affymetrix GeneChip Sugarcane Genome Array expression profiling. Funct Integr Genomics 7:153–167

    Article  CAS  PubMed  Google Scholar 

  • Casu RE, Hotta C, Souza GM (2010) Functional genomics: transcriptomics of sugarcane. In: Henry R, Kole C (eds) Genetics, genomics and breeding of sugarcane. CRC Press, Science Publishers, Enfield, pp 167–191

    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  CAS  PubMed  Google Scholar 

  • D’Hont A, Grivet L, Feldmann P, Rao S, Berding N, Glaszmann JC (1996) Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics. Mol Gen Genet 250:405–413

    PubMed  Google Scholar 

  • Damaj MB, Kumpatla SP, Emani C, Beremand PD, Reddy AS, Rathore KS, Buenrostro-Nava MT, Curtis IS, Thomas TL, Mirkov TE (2010a) Sugarcane Dirigent and O-methyltransferase promoters confer stem-regulated gene expression in diverse monocots. Planta 231:1439–1458

    Article  CAS  PubMed  Google Scholar 

  • Damaj MB, Beremand PD, Buenrostro-Nava MT, Ivy J, Kumpatla SP, Jifon J, Beyene G, Yu Q, Thomas TL, Mirkov TE (2010b) Isolating promoters of multigene family members from the polyploidy sugarcane genome by PCR-based walking in BAC DNA. Genome 53:840–847

    Article  CAS  PubMed  Google Scholar 

  • de 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 M-A (2005) Transcriptionally active transposable elements in recent hybrid sugarcane. Plant J 44:707–717

    Article  PubMed  Google Scholar 

  • de Souza AP, Gaspar M, da Silva EA, Ulian EC, Waclawovsky AJ, Nishiyama MY Jr, Dos Santos RV, Teixeira MM, Souza GM, Buckeridge MS (2008) Elevated CO2 increases photosynthesis, biomass and productivity, and modifies gene expression in sugarcane. Plant Cell Environ 31:1116–1127

    Article  PubMed  Google Scholar 

  • Elliott AR, Campbell JA, Brettell RIS, Grof CPL (1998) Agrobacterium-mediated transformation of sugarcane using GFP as a screenable marker. Aus J Plant Physiol 25:739–743

    Article  CAS  Google Scholar 

  • FAO (2008) Food and Agricultural Organisation of the United Nations. Website: http://faostat.fao.org/site/291/default.aspx

  • Felix JM, Papini-Terzi FS, Rocha FR, Vencio RZN, Vicentini R, Nishiyama MY Jr, Ulian EC, Souza GM, Menossi M (2009) Expression profile of signal transduction components in a sugarcane population segregating for sugar content. Trop Plant Biol 2:98–109

    Article  CAS  Google Scholar 

  • Ficklin SP, Luo F, Feltus FA (2010) The association of multiple interacting genes with specific phenotypes in rice using gene co-expression networks. Plant Physiol 154:13–24

    Article  CAS  PubMed  Google Scholar 

  • Garsmeur O, Charron C, Bocs S, Jouffe V, Samain S, Couloux A, Droc G, Zini C, Glaszmann J-C, Van Sluys M-A, D’Hont A (2010) High homologous gene conservation despite extreme autoploid redundancy in sugarcane. New Phytol in press. doi:10.1111/j.1469-8137.2010.03497.x

  • Glassop D, Roessner U, Bacic A, Bonnett GD (2007) Changes in the sugarcane metabolome with stem development. Are they related to sucrose accumulation? Plant Cell Physiol 48:573–584

    Article  CAS  PubMed  Google Scholar 

  • Goldemberg J (2008) The Brazilian biofuels industry. Biotech for Biofuels 1:6. doi:10.1186/1754-6834-1-6

    Google Scholar 

  • Gomes de Oliveira Dal’Molin C, Quek L-E, Palfreyman RW, Brumbley SM, Nielsen LK (2010) C4GEM—a genome-scale metabolic model to study C4 plant metabolism. Plant Physiol, in press. doi:10.1104/pp.110.166488

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

    CAS  PubMed  Google Scholar 

  • Groenewald J-H, Botha FC (2008) Down-regulation of pyrophosphate:fructose 6-phosphate 1-phosphotransferase (PFP) activity in sugarcane enhances sucrose accumulation in immature internodes. Transgenic Res 17:85–92

    Article  CAS  PubMed  Google Scholar 

  • Grof CPL, So CTE, Perroux JM, Bonnett GD, Forrester RI (2006) The five families of sucrose-phosphate synthase genes in Saccharum spp. are differentially expressed in leaves and stem. Funct Plant Biol 33:605–610

    Article  CAS  Google Scholar 

  • Gupta V, Raghuvanshi S, Gupta A, Saini N, Gaur A, Khan MS, Gupta RS, Singh J, Duttamajumder SK, Srtivastava S, Suman A, Khurana JP, Kapur R, Tyagi AK (2010) The water-deficit stress- and red-rot-related genes in sugarcane. Funct Integr Genomics 10:207–214

    Article  CAS  PubMed  Google Scholar 

  • Haas BJ, Zody MC (2010) Advancing RNA-Seq analysis. Nat Biotechnol 28:421–423

    Article  CAS  PubMed  Google Scholar 

  • He F, Zhou Y, Zhang Z (2010) Deciphering floral transition process by integrating a protein-protein interaction network and gene expression data. Plant Physiol 153:1492–1505

    Article  CAS  PubMed  Google Scholar 

  • Heller-Uszynska K, Uszynski G, Huttner E, Evers M, Carlig J, Caig V, Aitken K, Jackson P, Piperidis G, Cox M, Gilmour R, D’Hont A, Butterfield M, Glaszmann J-C, Kilian A (2010) Diversity arrays technology effectively reveals DNA polymorphism in a large and complex genome of sugarcane. Mol Breeding, in press. doi:10.1007/s11032-010-9460-y

  • Hotta CT et al (2010) The biotechnology roadmap for sugarcane improvement. Trop Plant Biol 3:75–87

    Article  CAS  Google Scholar 

  • Iskandar HM, Simpson RS, Casu RE, Bonnett GD, Maclean DJ, Manners JM (2004) Comparison of reference genes for quantitative real-time PCR analysis of gene expression in sugarcane. Plant Mol Biol Rep 22:325–337

    Article  CAS  Google Scholar 

  • Iskander HM, Casu RE, Fletcher AT, Schmidt S, Xu J, Maclean DJ, Manners JM, Bonnett GD (2011) Identification of drought-response genes and study of their expression during sucrose accumulation and water deficit in sugarcane. BMC Plant Biology 11:12. doi:10.1186/1471-2229-11-12

    Article  Google Scholar 

  • Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucl Acids Res 29:e25

    Article  CAS  PubMed  Google Scholar 

  • Jackson S, Chen ZJ (2010) Genomic and expression plasticity of polyploidy. Curr Op Plant Biol 13:153–159

    Article  CAS  Google Scholar 

  • Jackson MA, Rae AL, Casu RE, Grof CPL, Bonnett GD, Maclean DJ (2007) A bioinformatic approach to the identification of a conserved domain in a sugarcane legumain that directs GFP to the lytic vacuole. Funct Plant Biol 34:633–644

    Article  CAS  Google Scholar 

  • Jannoo N, Grivet L, Chantret N, Garsmeur O, Glaszmann J-C, Arruda P, D’Hont A (2007) Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome. Plant J 50:574–585

    Article  CAS  PubMed  Google Scholar 

  • Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53

    Article  CAS  PubMed  Google Scholar 

  • Joyce P, Kuwahata M, Turner N, Lakshmanan P (2010) Selection systems and co-cultivation medium are important determinants of Agrobacterium-mediated transformation of sugarcane. Plant Cell Rep 29:173–183

    Article  CAS  PubMed  Google Scholar 

  • Kaufmann K, Pajoro A, Angenent GC (2010) Regulation of transcription in plants: mechanisms controlling developmental switches. Nat Rev Genet 11:830–842

    Article  CAS  PubMed  Google Scholar 

  • Lawrence RJ, Pikaard CS (2003) Transgene-induced RNA interference: a strategy for overcoming gene redundancy in polyploids to generate loss-of-function mutations. Plant J 36:114–121

    Article  CAS  PubMed  Google Scholar 

  • le Cunff L, Garsmeur O, Raboin LM, Pauquet J, Telismart H, Selvi A, Grivet L, Philippe R, Begum D, Deu M, Costet L, Wing R, Glaszmann JC, D’Hont A (2008) Diploid/polyploid syntenic shuttle mapping and haplotype-specific chromosome walking towards a rust resistance gene (Bru1) in highly polyploidy sugarcane (2n 12× 115). Genetics 180:649–660

    Article  PubMed  Google Scholar 

  • Li X, Weng J-K, Chapple (2008) Improvement of biomass through lignin modification. Plant J 54:569–581

    Article  CAS  PubMed  Google Scholar 

  • Matsuoka S, Ferro J, Arruda P (2009) The Brazilian experience of sugarcane ethanol industry. In Vitro Cell Dev Biol Plant 45:372–381

    Article  Google Scholar 

  • McCormick AJ, Cramer MD, Watt DA (2008) Differential expression of genes in the leaves of sugarcane in response to sugar accumulation. Trop Plant Biol 1:142–158

    Article  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  CAS  PubMed  Google Scholar 

  • Mezker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31–45

    Article  Google Scholar 

  • Mudge SR, Osabe K, Casu RE, Bonnett GD, Manners JM, Birch RG (2009) Efficient silencing of reporter transgenes coupled to known functional promoters in sugarcane, a highly polyploidy crop species. Planta 229:549–558

    Article  CAS  PubMed  Google Scholar 

  • Nass LL, Pereira PAA, Ellis D (2007) Biofuels in Brazil: an overview. Crop Sci 47:2228–2237

    Article  Google Scholar 

  • Nogueira FTS, De Rosa VE Jr, 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  CAS  PubMed  Google Scholar 

  • Nogueira FTS, Schlögl PS, Camargo SR, Fernandez JH, De Rosa VE Jr, 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 

  • Osabe K, Mudge S, Graham M, Birch R (2009) RNAi mediated down-regulation of PDS gene expression in sugarcane (Saccharum), a highly polyploid crop. Trop Plant Biol 2:143–148

    Article  CAS  Google Scholar 

  • Papini-Terzi FS, Rocha FR, Vencio RZ, Oliveira KC, Felix JM, Vicentini R, Rocha CS, Simoes AC, Ulian EC, Zingaretti di Mauro SM, Da Silva AM, de Braganca Pereira CA, Menossi M, Mendes Souza G (2005) Transcription profiling of signal transduction-related genes in sugarcane tissues. DNA Res 12:27–38

    Article  CAS  PubMed  Google Scholar 

  • Papini-Terzi FS, Rocha FR, Vencio RZN, Felix JM, Branco DS, Waclawovsky AJ, Del Bem LEV, Lembke CG, Costa MDL, Nishiyama MY Jr, Vicentini R, Vicentz MGA, Ulian EC, Menossi M, Souza GM (2009) Sugarcane genes associated with sucrose content. BMC Genomics 10:120

    Article  PubMed  Google Scholar 

  • Patade VY, Rai AN, Suprassana P (2010) Expression of a sugarcane shaggy-like kinase (SuSK) gene identified through cDNA subtractive hybridisation in sugarcane (Saccharum officinarum L.) Protoplasma. doi:10.1007/s00709-010-0207-8

  • Paterson AH et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–548

    Article  CAS  PubMed  Google Scholar 

  • Paterson AH, Souza G, Van Sluys M-A, Ming R, D’Hont A (2010) Structural genomics and genome sequencing. In: Henry R, Kole C (eds) Genetics, genomics and breeding of sugarcane. CRC Press, Science Publishers, Enfield, pp 149–165

    Google Scholar 

  • Pinto LR, Garcia AAF, Pastina MM, Teixeira LHM, Bressiani JA, Ulian EC, Bidoia MAP, Souza AP (2010) Analysis of genomic and functional RFLP derived markers associated with sucrose content, fiber, and yield QTLs in a sugarcane (Saccharum spp.) commercial cross. Euphytica 172:313–327

    Article  CAS  Google Scholar 

  • Prabu G, Kawar PG, Pagariya MC, Prasad DT (2010) Identification of water-deficit stress-upregulated genes in sugarcane. Plant Mol Biol Rep. doi:10.1007/s11105-010-0230-0

    Google Scholar 

  • Rae AL, Grof CPL, Casu RE, Bonnett GD (2005a) Sucrose accumulation in the sugarcane stem: pathways and control points for transport and compartmentation. Field Crops Res 92:159–168

    Article  Google Scholar 

  • Rae AL, Perroux JM, Grof CPL (2005b) Sucrose partitioning between vascular bundles and storage parenchyma in the sugarcane stem: a potential role for the ShSUT1 sucrose transporter. Planta 220:817–825

    Article  CAS  PubMed  Google Scholar 

  • Raghuwanshi A, Birch RG (2010) Genetic transformation of sweet sorghum. Plant Cell Rep 29:997–1005

    Article  CAS  PubMed  Google Scholar 

  • Rocha FR, Papini-Terzi FS, Nishiyama MY Jr, Vencio RZN, Vicentini R, Duarte RDC, De Rosa VE Jr, Vinagre F, Barsalobres C, Medeiros AH, Rodrigues FA, Ulian EC, Zingaretti SM, Galbiatti JA, Almeida RS, Figueira AVO, Hemerly AS, Silva-Fihlo MC, Menossi M, Souza GM (2007) BMC Genomics 8:71

    Article  PubMed  Google Scholar 

  • Rossouw D, Bosch S, Kossmann J, Botha FC, Groenewald J-H (2007) Downregulation of neutral invertase activity in sugarcane cell suspension cultures leads to a reduction in respiration and growth and an increase in sucrose accumulation. Funct Plant Biol 34:490–498

    Article  CAS  Google Scholar 

  • Rossouw D, Kossmann J, Botha FC, Groenewald J-H (2010) Reduced neutral invertase activity in the culm tissues of transgenic sugarcane plants results in a decrease in respiration and sucrose cycling and an increase in the sucrose to hexose ratio. Funct Plant Biol 37:22–31

    Article  CAS  Google Scholar 

  • Simon SA, Zhai J, Nandety RS, McCormick KP, Zeng J, Mejia D, Meyers BC (2009) Short-read sequencing technologies for transcriptional analyses. Annu Rev Plant Biol 60:305–333

    Article  CAS  PubMed  Google Scholar 

  • Somerville C, Young H, Taylor C, Davis SC, Long SP (2010) Feedstocks for lignocellulosic biofuels. Science 329:790–792

    Article  CAS  PubMed  Google Scholar 

  • Stekel DJ, Git Y, Falciani F (2000) The comparison of gene expression from multiple cDNA libraries. Genome Res 10:2055–2061

    Article  CAS  PubMed  Google Scholar 

  • Travella S, Klimm TE, Keller B (2006) RNA interference-based gene silencing as an efficient tool for functional genomics in hexaploid bread wheat. Plant Physiol 142:6–20

    Article  CAS  PubMed  Google Scholar 

  • Trujillo LE, Sotolongo M, Menendez C, Ochogavia ME, Coll Y, Hernandez I, Borras-Hidalgo O, Thomma BPHJ, Vera P, Hernandez L (2008) SodERF3, a novel sugarcane ethylene responsive factor (ERF) enhances salt and drought tolerance when overexpressed in tobacco plants. Plant Cell Physiol 49:512–525

    Article  CAS  PubMed  Google Scholar 

  • Uys L, Botha FC, Hofmeyr J-HS, Rohwer JM (2007) Kinetic model of sucrose accumulation in maturing sugarcane culm tissue. Phytochemistry 68:2375–2392

    Article  CAS  PubMed  Google Scholar 

  • van der Merwe MJ, Groenewald J-H, Stitt M, Kossmann J, Botha FC (2010) Down-regulation of pyrophosphate: fructose 6-phosphate 1-phosphotransferase activity in sugarcane culms enhances sucrose accumulation due to elevated hexose-phosphate levels. Planta 231:595–608

    Article  PubMed  Google Scholar 

  • Vazquez F, Legrand S, Windels D (2010) The biosynthetic pathways and biological scopes of plant small RNAs. Trends Plant Sci 15:337–345

    Article  CAS  PubMed  Google Scholar 

  • Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270:484–487

    Article  CAS  PubMed  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 

  • Vicentini R, Menossi M (2009) The predicted subcellular localisation of the sugarcane proteome. Funct Plant Biol 36:242–250

    Article  CAS  Google Scholar 

  • Vicentini R, Felix JM, Dornelas MC, Menossi M (2009) Characterisation of a sugarcane (Saccharum spp.) gene homolog to the brassinosteroid insensitive1-associated receptor kinase 1 that is associated to sugar content. Plant Cell Rep 28:481–491

    Article  CAS  PubMed  Google Scholar 

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

    Article  Google Scholar 

  • Vickers JE, Grof CPL, Bonnett GD, Jackson PA, Knight DP, Roberts SE, Robinson SP (2005) Overexpression of polyphenol oxidase in transgenic sugarcane results in darker juice and raw sugar. Crop Sci 45:354–362

    Article  CAS  Google Scholar 

  • Wang J, Roe B, Macmil S, Yu Q, Murray JE, Tang H, Chen C, Najar F, Wiley G, Bowers J, Van Sluys M-A, Rokhsar DS, Hudson ME, Moose SP, Paterson AH, Ming R (2010) Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genomics 11:261

    Article  PubMed  Google Scholar 

  • Whittaker A, Botha FC (1999) Pyrophosphate: fructose 6-phosphate 1-phosphotransferase activity patterns in relation to sucrose storage across sugarcane varieties. Physiologum Plantarum 107:379–386

    Article  CAS  Google Scholar 

  • Wind J, Smeekens S, Hanson J (2010) Sucrose: metabolite and signalling molecule. Phytochemistry 71:1610–1614

    Article  CAS  PubMed  Google Scholar 

  • Wu L, Birch RG (2007) Doubled sugar content in sugarcane plants modified to produce a sucrose isomer. Plant Biotechnol J 5:109–117

    Article  CAS  PubMed  Google Scholar 

  • Wu L, Birch RG (2010) Physiological basis for enhanced sucrose accumulation in an engineered sugarcane cell line. Funct Plant Biol 37:1161–1174

    Article  CAS  Google Scholar 

  • Yamaguchi-Shinozaki K, Shinozaki K (2010) Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Ann Rev Plant Biol 57:781–803

    Article  Google Scholar 

  • Yilmaz A, Nishiyama MY, Fuentes BG, Souza GM, Janies D, Gray J, Grotewold E (2009) GRASSIUS: a platform for comparative regulatory genomics across grasses. Plant Physiol 149:171–180

    Article  CAS  PubMed  Google Scholar 

  • Zanca AS, Vicentini R, Ortiz-Morea FA, Del Bem LEV, da Silva MJ, Vicentz M, Nogueira FTS (2010) Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane. BMC Plant Biol 10:260

    Article  PubMed  Google Scholar 

  • Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z (2010) PMRD: plant microRNA database. Nucl Acids Res 38:D806–D813

    Article  CAS  PubMed  Google Scholar 

  • Zhu Q-H, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C (2008) A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res 18:1456–1465

    Article  CAS  PubMed  Google Scholar 

  • Zimmerman P, Hennig L, Gruissem W (2005) Gene-expression analysis and network discovery using Genevestigator. Trend Plant Sci 10:407–409

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Brisbane, 4067, Australia

    John M. Manners & Rosanne E. Casu

Authors
  1. John M. Manners
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rosanne E. Casu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to John M. Manners.

Additional information

Communicated by: Paulo Arruda

Rights and permissions

Reprints and permissions

About this article

Cite this article

Manners, J.M., Casu, R.E. Transcriptome Analysis and Functional Genomics of Sugarcane. Tropical Plant Biol. 4, 9–21 (2011). https://doi.org/10.1007/s12042-011-9066-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12042-011-9066-5

Keywords

Search

Navigation