The Biotechnology Roadmap for Sugarcane Improvement

Due to the strategic importance of sugarcane to Brazil, FAPESP, the main São Paulo state research funding agency, launched in 2008 the FAPESP Bioenergy Research Program (BIOEN, http://bioenfapesp.org). BIOEN aims to generate new knowledge and human resources for the improvement of the sugarcane and ethanol industry. As part of the BIOEN program, a Workshop on Sugarcane Improvement was held on March 18th and 19th 2009 in São Paulo, Brazil. The aim of the workshop was to explore present and future challenges for sugarcane improvement and its use as a sustainable bioenergy and biomaterial feedstock. The workshop was divided in four sections that represent important challenges for sugarcane improvement: a) gene discovery and sugarcane genomics, b) transgenics and controlled transgene expression, c) sugarcane physiology (photosynthesis, sucrose metabolism, and drought) and d) breeding and statistical genetics. This report summarizes the roadmap for the improvement of sugarcane.

[1]  Zhongfu Ni,et al.  Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. , 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.

[2]  D. Bulgarelli,et al.  Marker assisted selection in crop plants , 2005, Plant Cell, Tissue and Organ Culture.

[3]  A. McCormick,et al.  Sink strength regulates photosynthesis in sugarcane. , 2006, The New phytologist.

[4]  G. Bonnett,et al.  Genetic control of yield related stalk traits in sugarcane , 2008, Theoretical and Applied Genetics.

[5]  L. Nielsen,et al.  Production of polyhydroxybutyrate in sugarcane. , 2007, Plant biotechnology journal.

[6]  Lázaro Hernández,et al.  Sugarcane (Saccharum hybrid) genetic transformation mediated by Agrobacterium tumefaciens: Production of transgenic plants expressing proteins with agronomic and industrial value , 2000 .

[7]  M. L. Hewitt,et al.  Source–sink differences in genotypes and water regimes influencing sucrose accumulation in sugarcane stalks , 2009 .

[8]  A. McCormick,et al.  Regulation of photosynthesis by sugars in sugarcane leaves. , 2008, Journal of plant physiology.

[9]  P. Hooykaas Transformation Mediated by Agrobacterium tumefaciens , 2004 .

[10]  F. Botha,et al.  Sucrose metabolism in the culm of transgenic sugarcane with reduced soluble acid invertase activity , 2001 .

[11]  Mihaela M. Martis,et al.  The Sorghum bicolor genome and the diversification of grasses , 2009, Nature.

[12]  E. Nevo,et al.  Discovery and assay of single-nucleotide polymorphisms in barley (Hordeum vulgare) , 2002, Plant Molecular Biology.

[13]  R. Casu,et al.  Efficient silencing of reporter transgenes coupled to known functional promoters in sugarcane, a highly polyploid crop species , 2009, Planta.

[14]  Luguang Wu,et al.  Doubled sugar content in sugarcane plants modified to produce a sucrose isomer. , 2007, Plant biotechnology journal.

[15]  Identification of methyl jasmonate-responsive genes in sugarcane using cDNA arrays , 2005 .

[16]  S. Saumtally,et al.  Identification of a major quantitative trait locus (QTL) for yellow spot (Mycovellosiella koepkei) disease resistance in sugarcane , 2006, Molecular Breeding.

[17]  R. Stoughton,et al.  Genetics of gene expression surveyed in maize, mouse and man , 2003, Nature.

[18]  L. H. Allen,et al.  Growth at elevated CO(2) delays the adverse effects of drought stress on leaf photosynthesis of the C(4) sugarcane. , 2009, Journal of plant physiology.

[19]  Stefano Castiglione,et al.  Somaclonal variation in insect‐resistant transgenic sugarcane (Saccharum hybrid) plants produced by cell electroporation , 1999, Transgenic Research.

[20]  A. P. de Souza,et al.  Analysis of genetic similarity detected by AFLP and coefficient of parentage among genotypes of sugar cane (Saccharum spp.) , 2002, Theoretical and Applied Genetics.

[21]  R. Birch PLANT TRANSFORMATION: Problems and Strategies for Practical Application. , 1997, Annual review of plant physiology and plant molecular biology.

[22]  Z B Zeng,et al.  Estimating the genetic architecture of quantitative traits. , 1999, Genetical research.

[23]  M. Chan,et al.  An efficient protocol for sugarcane (Saccharum spp. L.) transformation mediated by Agrobacterium tumefaciens , 1998, Transgenic Research.

[24]  P. Arruda,et al.  Collection for Tropical Crop Sugarcane Analysis and Functional Annotation of an Expressed Sequence Tag , 2006 .

[25]  A. D'Hont,et al.  Unraveling the genome structure of polyploids using FISH and GISH; examples of sugarcane and banana , 2005, Cytogenetic and Genome Research.

[26]  R. Birch,et al.  Engineered detoxification confers resistance against a pathogenic bacterium , 1999, Nature Biotechnology.

[27]  L. H. Allen,et al.  Up-regulation of photosynthesis and sucrose metabolism enzymes in young expanding leaves of sugarcane under elevated growth CO2 , 2006 .

[28]  D. E. Van Dyk,et al.  Initial evaluation of sugarcane as a production platform for p-hydroxybenzoic acid. , 2004, Plant biotechnology journal.

[29]  C. Grof,et al.  Agrobacterium-mediated transformation of sugarcane using GFP as a screenable marker , 1998 .

[30]  K. C. Oliveira,et al.  Transcription profiling of signal transduction-related genes in sugarcane tissues. , 2005, DNA research : an international journal for rapid publication of reports on genes and genomes.

[31]  T. Mirkov,et al.  Evaluation of transgenic sugarcane against stalkborers. , 2000 .

[32]  Hugo Bruno Correa Molinari,et al.  Evaluation of the stress-inducible production of proline in transgenic sugarcane (Saccharum spp.): osmotic adjustment, chlorophyll fluorescence and oxidative stress , 2007 .

[33]  M. Manickavasagam,et al.  Agrobacterium-mediated genetic transformation and development of herbicide-resistant sugarcane (Saccharum species hybrids) using axillary buds , 2004, Plant Cell Reports.

[34]  S. Chapman,et al.  Identification of Differentially Expressed Transcripts from Maturing Stem of Sugarcane by in silico Analysis of Stem Expressed Sequence Tags and Gene Expression Profiling , 2004, Plant Molecular Biology.

[35]  Stefan R. Schulze,et al.  An EST survey of the sugarcane transcriptome , 2004, Theoretical and Applied Genetics.

[36]  Daniela Kajihara,et al.  Transcriptionally active transposable elements in recent hybrid sugarcane. , 2005, The Plant journal : for cell and molecular biology.

[37]  S. Mcfarlane,et al.  South African Sugarcane Research Institute: Embracing biotechnology for crop improvement research , 2008, Sugar Tech.

[38]  Jh Groenewald,et al.  MOLECULAR AGRICULTURE: PROSPECTS FOR THE PRODUCTION OF ALTERNATIVE COMMODITIES IN SUGARCANE THROUGH GENETIC ENGINEERING , 1995 .

[39]  Phillip Jackson,et al.  Overexpression of polyphenol oxidase in transgenic sugarcane results in darker juice and raw sugar , 2005 .

[40]  A. Syvänen Accessing genetic variation: genotyping single nucleotide polymorphisms , 2001, Nature Reviews Genetics.

[41]  N. B. Leibbrandt,et al.  Stability of gene expression and agronomic performance of a transgenic herbicide-resistant sugarcane line in South Africa , 2003 .

[42]  Xianming Wei,et al.  Associations between DNA markers and resistance to diseases in sugarcane and effects of population substructure , 2006, Theoretical and Applied Genetics.

[43]  J. Finnegan,et al.  Transgene Inactivation: Plants Fight Back! , 1994, Bio/Technology.

[44]  M. Silva-Filho,et al.  Expression of soybean proteinase inhibitors in transgenic sugarcane plants: effects on natural defense against Diatraea saccharalis , 2003 .

[45]  J. Irvine,et al.  Herbicide Resistant Transgenic Sugarcane Plants Containing the bar Gene , 1996 .

[46]  P. Joyce,et al.  Engineering for resistance to SCMV in sugarcane , 1998 .

[47]  J. Glaszmann,et al.  Resistance of Sugarcane Cultivar R 570 to Puccinia melanocephala Isolatesfrom Different Geographic Locations. , 2001, Plant disease.

[48]  R. Henry,et al.  Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. , 2009, Plant biotechnology journal.

[49]  J. Batley,et al.  Mining for Single Nucleotide Polymorphisms and Insertions/Deletions in Maize Expressed Sequence Tag Data1 , 2003, Plant Physiology.

[50]  S. Streatfield,et al.  Medical molecular farming: production of antibodies, biopharmaceuticals and edible vaccines in plants , 2001, Trends in Plant Science.

[51]  F. Nogueira,et al.  Identification of new ABA- and MEJA-activated sugarcane bZIP genes by data mining in the SUCEST database , 2008, Plant Cell Reports.

[52]  J. Glaszmann,et al.  Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics , 1996, Molecular and General Genetics MGG.

[53]  V. Savolainen,et al.  C4 Photosynthesis Evolved in Grasses via Parallel Adaptive Genetic Changes , 2007, Current Biology.

[54]  A. D'Hont,et al.  Genomic distribution and characterization of EST-derived resistance gene analogs (RGAs) in sugarcane , 2003, Molecular Genetics and Genomics.

[55]  E. Ulian,et al.  Elevated CO2 increases photosynthesis, biomass and productivity, and modifies gene expression in sugarcane. , 2008, Plant, cell & environment.

[56]  J. Glaszmann,et al.  Analysis of genome-wide linkage disequilibrium in the highly polyploid sugarcane , 2008, Theoretical and Applied Genetics.

[57]  G A Churchill,et al.  Statistical aspects of genetic mapping in autopolyploids. , 1999, Gene.

[58]  N. Inman-Bamber,et al.  Sugarcane water stress criteria for irrigation and drying off. , 2004 .

[59]  J. Messing Synergy of Two Reference Genomes for the Grass Family1 , 2009, Plant Physiology.

[60]  H. Daniell Environmentally friendly approaches to genetic engineering , 1999, In Vitro Cellular & Developmental Biology - Plant.

[61]  R. Magarey,et al.  Identification and Validation of Molecular Markers Associated with Pachymetra Root Rot and Brown Rust Resistance in Sugarcane Using Map- and Association-based Approaches , 2005, Molecular Breeding.

[62]  Brandon S. Gaut,et al.  Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.) , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[63]  P. Jackson,et al.  Construction of a genetic linkage map for Saccharum officinarum incorporating both simplex and duplex markers to increase genome coverage. , 2007, Genome.

[64]  R. Henry,et al.  The identification and characterisation of alleles of sucrose phosphate synthase gene family III in sugarcane , 2006, Molecular Breeding.

[65]  F. Botha,et al.  Preliminary analysis of expressed sequence tags for sugarcane. , 2000 .

[66]  J. Nap,et al.  Genetical genomics : the added value from segregation , 2001 .

[67]  M. Van Sluys,et al.  MudrA-like sequences from rice and sugarcane cluster as two bona fide transposon clades and two domesticated transposases. , 2007, Gene.

[68]  E. Ulian,et al.  Transformation and expression of a gene for herbicide resistance in a Brazilian sugarcane , 2000, Plant Cell Reports.

[69]  E. Ulian,et al.  Identification of genes responsive to the application of ethanol on sugarcane leaves , 2007, Plant Cell Reports.

[70]  M. Silva-Filho,et al.  Expression of the Cry1Ab Protein in Genetically Modified Sugarcane for the Control of Diatraea saccharalis (Lepidoptera: Crambidae) , 2003 .

[71]  R. Bock Transgenic plastids in basic research and plant biotechnology. , 2001, Journal of molecular biology.

[72]  Seshagiri Rao,et al.  Characterisation of the double genome structure of modern sugarcane cultivars ( , 1996 .

[73]  David Edwards,et al.  Discovering genetic polymorphisms in next-generation sequencing data. , 2009, Plant biotechnology journal.

[74]  Prakash Lakshmanan,et al.  Sugarcane biotechnology: The challenges and opportunities , 2005, In Vitro Cellular & Developmental Biology - Plant.

[75]  T. Mirkov,et al.  Posttranscriptional gene silencing in transgenic sugarcane. Dissection Of homology-dependent virus resistance in a monocot that has a complex polyploid genome , 1999, Plant physiology.

[76]  J. Glaszmann,et al.  A putative major gene for rust resistance linked with a RFLP marker in sugarcane cultivar ‘R570’ , 1996, Theoretical and Applied Genetics.

[77]  J. Engels,et al.  Prebreeding in sugarcane with an emphasis on the programme of the Mauritius Sugar Industry Research Institute. , 2002 .

[78]  B. Courtois,et al.  Comparative genetics in sugarcane enables structured map enhancement and validation of marker-trait associations , 2008, Molecular Breeding.

[79]  A. McCormick,et al.  Changes in photosynthetic rates and gene expression of leaves during a source-sink perturbation in sugarcane. , 2008, Annals of botany.

[80]  Ariel Arencibia,et al.  Production of transgenic sugarcane (Saccharum officinarum L.) plants by intact cell electroporation , 1995, Plant Cell Reports.

[81]  C. Grof,et al.  Green-fluorescent protein facilitates rapid in vivo detection of genetically transformed plant cells , 1999, Plant Cell Reports.

[82]  P. Arruda,et al.  Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome. , 2007, The Plant journal : for cell and molecular biology.

[83]  D. M. Smith,et al.  Water relations in sugarcane and response to water deficits , 2005 .

[84]  Mukesh Jain,et al.  Agronomic Evaluation of Sugarcane Lines Transformed for Resistance to Sugarcane mosaic virus Strain E , 2005 .

[85]  N. V. Nair,et al.  Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane. , 2003, Genome.

[86]  K. Fukui,et al.  Quantitative chromosome map of the polyploid Saccharum spontaneum by multicolor fluorescence in situ hybridization and imaging methods , 1999, Plant Molecular Biology.

[87]  J. Bernal,et al.  Evaluation of Lectin-Expressing Transgenic Sugarcane Against Stalkborers (Lepidoptera: Pyralidae): Effects on Life History Parameters , 2002, Journal of economic entomology.

[88]  R. Birch,et al.  Transgenic sugarcane plants via microprojectile bombardment , 1992 .

[89]  R. Z. Vêncio,et al.  Signal transduction-related responses to phytohormones and environmental challenges in sugarcane , 2007, BMC Genomics.

[90]  D. M. Hogarth,et al.  Sugarcane : research towards efficient and sustainable production , 1996 .

[91]  G. May,et al.  A tool for functional plant genomics: chimeric RNA/DNA oligonucleotides cause in vivo gene-specific mutations. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[92]  M. Yano,et al.  Natural variation in rice starch synthase IIa affects enzyme and starch properties. , 2004, Functional plant biology : FPB.

[93]  Hongmei Ma,et al.  Metabolic engineering of invertase activities in different subcellular compartments affects sucrose accumulation in sugarcane cells , 2000 .

[94]  J. Glaszmann,et al.  Sugarcane genome analysis with molecular markers, a first decade of research , 2001 .

[95]  F. Nogueira,et al.  RNA Expression Profiles and Data Mining of Sugarcane Response to Low Temperature1 , 2003, Plant Physiology.

[96]  Paulo Arruda,et al.  Sugarcane genomics: depicting the complex genome of an important tropical crop. , 2002, Current opinion in plant biology.

[97]  A. Figueira,et al.  Serial analysis of gene expression in sugarcane (Saccharum spp.) leaves revealed alternative C4 metabolism and putative antisense transcripts , 2007, Plant Molecular Biology.

[98]  G. Wenzel Molecular plant breeding: achievements in green biotechnology and future perspectives , 2006, Applied Microbiology and Biotechnology.

[99]  P. Maliga Plastid transformation in higher plants. , 2004, Annual review of plant biology.

[100]  V. Ramanatha Rao,et al.  Managing Plant Genetic Diversity , 2002 .

[101]  J. Comstock,et al.  Agronomic performance and genetic characterization of sugarcane transformed for resistance to sugarcane yellow leaf virus , 2009 .

[102]  A. D'Hont,et al.  Genetic mapping in sugarcane, a high polyploid, using bi-parental progeny: identification of a gene controlling stalk colour and a new rust resistance gene , 2006, Theoretical and Applied Genetics.

[103]  A. Risterucci,et al.  Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). I. Genome mapping with AFLP markers , 2001, Theoretical and Applied Genetics.

[104]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[105]  Anete P. Souza,et al.  Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases , 2005, Theoretical and Applied Genetics.

[106]  Mukesh Jain,et al.  Prospecting the utility of a PMI/mannose selection system for the recovery of transgenic sugarcane (Saccharum spp. hybrid) plants , 2007, Plant Cell Reports.

[107]  N. G. Inman-Bamber,et al.  Increasing sucrose accumulation in sugarcane by manipulating leaf extension and photosynthesis with irrigation , 2008 .

[108]  G. A. de la Riva,et al.  Herbicide-resistant sugarcane (Saccharum officinarum L.) plants by Agrobacterium-mediated transformation , 1998, Planta.

[109]  P. Jackson,et al.  A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar , 2005, Theoretical and Applied Genetics.

[110]  P. Joyce,et al.  Transgenic sugarcane with increased resistance to canegrubs. , 1999 .

[111]  H. Daniell,et al.  Overexpression of the Bt cry2Aa2 operon in chloroplasts leads to formation of insecticidal crystals , 2001, Nature Biotechnology.

[112]  M. Rossi,et al.  Survey of transposable elements in sugarcane expressed sequence tags (ESTs) , 2001 .

[113]  David C. Ison,et al.  Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes , 1998 .

[114]  M. Vincentz,et al.  Sugarcane genes associated with sucrose content , 2009, BMC Genomics.

[115]  R. C. Muchow,et al.  Dry matter partitioning of sugarcane in Australia and South Africa , 2002 .

[116]  S. Chapman,et al.  Genomics approaches for the identification of genes determining important traits in sugarcane , 2005 .

[117]  P. Govindaraj,et al.  Genetic diversity analysis of indian sugarcane breeding pool based on sugarcane specific STMS markers , 2005, Sugar Tech.

[118]  J. Dutoit The Fourth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC) , 2007 .

[119]  R. Tarchini,et al.  A Single Amino Acid Difference Distinguishes Resistant and Susceptible Alleles of the Rice Blast Resistance Gene Pi-ta , 2000, Plant Cell.

[120]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica) , 2002, Science.

[121]  Rosanne E. Casu,et al.  Identification of a novel sugar transporter homologue strongly expressed in maturing stem vascular tissues of sugarcane by expressed sequence tag and microarray analysis , 2003, Plant Molecular Biology.

[122]  Phillip Jackson,et al.  Breeding for improved sugar content in sugarcane , 2005 .

[123]  A. A. Garcia,et al.  Functional integrated genetic linkage map based on EST-markers for a sugarcane (Saccharum spp.) commercial cross , 2007, Molecular Breeding.