Comprehensive Resources for Tomato Functional Genomics Based on the Miniature Model Tomato Micro-Tom

Tomato (Solanum lycopersicum L., Solanaceae) is an excellent model plant for genomic research of solanaceous plants, as well as for studying the development, ripening, and metabolism of fruit. In 2003, the International Solanaceae Project (SOL, www.sgn.cornell.edu ) was initiated by members from more than 30 countries, and the tomato genome-sequencing project is currently underway. Genome sequence of tomato obtained by this project will provide a firm foundation for forthcoming genomic studies such as the comparative analysis of genes conserved among the Solanaceae species and the elucidation of the functions of unknown tomato genes. To exploit the wealth of the genome sequence information, there is an urgent need for novel resources and analytical tools for tomato functional genomics. Here, we present an overview of the development of genetic and genomic resources of tomato in the last decade, with a special focus on the activities of Japan SOL and the National Bio-Resource Project in the development of functional genomic resources of a model cultivar, Micro-Tom.

[1]  M. Zanor,et al.  Integrated Analysis of Metabolite and Transcript Levels Reveals the Metabolic Shifts That Underlie Tomato Fruit Development and Highlight Regulatory Aspects of Metabolic Network Behavior1[W] , 2006, Plant Physiology.

[2]  Koh Aoki,et al.  Ethylmethanesulfonate (EMS) mutagenesis of Solanum lycopersicum cv. Micro-Tom for large-scale mutant screens , 2007 .

[3]  Hideki Takahashi,et al.  Tomato as a model plant for plant-pathogen interactions , 2007 .

[4]  S. Tanksley,et al.  An interspecific backcross of Lycopersicon esculentum x L. hirsutum: linkage analysis and a QTL study of sexual compatibility factors and floral traits. , 1997, Genetics.

[5]  P. Bramley.  Regulation of carotenoid formation during tomato fruit ripening and development. , 2002, Journal of experimental botany.

[6]  Hua Yan,et al.  MicroTom—a high-throughput model transformation system for functional genomics , 2006, Plant Cell Reports.

[7]  John Quackenbush,et al.  The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes , 2004, Nucleic Acids Res..

[8]  Sarah Melamed,et al.  A new model system for tomato genetics , 1997 .

[9]  Jonathan D. G. Jones,et al.  The Tomato Cf-2 Disease Resistance Locus Comprises Two Functional Genes Encoding Leucine-Rich Repeat Proteins , 1996, Cell.

[10]  Daniel T. Lavelle,et al.  Tomato Prf Is a Member of the Leucine-Rich Repeat Class of Plant Disease Resistance Genes and Lies Embedded within the Pto Kinase Gene Cluster , 1996, Cell.

[11]  A. Ohyama,et al.  Suppression of Acid Invertase Activity by Antisense RNA Modifies the Sugar Composition of Tomato Fruit , 1995 .

[12]  Jonathan D. G. Jones,et al.  The tomato Dwarf gene isolated by heterologous transposon tagging encodes the first member of a new cytochrome P450 family. , 1996, The Plant cell.

[13]  M. Ganal,et al.  The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1. , 1998, Development.

[14]  J. D. Jones,et al.  Characterization of the tomato Cf-4 gene for resistance to Cladosporium fulvum identifies sequences that determine recognitional specificity in Cf-4 and Cf-9. , 1997, The Plant cell.

[15]  Mark H. Wright,et al.  The SOL Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond1 , 2005, Plant Physiology.

[16]  R. Horsch,et al.  Leaf disc transformation of cultivated tomato (L. esculentum) using Agrobacterium tumefaciens , 1986, Plant Cell Reports.

[17]  G. Martin,et al.  Transcriptome and Selected Metabolite Analyses Reveal Multiple Points of Ethylene Control during Tomato Fruit Developmentw⃞ , 2005, The Plant Cell Online.

[18]  S. Henikoff,et al.  Targeting induced local lesions IN genomes (TILLING) for plant functional genomics. , 2000, Plant physiology.

[19]  J. Giovannoni,et al.  MOLECULAR BIOLOGY OF FRUIT MATURATION AND RIPENING. , 2001, Annual review of plant physiology and plant molecular biology.

[20]  Wei Hu,et al.  A combination of overgrowth-control antibiotics improves Agrobacterium tumefaciens-mediated transformation efficiency for cultivated tomato (L. esculentum) , 2001, In Vitro Cellular & Developmental Biology - Plant.

[21]  D. Shibata,et al.  Genomic Databases for Tomato , 2007 .

[22]  G. Bishop,et al.  Genetic and physiological characterization of tomato cv. Micro-Tom. , 2006, Journal of experimental botany.

[23]  D. Shibata,et al.  Non-biased distribution of tomato genes with no counterparts in Arabidopsis thaliana in expression patterns during fruit maturation , 2006 .

[24]  L. Melchers,et al.  Factors influencing transformation frequency of tomato (Lycopersicon esculentum) , 1993, Plant Cell Reports.

[25]  D. R. Wagner,et al.  Activation Tagging in Tomato Identifies a Transcriptional Regulator of Anthocyanin Biosynthesis, Modification, and Transport Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012963. , 2003, The Plant Cell Online.

[26]  Naama Menda,et al.  In silico screening of a saturated mutation library of tomato. , 2004, The Plant journal : for cell and molecular biology.

[27]  S. Tanksley,et al.  Mapping quantitative trait loci in inbred backcross lines of Lycopersicon pimpinellifolium (LA1589). , 2002, Genome.

[28]  Nathan M. Springer,et al.  Discovery of induced point mutations in maize genes by TILLING , 2004, BMC Plant Biology.

[29]  T. Wood,et al.  A deep-coverage tomato BAC library and prospects toward development of an STC framework for genome sequencing. , 2000, Genome research.

[30]  D. Zamir,et al.  Cloning of tangerine from tomato reveals a carotenoid isomerase essential for the production of beta-carotene and xanthophylls in plants. , 2002, The Plant cell.

[31]  Hideyuki Suzuki,et al.  Expressed sequence tags of full-length cDNA clones from the miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom , 2005 .

[32]  Xuemei Tang,et al.  Tomato Expression Database (TED): a suite of data presentation and analysis tools , 2005, Nucleic Acids Res..

[33]  W. Gruissem,et al.  Fruits: A Developmental Perspective. , 1993, The Plant cell.

[34]  M. Ganal,et al.  Effect of ticarcillin/potassium clavulanate on callus growth and shoot regeneration in Agrobacterium-mediated transformation of tomato (Lycopersicon esculentum Mill.) , 1998, Plant Cell Reports.

[35]  R. Van der Hoeven,et al.  Identification, Analysis, and Utilization of Conserved Ortholog Set Markers for Comparative Genomics in Higher Plants Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010479. , 2002, The Plant Cell Online.

[36]  G. Sita,et al.  Agrobacterium-mediated transformation of tomato (Lycopersicon esculentum var. Pusa Ruby) with coat-protein gene of Physalis mottle tymovirus. , 2000 .

[37]  G. Martin,et al.  ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development. , 2004, The Plant journal : for cell and molecular biology.

[38]  Stephen J. O'Brien,et al.  Genetic Maps: Locus Maps of Complex Genomes , 1990 .

[39]  S. Tanksley,et al.  Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium , 1996, Theoretical and Applied Genetics.

[40]  Xin Li,et al.  A fast neutron deletion mutagenesis-based reverse genetics system for plants. , 2001, The Plant journal : for cell and molecular biology.

[41]  P. D. de Wit,et al.  Receptor-like proteins involved in plant disease resistance. , 2005, Molecular plant pathology.

[42]  G. Martin,et al.  High density molecular linkage maps of the tomato and potato genomes. , 1992, Genetics.

[43]  A. Bennett,et al.  Sink metabolism in tomato fruit : I. Developmental changes in carbohydrate metabolizing enzymes. , 1988, Plant physiology.

[44]  G. Martin,et al.  Deductions about the Number, Organization, and Evolution of Genes in the Tomato Genome Based on Analysis of a Large Expressed Sequence Tag Collection and Selective Genomic Sequencing Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010478. , 2002, The Plant Cell Online.

[45]  A. Frary,et al.  An examination of factors affecting the efficiency of Agrobacterium-mediated transformation of tomato , 1996 .

[46]  D. Shibata,et al.  Expressed sequence tags from the laboratory-grown miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom and mining for single nucleotide polymorphisms and insertions/deletions in tomato cultivars. , 2005, Gene.

[47]  S. Tanksley,et al.  QTL analysis of transgressive segregation in an interspecific tomato cross. , 1993, Genetics.

[48]  Hiroshi Ezura,et al.  A highly efficient transformation protocol for Micro-Tom, a model cultivar for tomato functional genomics. , 2006, Plant & cell physiology.

[49]  K. Hirschi,et al.  Efficient and genotype-independent Agrobacterium--mediated tomato transformation. , 2003, Journal of plant physiology.

[50]  S. Tanksley,et al.  Utilization of tomato microarrays for comparative gene expression analysis in the Solanaceae. , 2005, Journal of experimental botany.

[51]  D. Shibata,et al.  Catalog of Micro-Tom tomato responses to common fungal, bacterial, and viral pathogens , 2005, Journal of General Plant Pathology.

[52]  J. Giovannoni,et al.  Fruit ripening mutants yield insights into ripening control. , 2007, Current opinion in plant biology.

[53]  Jonathan D. G. Jones,et al.  Analysis of the chromosomal distribution of transposon-carrying T-DNAs in tomato using the inverse polymerase chain reaction , 1994, Molecular and General Genetics MGG.

[54]  S. Tanksley,et al.  QTL analysis of horticultural traits differentiating the cultivated tomato from the closely related species Lycopersicon pimpinellifolium , 1996, Theoretical and Applied Genetics.

[55]  E. Emmanuel,et al.  Tomato mutants as tools for functional genomics. , 2002, Current opinion in plant biology.

[56]  S. Kanaya,et al.  Summary , 1940, Intellectual Property in the Conflict of Laws.

[57]  Y. Larondelle,et al.  Transgenic tomato lines containing Ds elements at defined genomic positions as tools for targeted transposon tagging , 1994, Molecular and General Genetics MGG.

[58]  David A. Jones,et al.  The Tomato Cf-5 Disease Resistance Gene and Six Homologs Show Pronounced Allelic Variation in Leucine-Rich Repeat Copy Number , 1998, Plant Cell.

[59]  Yuval Eshed,et al.  A genomic library of Lycopersicon pennellii in L. esculentum: A tool for fine mapping of genes , 2004, Euphytica.

[60]  Hsiao-Ching Yen,et al.  An Ethylene-Inducible Component of Signal Transduction Encoded by Never-ripe , 1995, Science.

[61]  F. Takken,et al.  Identification and Ds-tagged isolation of a new gene at the Cf-4 locus of tomato involved in disease resistance to Cladosporium fulvum race 5. , 1998, The Plant journal : for cell and molecular biology.

[62]  Takeshi Saito,et al.  Generation of gamma irradiation-induced mutant lines of the miniature tomato (Solanum lycopersicum L.) cultivar ‘Micro-Tom‘ , 2007 .

[63]  Y. Elkind,et al.  Technical advance: a high throughput system for transposon tagging and promoter trapping in tomato. , 2000, The Plant journal : for cell and molecular biology.

[64]  T. C. Nesbitt,et al.  fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. , 2000, Science.

[65]  Lukas A. Mueller,et al.  The Tomato Sequencing Project, the First Cornerstone of the International Solanaceae Project (SOL) , 2005, Comparative and functional genomics.

[66]  Brent K. Harbaugh,et al.  Micro-Tom. A miniature dwarf tomato , 1989 .

[67]  A. Frary,et al.  An examination of factors affecting the efficiency ofAgrobacterium-mediated transformation of tomato , 1996, Plant Cell Reports.

[68]  Nozomu Sakurai,et al.  MiBASE : A database of a miniature tomato cultivar Micro-Tom , 2006 .

[69]  Sergio Contrino,et al.  ArrayExpress—a public repository for microarray gene expression data at the EBI , 2004, Nucleic Acids Res..

[70]  G. Martin,et al.  Molecular basis of Pto-mediated resistance to bacterial speck disease in tomato. , 2003, Annual review of phytopathology.

[71]  J. Yoder,et al.  Classical and molecular genetics of tomato: highlights and perspectives. , 1988, Annual review of genetics.

[72]  J. D. Jones,et al.  Isolation of the tomato Cf-9 gene for resistance to Cladosporium fulvum by transposon tagging. , 1994, Science.