Structural and Functional Genomics of Tomato Barone et al. 2008

1. Structural and Functional Genomics of TomatoBarone et al. 2008 • Tomato (Solanum Lycopersicon) • economically important crop worldwide, • intensively investigated and • model system for genetic studies in plants. • Characteristics: • Simple diploid genetics: 12 chromosome pairs and 950 Mb genome size. • Short generation time • Routine transformation technology • Rich genetic and genomic resources.

2. Resources for genetic/genomic research include: • Wild species and mutant collections • marker collections • F2 synteny mapping population and permanent recombinant inbred (RI) mapping populations • BAC libraries and an advanced physical map • TILLING populations and • tomato microarrays, gene silenced tomato lines, and VIGS libraries (for transient silencing).

3. The International Solanaceae Genomics Project (SOL) • Goals and Objective: create a coordinated network of knowledge about the Solanaceae family • Key components and milestones: • 1) Sequence the reference tomato genome on a BAC by BAC basis • 2) Develop deep EST databases from various Solanaceae tissues and shotgun genomic sequencing of other Solanaceae with data integration. • 4) Construct a set of interspecific introgression resources (e.g. introgression lines, backcross inbred lines etc.) for all Solanaceae crop species in order to provide the genetic material from which genes/QTL can be studied. • 5) Establish saturation mutagenesis genetic resources, • 6) Construct a comprehensive phylogenetic and geographical distribution information network • 9) Improve the efficiency of plant breeding based on the use of wild species variation, marker assisted selection, and mutagenesis • 11) Develop an international bioinformatics platform

4. STRUCTURAL GENOMICS • Molecular Markers Restriction fragment length polymorphisms (RFLPs), simple sequence repeats (SSRs), cleaved amplified polymorphic sequence (CAPS), amplified fragment length polymorphisms (AFLPs), and single nucleotide polymorphism (SNP), known function genes (KFG) and EST-derived markers (TM) among others. A database of all the available markers can be found in: http://www.sgn.cornell.edu/search/direct_search.pl?search=markers

5. STRUCTURAL GENOMICS • Genetic and Physical Maps • Availability of genetic maps covering the entire tomato genome. • Comparative mapping: tomato-potato/pepper/eggplant. • COSII markers: determine the level of synteny between Arabidopsis genome and the genomes of tomato and other Solanceous species. • Genetic linkage maps, cytological and cytogenetic maps are available for tomato. • Mapped markers and of FISHed BAC allowed the construction of a high-density integrated genetic and physical map.

6. STRUCTURAL GENOMICS • QTL mapping and exploitation of natural biodiversity In tomato a whole genome molecular linkage map was used to identify quantitative trait loci (QTL). the “advanced backcross QTL mapping method” was proposed by Tanksley and Nelson In tomato, the first exotic library ensuring whole genome coverage was developed by Eshed and Zamir from the cross between the wild green-fruited species S. pennellii (acc. LA716) and the cultivated tomato S. lycopersicum (cv. M82).

7. STRATEGIES FOR TOMATO GENOME SEQUENCING • A draft sequence has been constructed for approximately 24% of the tomato euchromatic genome space, including all the twelve chromosomes. A sequencing strategy on a BAC by BAC basis of approximately 220Mb euchromatin was proposed. Starting in 2005, during the last two years of tomato sequencing activity, the participant countries set up their own sequencing pipelines and started to construct the sequence scaffold of assigned chromosomes.

8. FUNCTIONAL GENOMICS • Over 600 characterized monogenic mutations are available in a variety of genetic backgrounds at the Tomato Genetics Resource Center (http://tgrc.ucdavis.edu). • 6000 EMS-induced and 7000 fast neutron-induced mutant lines has been obtained. A detailed phenotypic description of the mutants is available online (http://zamir.sgn.cornell.edu/mutants). • TILLING (targeting induced local lesions IN genomes) platforms for tomato are under development in several countries, including the US, France, Italy, and India.

9. FUNCTIONAL GENOMICS • Gene silencing (RNAi and VIGS) • Fruit-specific silencing of genes by RNAi (remains confined in the fruit). • Virus induced gene silencing (VIGS) used in roots and fruits. Of the viral vectors used Tobacco Rattle Virus has the widest host range (Solanum species and Arabidopsis).

10. FUNCTIONAL GENOMICS • Transient expression of exogenous genes • Particle Bombardment • Agroinfiltration • Transcriptional profiling • Microarray platforms: Tom1, Tom2 and Affymetrix Genechip.

11. BIOINFORMATICS • International Tomato Annotation Group (ITAG): Annotation pipeline to provide a high-quality information-enriched tomato genome. (http://www.sgn.cornell.edu/sequencing/ITAG/status html.pl)

12. BIOINFORMATICS The CAB group within the EU-SOL project (http://www.eu-sol.net) is committed to collect all EST data from Solanaceae species available in dbEST (Table 1) and to provide EST alignments to the tomato genome draft sequences under production. Also ESTs from two species of the Coffee genus (Rubiaceae) The CAB group developed ISOL@, an Italian bioinformatics resource for Solanaceae genomics.