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Sequencing the Tomato Genome A model Solanaceous species

Sequencing the Tomato Genome A model Solanaceous species. Uses of the tomato genome sequence Representative genome of Solanaceae, will be extremely useful in comparative genomics and data mining Greatly facilitate map based cloning of important fruit quality genes in tomato

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Sequencing the Tomato Genome A model Solanaceous species

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  1. Sequencing the Tomato Genome A model Solanaceous species

  2. Uses of the tomato genome sequence • Representative genome of Solanaceae, will be extremely useful in comparative genomics and data mining • Greatly facilitate map based cloning of important fruit quality genes in tomato • Tomato and potato carry a rich diversity of genes for biotic and abiotic stress tolerance • Underpin current research interests in Solanaceaous species in the UK • Tomato VIGS for functional genomics

  3. UK User Community Steve Adams Warwick HRI Sue Angell JIC David Baulcombe SL Mike Bevan JIC Paul Birch SCRI Gerard Bishop Aberystwyth Margaret Boulton JIC Peter Bramley London Pierre Broun York Glenn Bryan SCRI Steve Colliver Unilever Bill Davies Lancaster Mark Dixon Southampton Andy Fleming Sheffield Rupert Fray Nottingham Michael Fay Kew Christine Foyer Rothamsted Paul Fraser London Don Grierson Nottingham Gareth Griffith Aberystwyth Mark Hooks Bangor Jonathan Jones SL Graham King Warwick HRI Sandy Knapp NHM Grantley Lycett Nottingham Ken Manning Warwick HRI Cathie Martin JIC S McQueen-Mason York Andy Maule JIC Phil Mullineaux JIC Hugh Nimmo Glasgow Ian Puddephat Syngenta Kevin Pyke Nottingham Paul Quick Sheffield John Rathjen SL Mike Roberts Lancaster Tim Robbins Nottingham Graham Seymour Warwick HRI Aileen Smith Aberystwyth John Stanley JIC Ian Taylor Nottingham Jane Taylor Lancaster Mark Taylor SCRI Colwyn Thomas UEA Andrew Thompson Warwick HRI Deri Tomos Bangor Miltos Tsiantis Oxford Greg Tucker Nottingham Jutta Tuerck ATC Robbie Waugh SCRI

  4. Internationally Competitive UK research that will benefit Fruit Quality, Human Transcription factors Health and Nutrition /HomeoticGenes Potato Genomics Industrial Applications Disease Resistance VIGS Carotenoid Biosynthesis Plastid Development ABA Biosynthesis BRs and systemins Epidermal Differentiation Metabolomics, Sugar metabolism Cell walls & Development Secondary Metabolism Natural products Bioinformatics/ Comparative Genomics Single cell 'omics

  5. Relevance to BBSRC Mission and Priority areas • In line with mission to support basic research which will impact on UK quality of life • Fully aligned with priorities for several BBSRC • committees including PMS, Agri-Food, GDB, EBS • e.g. Comparative Functional Genomics, Bioinformatics Genes to Food Products • Letters of support from Syngenta, Unilever, ATC, • BPC , TGA

  6. The UK Sequencing initiative is part of an International Consortium International Steering Committee led by Dani Zamir and Marc Zabeau, UK contacts, Gerard Bishop and Graham Seymour USA UK Netherlands China Korea France Italy Spain

  7. UK Contribution to Sequence the Gene - Rich Regions on Chromosome 4 • Why 4? • Contains important QTLs in Potato and Tomato relevant to UK user community (esp. SCRI) • Gene space on this chromosome can be sequenced at reasonable cost

  8. 12601ab1 IV PCN resistance 10 20 30 40 0 PACMAAC_288.4 0 DPAGMAGT_179.5 8 DPACMAGG_467.0 12 PATMCAT_198.0 20 DPCGMCAA_102.0 27 STM3016 30 PCAMAAC_289.0 32 DPGAMCAG_155.0 34 PATMAGG_92.3 DPACMATA_125.0 35 EAACMCTG_159.5 37 EACAMCAC_160.5 41 PACMACT_198.4 DPGAMCAC_219.5 42 EAACMCCA_200.0 43 EACAMCAC_153.0 44 S140 PCTMCAC_85.5 46 PGAMATC_195.9 48 PATMAGG_258.0 49 PACMATG_317.5 50 PCTMCAC_222.0 51 PATMACG_202.0 53 PACMAAG_309.3 54 PCCMACG_110.0 PAGMACG_134.0 56 PACMAAC_185.0 58 PCCMATA_530.0 PATMACG_295.0 63 PCCMATA_179.0 QTL loci on potato Ch 4 include those for late blight and potato cyst nematode • AFLP markers cloned & sequenced • Markers screened against potato BAC libraries • AFLPs • SSRs • RGCs • ~70 BACs identified to date • BAC fingerprinting in early 2004 • EU APOPHYS project • Global potato physical map Target region Glenn Bryan and Robbie Waugh, SCRI

  9. QTL loci on tomato Ch4 include those for fruit texture and colour Texture, Texture, Colour Early Ripening

  10. Sequencing Strategy

  11. Sequencing Strategy

  12. UK Contribution to Sequence the Gene - Rich Regions on Chromosome 4 • Aim to sequence chr4 ~25-30 Mb of gene- space

  13. Release of Sequence • Immediate release into public domain • through EMBL/GenBank

  14. Bioinformatics • International bioinformatics steering group established chaired by Lukas Mueller at Cornell • Training provided by Cornell • Ch4 sequence will be annotated in UK at • HRI / Imperial • Annotated Sequence release through • Solanaceae Genome Network (SGN) website • and database. Mirror site in UK.

  15. Dissemination of information to UK community • Annotated Sequence released through • Solanaceae Genome Network (SGN) website • and database. Mirror site in UK • UK website will adapt to needs/requests of UK user community • UK site to contain useful listings including, current grants genetic and genomic resources, conferences etc… • UK Solanaceae Community meetings • to be organised. First meeting to be hosted at Unilever.

  16. Key Milestones • Sequence of Chr12 and annotation • UK portal for UK users running • Finished Sequence of Chr 4 • Finished Annotation of Chr 4 • All data on UK and SGN web site

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