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Sequencing the Tomato Genome A model Solanaceous species Uses of the tomato genome sequence 1) Representative genome of Solanaceae, will be extremely useful in comparative genomics and data mining 2) Greatly facilitate map based cloning of important fruit quality genes in tomato 3) Tomato and potato carry a rich diversity of genes for biotic and abiotic stress tolerance 4) Underpin current research interests in Solanaceaous species in the UK 5) Tomato VIGS for functional genomics UK User Community Steve Adams Sue AngellJIC David Baulcombe Mike Bevan Paul Birch Gerard Bishop Margaret Boulton Peter Bramley Pierre Broun Glenn Bryan Steve Colliver Bill Davies Mark Dixon Andy Fleming Rupert Fray Michael Fay Christine Foyer Paul Fraser Don Grierson Gareth Griffith Mark Hooks Jonathan Jones Graham King Sandy Knapp Grantley Lycett Ken Manning Warwick HRI SL JIC SCRI Aberystwyth JIC London York SCRI Unilever Lancaster Southampton Sheffield Nottingham Kew Rothamsted London Nottingham Aberystwyth Bangor SL Warwick HRI NHM Nottingham Warwick HRI Cathie Martin S McQueen-Mason Andy Maule Phil Mullineaux Hugh Nimmo Ian Puddephat Kevin Pyke Paul Quick John Rathjen Mike Roberts Tim Robbins Graham Seymour Aileen Smith John Stanley Ian Taylor Jane Taylor Mark Taylor Colwyn Thomas Andrew Thompson Deri Tomos Miltos Tsiantis Greg Tucker Jutta Tuerck Robbie Waugh JIC York JIC JIC Glasgow Syngenta Nottingham Sheffield SL Lancaster Nottingham Warwick HRI Aberystwyth JIC Nottingham Lancaster SCRI UEA Warwick HRI Bangor Oxford Nottingham ATC SCRI Internationally Competitive UK research that will benefit Fruit Quality, Human Health and Nutrition Transcription factors /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 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 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 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 QTL loci on potato Ch 4 include those for late blight and potato cyst nematode Target region DPACMAGG_467.0 12 PATMCAT_198.0 20 DPCGMCAA_102.0 STM3016 PCAMAAC_289.0 DPGAMCAG_155.0 PATMAGG_92.3 DPACMATA_125.0 EAACMCTG_159.5 EACAMCAC_160.5 PACMACT_198.4 DPGAMCAC_219.5 EAACMCCA_200.0 EACAMCAC_153.0 S140 PCTMCAC_85.5 PGAMATC_195.9 PATMAGG_258.0 PACMATG_317.5 PCTMCAC_222.0 PATMACG_202.0 PACMAAG_309.3 PCCMACG_110.0 PAGMACG_134.0 PACMAAC_185.0 PCCMATA_530.0 PATMACG_295.0 27 30 32 34 35 37 41 42 43 44 46 48 49 50 51 53 54 56 58 PCCMATA_179.0 63 Glenn Bryan and Robbie Waugh, SCRI 40 – Global potato physical map 8 30 • ~70 BACs identified to date • BAC fingerprinting in early 2004 • EU APOPHYS project DPAGMAGT_179.5 20 – AFLPs – SSRs – RGCs PCN resistance 10 0 • AFLP markers cloned & sequenced 12601ab1 IV • Markers screened against potato BAC librariesPACMAAC_288.4 0 QTL loci on tomato Ch4 include those for fruit texture and colour Texture, Texture, Colour Early Ripening Sequencing Strategy Sequencing Strategy UK Contribution to Sequence the Gene - Rich Regions on Chromosome 4 • Aim to sequence chr4 ~25-30 Mb of genespace Release of Sequence • Immediate release into public domain through EMBL/GenBank 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. 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. 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