Presentation on theme: "Sequencing the Tomato Genome A model Solanaceous species."— Presentation transcript:
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 AdamsWarwick HRI Sue AngellJIC David Baulcombe SL Mike BevanJIC Paul BirchSCRI Gerard BishopAberystwyth Margaret BoultonJIC Peter BramleyLondon Pierre BrounYork Glenn BryanSCRI Steve ColliverUnilever Bill DaviesLancaster Mark DixonSouthampton Andy FlemingSheffield Rupert FrayNottingham Michael FayKew Christine FoyerRothamsted Paul FraserLondon Don Grierson Nottingham Gareth GriffithAberystwyth Mark HooksBangor Jonathan Jones SL Graham KingWarwick HRI Sandy KnappNHM Grantley LycettNottingham Ken ManningWarwick HRI Cathie MartinJIC S McQueen-MasonYork Andy MauleJIC Phil MullineauxJIC Hugh NimmoGlasgow Ian PuddephatSyngenta Kevin PykeNottingham Paul QuickSheffield John RathjenSL Mike RobertsLancaster Tim RobbinsNottingham Graham SeymourWarwick HRI Aileen SmithAberystwyth John StanleyJIC Ian TaylorNottingham Jane TaylorLancaster Mark TaylorSCRI Colwyn ThomasUEA Andrew ThompsonWarwick HRI Deri TomosBangor Miltos TsiantisOxford Greg TuckerNottingham Jutta Tuerck ATC Robbie WaughSCRI
Fruit Quality, Human Transcription factors Health and Nutrition /HomeoticGenes Potato Genomics Industrial Applications Disease ResistanceVIGS Carotenoid BiosynthesisPlastid Development ABA BiosynthesisBRs and systemins Epidermal Differentiation Metabolomics, Sugar metabolism Cell walls & Development Secondary Metabolism Natural products Bioinformatics/ Comparative GenomicsSingle cell 'omics Internationally Competitive UK research that will benefit
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 USAUK NetherlandsChina KoreaFrance ItalySpain
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 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 PATMAGG_92.3 34 DPACMATA_125.0 35 EAACMCTG_159.5 37 EACAMCAC_160.5 PACMACT_198.4 41 DPGAMCAC_219.5 42 EAACMCCA_200.0 43 EACAMCAC_153.0 S140 44 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 PCCMACG_110.0 54 PAGMACG_134.0 56 PACMAAC_185.0 PCCMATA_530.0 58 PATMACG_295.0 PCCMATA_179.0 63 0 10203040 12601ab1 IV PCN resistance 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
Texture, Colour Early Ripening Texture, QTL loci on tomato Ch4 include those for fruit texture and colour
UK Contribution to Sequence the Gene - Rich Regions on Chromosome 4 Aim to sequence chr4 ~25-30 Mb of gene- space
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