Sequencing the Tomato GenomeA 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 CommunitySteve Adams Warwick HRISue Angell JICDavid Baulcombe SLMike Bevan JICPaul Birch SCRIGerard Bishop AberystwythMargaret Boulton JICPeter Bramley LondonPierre Broun YorkGlenn Bryan SCRISteve Colliver UnileverBill Davies LancasterMark Dixon SouthamptonAndy Fleming SheffieldRupert Fray NottinghamMichael Fay KewChristine Foyer RothamstedPaul Fraser LondonDon Grierson NottinghamGareth Griffith AberystwythMark Hooks BangorJonathan Jones SLGraham King Warwick HRISandy Knapp NHMGrantley Lycett NottinghamKen Manning Warwick HRI
Cathie Martin JICS McQueen-Mason YorkAndy Maule JICPhil Mullineaux JICHugh Nimmo GlasgowIan Puddephat SyngentaKevin Pyke NottinghamPaul Quick SheffieldJohn Rathjen SLMike Roberts LancasterTim Robbins NottinghamGraham Seymour Warwick HRIAileen Smith AberystwythJohn Stanley JICIan Taylor NottinghamJane Taylor LancasterMark Taylor SCRIColwyn Thomas UEAAndrew Thompson Warwick HRIDeri Tomos BangorMiltos Tsiantis OxfordGreg Tucker NottinghamJutta Tuerck ATCRobbie Waugh SCRI
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 MetabolismNatural products
Bioinformatics/Comparative Genomics Single cell 'omics
Internationally Competitive UK researchthat 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 BBSRCcommittees including PMS, Agri-Food, GDB,
EBSe.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 blightand potato cyst nematode
PACMAAC_288.4 0
DPAGMAGT_179.5 8
DPACMAGG_467.0 12
PATMCAT_198.0 20
DPCGMCAA_102.0 27STM3016 30
PCAMAAC_289.0 32DPGAMCAG_155.0
PATMAGG_92.3 34DPACMATA_125.0 35EAACMCTG_159.5 37EACAMCAC_160.5
PACMACT_198.4 41DPGAMCAC_219.5 42EAACMCCA_200.0 43EACAMCAC_153.0
S140 44PCTMCAC_85.5 46
PGAMATC_195.9 48PATMAGG_258.0 49PACMATG_317.5 50PCTMCAC_222.0 51PATMACG_202.0 53PACMAAG_309.3PCCMACG_110.0 54PAGMACG_134.0 56PACMAAC_185.0PCCMATA_530.0 58PATMACG_295.0
PCCMATA_179.0 63
0
10
20
30
40
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
Sequencing Strategy
Sequencing Strategy
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 domainthrough 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) websiteand database. Mirror site in UK.
Dissemination of information to UK community
• Annotated Sequence released through Solanaceae Genome Network (SGN) websiteand 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 meetingsto 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