Sequencing the Tomato Genome

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Sequencing the Tomato Genome A model Solanaceous
species
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• 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

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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
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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
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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

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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
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• 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

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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
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QTL loci on tomato Ch4 include those for fruit
texture and colour
Texture,
Texture, Colour Early Ripening
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Sequencing Strategy
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Sequencing Strategy
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• UK Contribution to Sequence the Gene - Rich
  Regions on Chromosome 4
• Aim to sequence chr4 25-30 Mb of gene- space

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

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• 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.

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• 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.

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• 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