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