Transcript No Slide Title

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