Download Presentation - IAC 2016, New Delhi

1st International Agrobiodiversity Congress 2016
November 7, 2016, New Delhi
Plant DNA Resources in
RIKEN BRC to Bridge the Gap
between Gene Function and
Phenotype
Hiroshi ABE
Masatomo KOBAYASHI
Experimental Plant Division,
RIKEN BioResource Center
National BioResoure Project started in 2002
National BioResoure Project started in 2002
9 projects
Chryaanthemum
Moning glory
Arabidopsis
Barley Wheat
Lotus
Rice
Algae
Glycine
Tomato
Many institute and university
are involved in NBRP plant
Arabidopsis thaliana
Experimental model plant
・Small size
・Growing fast (6-8 weeks/a generation)
・Growing easily under fluorescent lamp
Full genome sequence (in 2000)
・Enormous genome resources
(>>Knock out mutants:
More than 95% of Arabidopsis 26000 genes)
Activity of RIKEN BRC
Core Facility of Arabidopsis in Japan
Plant cell lines
Seeds
DNA stocks
Knock out lines
Mutants
Natural accessions
Full-length cDNA
and TAC clones
Mission and Aim
1. Collection, preservation and distribution
of Arabidopsis seeds, plant cultured
cells and DNA materials
2. Development of technologies, such as
long term preservation of resources and
genetic/phenotypic characterization of
natural accessions, KO line…
3. International collaboration through the
Multinational Arabidopsis Steering
Committee (MASC)
Seeds
Arabidopsis transposon-tagged mutant lines
Arabidopsis activation-tagged lines
Arabidopsis FOX lines
SASSC seeds including natural accessions
Individual mutant and transgenic lines
Brachypodium distachyon Bd21
Clones
Arabidopsis full-length cDNA (RAFL) clones
Arabidopsis TAC clones
Brachypodium distachyon full-length cDNA clones
Physcomitrella patens full-length cDNA clones
Poplar full-length cDNA clones
Striga hermonthica full-length cDNA clones
Cassava full-length cDNA clones
Tobacco EST clones
Thellungiella halophila full-length cDNA clones
Brassica rapa EST clones
Individual DNA materials
Plant Cultured Cells
20,790
36,675
21,739
1,207
26
1
251,382
10,752
39,746
149,363
23,100
35,198
19,968
22,221
19,429
12,069
288
54
Seeds
Arabidopsis transposon-tagged mutant lines
Arabidopsis activation-tagged lines
Arabidopsis FOX lines
SASSC seeds including natural accessions
Individual mutant and transgenic lines
Brachypodium distachyon Bd21
Clones
Arabidopsis full-length cDNA (RAFL) clones
Arabidopsis TAC clones
Brachypodium distachyon full-length cDNA clones
Physcomitrella patens full-length cDNA clones
Poplar full-length cDNA clones
Striga hermonthica full-length cDNA clones
Cassava full-length cDNA clones
Tobacco EST clones
Thellungiella halophila full-length cDNA clones
Brassica rapa EST clones
Individual DNA materials
Plant Cultured Cells
20,790
36,675
21,739
1,207
26
1
994,697 resources
251,382
10,752
39,746
149,363
23,100
35,198
19,968
22,221
19,429
12,069
288
54
Situation about International Distribution
Overseas
19,208
Domestic
17,973
Distribution: more than a half of the
resources have been distributed to
overseas countries
Recipient laboratory: total 601 institutes (departments) in 40
countries
USA
149
India 10
Denmark 10
Switzerland 14
Netherland 15
Germany
83
Sweden 22
Canada 25
Spain 27
France 27
China 29
Since 2002
Korea
35
UK
50
USA
Korea
Spain
The Netherland
India
Taiwan
Chile
Austria
Mexico
Ireland
Greece
Iran
Saudi Arabia
Viet Nam
Germany
China
Canada
Switzerland
Australia
Belgium
Poland
Norway
Finland
Portugal
New Zealand
Malaysia
Turkey
UK
France
Sweden
Denmark
Israel
Italy
Argentina
Czech Republic
Hungary
Brazil
Singapore
Pakistan
Uruguay
Plant DNA Resources in
RIKEN BRC to Bridge the Gap
between Gene Function and
Phenotype
“What kind of DNA resources
are useful for
bridging the gene function
and phenotype?”
Plant DNA Resources in
RIKEN BRC to Bridge the Gap
between Gene Function and
Phenotype
Full-length cDNAs (FL cDNAs)
Very useful for further analyses of gene
function, and also large scale gene discovery
projects, or other -omics research
5’UTR
ORF
3’UTR
RIKEN Arabidopsis FL (RAFL) clones
251,382 Clones
・Standard clones in Arabidopsis community
・About 15,000 non-redundant clones
Seki et al. Science (2002) 296, 141-145.
Overexpression of RAFL09-94-K24, encoding receptor-like
protein kinase 1 (RPK1) protein
Drought tolerance!!
Gene Function to Phenotype
Osakabe et al. J. Biol. Chem. (2010) 285, 9190-9201
FOX hunting system
(Full-length cDNA Over-eXpressing gene hunting system)
Arabidopsis
FL cDNA clones
Developed in RIKEN
Plant Science Center
FOX hunting system
WT
FOX
lines
Ichikawa et al. (2006)
Plant Journal 45. 974-985
RIKEN Arabidopsis FL (RAFL) clones
251,382 Clones
・Standard clones in Arabidopsis community
・About 15,000 non-redundant clones
60% of Arabidopsis whole genes
RIKEN Arabidopsis Transcription
factor (RARTR) clones
・400 FL cDNAs for Arabidopsis transcription
factors, absent in RAFL clones
Fujita et al. (2007) BBRC 364. 250-257
FOX system using RIKEN Arabidopsis
Transcription factor (RARTR) clones
Overexpression of Arabidopsis AtbZIP60
confer salt stress tolerance
Control
FOX line1
FOX line2
Fujita et al. (2007) BBRC 364. 250-257
Arabidopsis FOX lines
21,739 lines are available!!
Distributing as seed pool
for phenotype screening
…….
50 Overexpressor lines
1 seed pool
…….
20 seed pool
1 set (20 sets are available)
FOX hunting system is available for every FL clones
(Rice FOX hunting lines)
Rice
FL cDNA clones
About 4000 lines of Rice FOX are available from RIKEN BRC
FL cDNA clones in RIKEN BRC,
Experimental Plant Devision
Full Length Clones
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Arabidopsis clones
Brachypodium distachyon clones
Poplar clones
Cassava clones
Brassica rapa clones
Physcomitrella patens clones
Striga hermonthica clones
Thellungiella halophila clones
251,382
39,746
23,100
19,968
12,069
149,363
35,198
19,429
Application of Arabidopsis gene annotation
to other plants
Arabidopsis genes
Genome resources
Fulfilling gene annotation
SABRE database
Systematic consolidation of Arabidopsis and other Botanical
Resources (FL clones) to cross-search through Arabidopsis
information.
Arabidopsis genes and other
FL clones were related by
homology search
Cross-search of
plant genetic resources
Skewer every FL clones using Arabidopsis gene
information
SABRE :
Arabidopsis gene DB
Systematic consolidation of
Arabidopsis and other
Botanical
REsource
The
Arabidopsis
Information
Resource
Connection using homology
(blastn, blastx)
P. patens
Arabidopsis
Tabacco
P. nigra
DNA resources in RIKEN BRC
Platform to connect
every cDNA resources
SABRE2 database
In addition to the RIKEN BRC clones, user can search the
NBRP plant clone informations such as Tomato, Rice…
RIKEN BRC clones (8 plant species)
Other NBRP clones (7 plant species)
Infrastructure development to
applicate Arabidopsis information
to other plants.
Arabidopsis
Other plant
To Bridge the Gap between Gene
Function and Phenotype…
Our strategy
(DNA resources)
・Arabidopsis FL clones
・Other FL clones
(Plant resources)
・FOX hunting lines
(Database)
・SABRE2, ABRANA
To Bridge the Gap between Gene
Function and Phenotype…
In addition to the
Full length cDNA clones,
we have to totally develop
the bioresources!
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