Download iplant collaborative

Bridging the gap between models
and crops
A systems approach to
understand biological
mechanism
LHY/
CCA1
PRR7/
PRR9
Y (GI)
Rapid method to identify
the mutated gene
responsible for a trait
High throughput sequencing
to develop next generation
genetic tool for crops
TOC1
X
Prof Anthony Hall
Iplant UK
• £2M BBSRC funded project with TGAC, Warwick, Nottingham
and Liverpool- Funded as a capital investment
• Putting the Iplant system on top of TGAC Hardware,
providing community access
• Work with the community to ensure take up of the system
and develop resources around imaging, systems biology and
NGS
Liverpool 2 X 18month post-docs, £135K to build iplant node
• Liverpool developing workflows NGS around wheat and
Arabidopsis
• In addition to develop community led workflow around NGS
Iplant UK-TGAC-hardware
TGAC 2 X 18month post-docs, £1M to build iplant storage and
memory node with high speed connection
Rob Davey, Erik van den Bergh, Tim Stitt
• Build iplant on top of UK infra structure
• Assist with building test nodes at regional sites
Iplant UK-Liverpool-NGS
Liverpool 2 X 18month post-docs, £135K to build iplant node
Anthony Hall, Ryan Johnson, Ritesh Kreshna
• Update and maintain existing NGS workflows
• Liverpool developing workflows NGS around wheat and
Arabidopsis. Mapping-by-sequencing; RNA-seq for wheat; de
novo assemble for pan-genome and non-reference assembly
• In addition to develop community led workflows around NGS
Iplant UK-Warwick-System biology
Warwick- 2 X 18month post-docs, £135K to build iplant node
David Wild, Sam Mason
• Converting code to run effectively in iplant ie. Matlab code.
• Build systems biology software packages in the iplant
environment
• Network analysis; promoter analysis tools
Iplant UK-Nottingham-image analysis
Nottingham - 2 X 18month post-docs, £135K to build iplant
node
Tony Pridmore
• Build root imaging analysis work flows in iPlant
• Root phenotyping tool bench
Iplant UK-GARNET
GARNet- Jim Murray, Ruth Bastow, Geraint Parry
• Host future iplant workshops
• Produce iplant blog
• Articles about using iPlant in GARNISH
• Advertise and promote iPlant
• Current have 952 registered UK users
Diverse collection of germplasm
iPlant collaborative
Across site/community
access to data, data
analysis workflows and
storage.
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Biomass diversity panel
Primary synthetic diversity panel
BREAD wheat diversity panel
Watkins core collection
Mapping populations Transfer x
DBW10 and Seri / Babax
LIV LAN
Epigenetic variation (EWAS)
Genome wide Epigenetic variation
(INTREPID project) across the
Watkins collection will be correlated
with phenotypic variation in
Photosynthetic efficiency.
Output: association of epitype with PS phenotypes
PROJECT IMPACT
• Informatics tools and a complete
dataset in the hands of crop breeders
and physiologists
• Molecular (KASP-assays) and phenotypic
markers for breeding programs
• Potentially, genes/pathways as new
targets for research and engineering
USING
NEXT
GENERATION
GENETIC
APPROACHES TO EXPLOIT PHENOTYPIC
VARIATION IN PHOTOSYNTHETIC EFFICIENCY
TO INCREASE WHEAT YIELD
LIV
Field phenotypinggenotyping-GWAS
• Field phenotyping of 1500 lines
using spectral indices and canopy
temperature
• Genotyping using 12Mb exome
capture
• GWAS
Outputs: ID genomic regions, tail
panel conferring enhanced PS
LIV LAN
Fine phenotyping and
BSA
• Fine phenotyping of phenotypic
tails in the greenhouse and field.
• DNA from tails pooled to identify
potential genes/marks underlying
trait.
Output: Physiological description of
enhanced P/sin cultivar; identification
of linked markers or genes
LIV
Mapping-by-sequencing
Screen mapping populations for
specific enhanced PS traits
Mapping-by-sequencing pools to
identify genes/ markers associated
with enhanced PS
Output: identification of linked
markers or genes