Rapid method to identify the mutated gene

responsible for a trait

A systems approach to understand biological

mechanism

High throughput sequencing to develop next generation

genetic tool for crops

TOC1

X

LHY/ CCA1

PRR7/ PRR9

Y (GI)

Bridging the gap between models and crops

Prof Anthony Hall

• £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 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-TGAC-hardware

Liverpool 2 X 18month post-docs, £135K to build iplant nodeAnthony 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-Liverpool-NGS

Warwick- 2 X 18month post-docs, £135K to build iplant nodeDavid 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-Warwick-System biology

Nottingham - 2 X 18month post-docs, £135K to build iplant nodeTony Pridmore• Build root imaging analysis work flows in iPlant• Root phenotyping tool bench

Iplant UK-Nottingham-image analysis

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

Iplant UK-GARNET

Diverse collection of germplasm

Field phenotyping-genotyping-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

iPlant collaborativeAcross site/community access to data, data analysis workflows and storage.

Epigenetic variation (EWAS)

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

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

Screen mapping populations for specific enhanced PS traitsMapping-by-sequencing pools to identify genes/ markers associated with enhanced PS

Genome wide Epigenetic variation (INTREPID project) across the Watkins collection will be correlated with phenotypic variation inPhotosynthetic efficiency.

Output: association of epi-type with PS phenotypes

• Biomass diversity panel• Primary synthetic diversity panel• BREAD wheat diversity panel• Watkins core collection • Mapping populations Transfer x

DBW10 and Seri / Babax

LAN

LAN

LIV

LIV

LIV

Mapping-by-sequencing

LIV

Output: identification of linked markers or genes

USING NEXT GENERATION GENETIC APPROACHES TO EXPLOIT PHENOTYPIC VARIATION IN PHOTOSYNTHETIC EFFICIENCY TO INCREASE WHEAT YIELD