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 Bridging the gap between models and crops Prof Anthony Hall
Established in 2008 by the NSF and a $50M grant, renewed in UK iPLANT IPLANT COLLABORATIVE
£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 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-Liverpool-NGS
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-Warwick-System biology
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-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 collaborative Across 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 traits Mapping-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 in Photosynthetic 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 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