Integrative bioinformatics platform, data integration and modelling

Technological and analytical advances in plant science are increasingly data intensive. While this offers new opportunities for understanding plant biology and for precision plant breeding, it also brings challenges for data management and staff training. We propose to build a common platform for data analysis which will function across the Energy Grasses & Biorefining and Crop Genetics, Genomics & Germplasm ISPGs. The aim is to develop storage and archiving capacity and relational integration between datasets. Databases will be built to manage genomic and phenotypic data. These databases will complement the breeding database and visualisation system MSCAN, a MySQL database system with a web-based interface. Software tools will be developed to allow cross database queries to retrieve data for analysis and visualisation. The aim is to promote synergistic activities within and across the ISPGs, with the wider research community and to enable the application of computational, mathematical and statistical tools to better understand the relationship of genotype, phenotype and the environment. Integrated datasets will be systematically analysed using bioinformatics, statistics and data mining methodologies to facilitate mass genotyping, and the identification of SNPs and other polymorphisms. We will use the informatics platform to identify ideotypes which combine optimum combinations of traits for different environments and end use. The crop models will allow analyses to predict the sensitivity of target traits under current and future climates. These outputs provide inputs for life-cycle and economic analyses, which will be linked right through to genotypes.