The High Resolution Plant Phenomics Centre (HRPPC) is part of the Australian Plant Phenomics Facility and focuses on deep phenotyping and reverse phenomics through development of next generation tools to measure performance of plants ranging from model species to crops. A major aim of the HRPPC model plant module is to find genes of agricultural importance using high resolution phenotyping of model plant species. One such project is an international collaboration using the model species Brachypodium distachyon to accelerate the breeding of next generation biofuel crops and discover genes responsible for important traits in wheat. Brachypodium, unlike switchgrass or miscanthus, has all the attributes of a model species (small, fully sequenced genome and short life cycle) allowing high throughput screening. We developed various non-invasive and destructive assays for growth, biomass, photosynthesis and root growth and architecture. Large phenotypic variability of biomass accumulation was observed in a set of 160 natural accessions of Brachypodium. Root growth and architecture was characterised in these ecotypes and show significant variation in total root length, root type distribution (nodal and seminal) or shoot/root ratio. Contrasting ecotypes are currently under investigation using high resolution imaging analysis techniques to identify the optimal combination of these phenotypic traits under limiting water and nutrients and to determine the underlying genomic regions responsible. Since Brachypodium is a typical grass and shares a high degree of genetic similarity and markers with commercial crops, it would be possible to extend the knowledge gained from this project to improve more complex plants species.