Genomics Phase 2 Digital Initiative

As the world’s population grows to 9.7 billion by 2050, Australian agricultural production and food security faces opportunities as well as challenges. This has been complicated by global climate change causing extreme weather impacting seasons and water supply, coupled with the unwanted introduction of pest and invasive species. The scientific field of molecular biology will be key to meeting these challenges and making the most of the opportunities.

Molecular biology is concerned with the relationship between DNA (the genome), RNA (the transcriptome), and proteins (the proteome) to find the underlying cause for significant crop traits, such as disease susceptibility, drought resistance and protein content. Such knowledge will underpin new technologies that will enable Australian agriculture to not only survive but to thrive in this environment.

The integrated study of “omic” data at population scale, known as pan’omics, has been undergoing a paradigm shift brought about by recent technological advances. Continual improvements in genomic sequencing are making the collection and use of chromosomal-scale, multi-individual data sets for genomic investigations and genomic-assisted breeding conceivable and affordable. The increasing availability of transcriptomic and proteomic data is supporting fresh approaches to determining the biological cause of traits. Laborious and time-intensive manual collection and analysis of phenotypic (trait) information can now be replaced by a combination of autonomous vehicles, machine-learning/artificial-intelligence, and augmented reality. The SIEF Genomics Digital Initiative’s two programs directly address the opportunities and challenges within these advances.

The Pan’omics Toolbox  has developed new techniques and technologies for the collection, representation, analysis, and visualisation of pangenomic data sets. This improves both comparative and functional genomic analyses, leading to new understandings of the biological cause of significant traits, and supporting genomic-assisted breeding programs. This involved both novel research – the development of new pangenome representation and analysis techniques – as well as the development of practical tools designed to support molecular biologists in the production, use, and analysis of pangenomic data. The Toolbox is sufficiently mature to be used by leading-edge researchers for comparative genomic analysis and is being used internally within CSIRO. An ongoing research program in partnership with the Australian National University is investigating its use for functional genomic analysis. It is projected that with further development the Toolbox could be commercialised within two years.

The Video Phenomics has developed an artificial intelligence (AI)-based prototype phenotyping platform by utilising advanced computer vision and machine learning methods. This automates the detection and quantification of crop traits using farm data collected from equipment such as drones, mounted with sensors like cameras and LIDAR. Information collected in collaboration with a leading cereal breeding company, InterGrain, included crop emergence, spike and spikelet counts, height and biomass index for crop performance monitoring and yield estimation. Outputs include a prototype phenotyping platform with a web portal that allows end users to upload image and video data and generate reports, using AI-based models for analysing the image and video data to extract crop traits. These AI models have been assessed using data acquired from multiple crops at different sites. Augmented Reality (AR) techniques have been developed to accelerate the on-farm collection, curation and visualisation of trait data and the platform will potentially improve phenotyping data collection efficiency. The information retrieved from the crop traits can be used for breeders and farmers to make informed decisions around breeding selections. By partnering with industry, the team will continue to work toward industry uptake.

The outcomes of the SIEF Genomics Initiative will significantly improve the ability of scientists, breeders, and farmers to meet the challenges and opportunities raised by population growth, climate change and globalisation. The pathway to impact for the Initiative will involve a combination of industry partnerships, cooperative research with other institutions, and application to internal CSIRO research and development programs. Both the Pan’omics Toolbox and the Video Phenomics platform provide opportunities to transform the crop breeding process and enhance traditional farming practices leading to increased profitability and food security.