Genomics Digital Initiative

 

Ears of wheat (Source: CSIRO)

Genomic science is entering an era where high resolution data across large populations are now achievable. This opens the potential for a paradigm shift in the role that genomic data can play in knowledge gain and industry innovation. Genomics based scientific advances within the agricultural sector promises new avenues for the genetic improvement of agricultural stock and improved productivity, resilience and value generation in breeding programs in Australia and globally. These avenues, for example genomic breeding strategies and genetic engineering, rely on accurate data science approaches and software prediction tools. Unfortunately, current data methods are under-equipped to analyse and exploit population scale genomics data. There is an urgent need to develop new data science approaches that can derive new understanding of biological systems. These new digital approaches seek to enhance and accelerate the ability to map function between the genomes of a population to their respective observable characteristics or phenome, such as flowering time or number of wheat spikes.

To achieve these outcomes, the Genomics Digital Initiative pilot focussed on the exploration and development of advanced technologies and data science techniques to improve on current approaches for data capture, analysis and, visualisation and translation of results, for complex and high dimensional population-scale genomics datasets. The pilot focussed on wheat genomics as a proof of value analysis. Wheat was chosen as valuable test case for complex population genomics due to the large and polyploid nature of the wheat genome, its existing data resources within CSIRO and the importance of the wheat industry to the Australian economy.

The Genomics Pilot successfully generated a number of transferable and reusable outcomes including immersive visualization tools, graph based approaches for analysing complex genomics data, foundational research into graph based representations of population scale data, and the automation of data collection processes through the creation of a prototype artificial intelligence (AI) algorithm.

Due to the pilot nature of the Digital Initiative, further research and development is required to ensure outcomes will make an impact for Australian wheat producers. However, a number of key outcomes set the foundations for technology platforms with clear impact pathways. The AI prototype platform has attracted strong industry interest and through further research and development may provide a clear opportunity to transform the breeding process in cereal crops. The foundational graph research provides the basis of a potential pathway and novel software platform for the full exploitation of population scale genomics, and more generally ‘omics (for example proteomics and transcriptomics). Both of these platforms are proposed to form the next phase, building upon the key outcomes from this pilot Initiative.