Developing targeted gene-panel sequencing techniques for the early detection and identification of S. endobioticum in soil and water samples and exploring its applications in pathotyping and viability confirmation

Funding period: 2023-2027

Lead: Sean Li

Total GRDI funding: $214,000

Targeted gene-panel sequencing techniques are used efficiently in the medical field to facilitate the development of precision oncology treatment based on a tumour's molecular profile. The gene panel captures and enriches genes of interest before sequencing, increasing the sensitivity and specificity for the detection of target pathogens and reducing per-sample costs. This research is based on the databases of genomics and transcriptomics sequencing data collected during the Genome Atlantic Environmental fund project on potato wart and potato varieties. Soil and water management are key elements to help prevent the spread of potato wart. In this research project, the early and reliable detection of Synchytrium endobioticum and its identification for pathotyping and viability assessment are targeted on the basis of metagenomics and associated bioinformatics tools developed recently at CFIA for analyzing potato, soil and water samples.