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sector_ico_Agrifood_trans Agrifood

Application of single-cell genomics to unravel origin and evolution of devastating crop pathogens

  • Project Leaders: Gurcharn Brar, Guus Bakkeren
  • Institutions: University of British Columbia (UBC)
  • Budget: $80000
  • Program/Competition: Sector Innovation Program
  • Genome Centre(s): Genome British Columbia
  • Fiscal Year: 2020
  • Status: Active

Crop pathogens jeopardize global food production by reducing yield and quality. Stripe rust, caused by the fungus Puccinia striiformis f. sp. tritici (Pst), is one of the five most devastating pathogens of wheat and barley in Canada, including BC’s Peace Region, with an estimated ~1-3% (more in epidemic years) yield loss annually which translates into millions of dollars.  

The pathogen evolves rapidly to overcome resistance in cultivars and mutations in the genome are thought to be the cause.  Mechanisms causing these fungi to change their genetic make-up have recently been found. Species such as Pst can create variation through mating between individuals from different genetic groups on a different plant species but can also re-assort their genetic material by exchanging nuclei between individuals while they both grow in the plant. This latter process is called somatic hybridization and we have preliminary evidence that this happened in Pst lineages in Canada. However, the extent of genetic variation it creates and its role in pathogen evolution is not well-understood.

It is important to study the origin and evolution of lineages because the genetic re-assortment among individuals often leads to more virulent pathogens which can then cause disease on wheat cultivars previously resistant to earlier variants.  The sequencing of whole genomes of single cells will allow us to precisely study the content and origin of each nucleus and hence the genetic make-up of the lineages we find among field samples.  

This research will lay the foundation for the use of rapid, single-cell genomics-based tools for ongoing pathogen surveys of cereal rusts.  Understanding the role of somatic hybridization in wheat rust pathogens in the field will help us understand better how and where new, possibly more virulent lineages appear and their impact on wheat production, and lead to improved diagnostics and better management strategies. This work will also inform and complement ongoing Canadian-led genomics research in wheat with respect to breeding for resistance against these diseases.