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bioRxiv · 10.1101/2024.12.26.630446

Clonal expansion from standing genetic variation underpins the evolution of an emerging plant pathogen in Australia

Sparks, A. L.·Adorada, D. L.·Colombi, E.·Kelly, L.·Young, A.·Knight, N. L.·Vaghefi, N.
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Abstract

Pathogens can evolve rapidly, leading to the emergence of novel strains that can overcome commercially deployed host plant resistance. Understanding the genetic and phenotypic diversity and population dynamics of plant pathogens is crucial to inform breeding programs targeting resistance. Tan spot, otherwise known as bacterial wilt, caused by Curtobacterium flaccumfaciens pv. flaccumfaciens, is a destructive disease of mungbean in Australia. Since the 1990s, several mungbean cultivars with partial resistance to tan spot have been released; however, cultivars initially rated as moderately resistant were later rated as moderately susceptible to tan spot. This study investigated the genetic and phenotypic diversity and temporal evolutionary dynamics of C. flaccumfaciens pv. flaccumfaciens in Australian mungbean fields. Whole-genome sequencing of 119 isolates collected from mungbean and other legumes (1986-2019) enabled analyses of pathogen evolution in Australia and in a global context. Results revealed that clonal expansion from standing genetic variation, rather than introduction of novel genotypes, has driven the evolution of this pathogen in Australia since the 1980s. Glasshouse trials confirmed the role of a plasmid in pathogenicity of C. flaccumfaciens pv. flaccumfaciens but found no significant differences in aggressiveness between clonal lineages. This study underscores the importance of understanding pathogen diversity and aggressiveness to guide breeding programs for effective and durable disease resistance and highlights the need for further studies on the competitive fitness of isolates and characterisation of private alleles linked to dominant clonal lineages. SignificanceTan spot is an increasingly significant pathogen affecting beans and mungbean worldwide, with a broad host range and quarantine importance in many countries underscoring the need for effective breeding strategies to manage the disease. Our research provides insights into genetic and phenotypic diversity of this important plant pathogen and temporal changes in its population structure in Australia, which are crucial for developing informed breeding strategies and managing the spread and impact of the disease. This work also underscores the critical need for robust, validated screening protocols and selection of aggressive, locally representative isolates for resistance breeding to ensure accurate assessment of resistance in crops for effective and durable resistance.

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Sparks, A. L., Adorada, D. L., Colombi, E., Kelly, L., Young, A., Knight, N. L., Vaghefi, N.. 2024-12-27. Clonal expansion from standing genetic variation underpins the evolution of an emerging plant pathogen in Australia. https://doi.org/10.1101/2024.12.26.630446

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