Analysis of Population‐Level Avirulence and Virulence Genetic Frequencies Provides Insight Into Resistance Gene Rotation and Plant Disease Epidemiology

ABSTRACT Blackleg disease, caused by Leptosphaeria maculans , leads to significant yield losses to canola ( Brassica napus ) production worldwide. Whilst the impact of this disease can be minimised by genetic resistance in B. napus , pathogen populations evolve quickly to overcome this resistance and restore virulence. To prevent yield losses due to the evolution of virulence, population‐level monitoring is required so that timely warnings can be provided to growers and breeders. Here, we develop high‐throughput sequencing‐based molecular markers for L . maculans avirulence or virulence towards five B. napus resistance genes that allow their frequency to be determined within entire populations, rather than individual isolates. Using these markers on Australian spore populations, we show that avirulence alleles are present in populations at low frequencies, even when the corresponding resistance gene is deployed in the plant host. Furthermore, virulence frequencies can vary dramatically from different pieces of stubble (crop debris) within the same paddock. These results show that population‐level markers are an effective tool for monitoring virulence and highlight the significant gaps in the current understanding of the breakdown of plant genetic resistance, whereby it is unclear what percentage of the population is required to be avirulent for a resistance gene to be effective.