Molecular evolution of the AvrLm7 avirulence gene of Leptosphaeria maculans under resistance gene selection in the field is driven by its genomic location, sexual reproduction and cropping practices

Leptosphaeria maculans, the agent of stem canker of oilseed rape, develops “gene-for-gene” interactions with its host plant, and shows a high evolutionary potential to “breakdown” novel resistance sources in the field. The newly marketed Rlm7 resistance allowed us (i) to monitor the evolution of populations faced to this resistance over three consecutive years, (ii) to identify the nature and sequence of molecular events responsible for the loss of the corresponding AvrLm7 avirulence, and (iii) to compare the durability of Rlm7 in two contrasted cropping systems, i.e. a “cautious” system involving a diversified crop sequence and ploughing of oilseed rape stubble after harvest, and a “risky” system without crop sequence and with simplified tillage. Population genetics approaches were used to evaluate the main population traits linked with birth and dissemination of the virulent mutations in the populations. A total of 1967 isolates were collected, over the three years, either on a cv. harbouring Rlm7 or on a cv. devoid of it, then phenotyped and genotyped. During this period the ratio of avrLm7 virulent isolates in local populations, as estimated from isolates collected on the susceptible cv., increased from 0 [0.0, 1.9] % to 36.2 [30.0, 42.7] % in the field submitted to the “risky” system. All possible molecular events leading to virulence were found within our sampling with an over-representation of complete deletions and wide-scale RIP mutations of the coding sequence. In contrast, less than 1% of avrLm7 isolates were collected on the susceptible cv. in the field submitted to the “cautious” system. The high mutability of AvrLm7 appeared to be mainly driven by its repeat-rich genome environment combined with the obligatory annual sexual stage that promotes large-scale deletions, translocations, duplications and RIP events, rather than gene flow, which appears to be a minor threat for the resistance breakdown in the L. maculans-B. napus pathosystem. The major role of the sexual stage in generating virulent isolates may explain the increased durability of Rlm7 in the “cautious” system where ploughing prevents mating by burying stem residues on which pseudothecia and ascospores are produced. This study permitted to quantify the role of cropping practices in the preservation of the efficacy of a new specific resistance. This information can now by used to develop models aimed at helping the design of durable management strategies. At the national level, the frequency of avrLm7 isolates in 2010-2011 still remains at a low level (less than 4%) in spite of 5 years of commercialization of Rlm7 and its deployment on around 20% of oilseed rape acreage since 2008. The reasons for this limited expansion of virulent isolates will be discussed