The deployment of virus-resistant crops often leads to the emergence of resistance-breaking (RB) pathogens that suppress the yield benefit provided by the resistance. Although breakdowns are well known for plant genes conferring total, i.e. qualitative, resistance to the virus, they are still poorly understood for plant genetic factors conferring partial, i.e. quantitative resistance. Furthermore, it has been proved for several pathosystems that combining qualitative and quantitative resistances can increase the durability of the qualitative resistance. Two mechanisms can explain this result : either (i) an increase of genetic drift in the virus population, or (ii) a decrease of the selection advantage of the RB mutant. Here, we aim at disentangling the role of these two mechanisms on the durability of plant qualitative resistances to viruses.

 

To investigate this, we follow by high-throughput sequencing the within-host demo-genetic dynamics of five Potato virus Y (PVY) variants in sixteen contrasted pepper plant genotypes, carrying a qualitative resistance and different combinations of quantitative resistances. PVY variants carry distinct mutations, each mutation conferring weak to strong adaptation to the qualitative resistance. We measure the within-host virus variants frequencies and the relative virus population size at different time points. We estimate the fitness of each virus variant by fitting a Lotka-Volterra model of competition between variants to these data. We assess the strength of genetic drift by analysing and modeling between-host variances of the variants frequencies at each time point. With this modeling approach, we can determine how quantitative resistance can increase the durability of qualitative resistance, and provide criteria to screen host genotypes with sustainable pathogen resistance.

quantitative resistance, genetic drift, selection advantage, viral population dynamics, durable resistance.