Thesis subject
Elucidating the population dynamics of a plant pathogenic protist
Plasmodiophora brassicae is one of the most important Brassica crop pathogens, causing clubroot disease. Control is difficult as different pathotypes of P. brassicae exist that can avoid the currently most successful control strategy of breeding resistant hosts. The resistance of plants is pathotype specific and frequently broken in the field. It is not known if the use of resistant plants forces the pathogen to evolve into new pathotypes, or if less abundant more aggressive pathotypes become dominant by the presence of resistant plants.
Pre-work showed that there are at least 2 different rRNA types (ribotypes) of P. brassicae that can occur in one plant. In this project you will use long read Nanopore sequencing to characterize the rRNA sequence variation of isolates and analyse the ratio of the ribotypes in different host plants. In a greenhouse experiment you determine if and how the intraspecific population structure changes when the pathogen is multiplied in different host plants.
You will gain experience in state- of-the-art long-read Nanoporesequencing using the MinION. You will use this technology to examine the intraspecific population dynamics of an important Brassica pathogen. You will use this information to develop ribotype specific primers and perform qPCRs. You are most welcome to develop and add your own ideas to the project. Your findings might become part of a scientific publication and can have a direct impact for optimized breeding strategies.