Melanie Montes:
Population Genetics of Phytophthora infestans

Date: 20-03-2017    Supervisor: Søren Rosendahl & Rasmus Kjøller

The pathogen Phytophthora infestans (Mont. de Bary) is the causal agent of late blight on solanaceous plant species, and is responsible for huge losses in potato crops each year. Potato fields are therefore extensively sprayed with control chemicals, often over 10 times in a single growing season. Currently the decision of when to spray fungicides is largely based on meteorological data, but the hopes of this thesis were to lay the foundation for a genetics-based early warning system that would use markers for phenotypic traits, such as virulence or resistance to certain fungicides, to make more informed management decisions.

The first step was to characterize the population structure of P. infestans in order to gage the adaptive potential of the population and hence the plausibility of such a system. In Chapter 2 this was done for the 2013 Danish population using a system of 10 short sequence repeat (SSR) markers and single nucleotide polymorphism (SNP)-based mitochondrial haplotyping of over 80 isolates. Both mating types, A1 and A2, necessary for sexual reproduction were present in most fields, but tests for recombination showed that clonal reproduction is still dominating in Danish populations. The dynamics of resistance to the fungicide Metalaxyl-M throughout the growing season were also characterized. Resistance phenotypes were linked to specific SSR alleles, which demonstrates the potential for a more precise SNP-based marker system for predicting resistance.

In Chapter 3 the population structure of the 2014 outbreak of P. infestans in Denmark was described in more detail through the use of Restriction-site Associated DNA sequencing (RADseq), for the first time in P. infestans, to generate a much higher number (55 288) of SNP markers spread throughout the whole genome. This dataset also allowed for the determination of ploidy, and it was found that the Danish population consists primarily of diploids, with signs of possible aneuploidy. Despite an increased potential for sexual reproduction in diploid individuals, it was confirmed that the population displayed significant linkage disequilibrium and was clonal. The structure also pointed toward limited gene flow between fields, which could explain why one doesn't observe single clonal genotypes taking over the entire region.

Finally, Chapter 4 presents a pilot study and one of the first attempts at collecting aerial sporangia from the field using a spore sampler, and quantifying them using quantitative real-time PCR (qPCR). It was found that in 2014 weather data was a better predictor of outbreaks in the field than the aerial spore number quantified using a single nearby spore trap and this qPCR technique. The system did however show enough sensitivity to detect a single spore, and while spore number alone may not be a useful predictor, there may be a future application in amplifying specific markers for phenotypic traits.