Population genetics

1.3.1. Theoretical background of pathogen population genetics

The ability of fungal pathogens to compromise yield quantity and quality by overcoming host resistance or developing fungicide resistance is determined by the biological and genetic properties of the population as a whole (McDonald and McDermott 1993). According to McDonald and Linde (2002), the genetic structure of a population is defined as the “amount and distribution of genetic variation within and among populations”. This in turn is a result of the evolutionary forces mode of reproduction, gene flow, genetic drift, mutation and selection acting on the population (McDonald and Linde 2002). The most dangerous pathogens are those that are able to adapt to changing environmental conditions quickly (McDonald and Linde 2002). These pathogens possess a high evolutionary potential that is determined by a mixed reproduction system, a short generation span, a high propagation rate, a high mutation rate, a large effective population size and long-distance dispersal of spores (high amount of gene flow).

A high mutation rate is the main driver for the development of new alleles and thus for genetic variation. Mutations usually occur rarely (mutation rates of 10^-6 are common), but in populations consisting of millions of individuals as in fungal populations, they can have a substantial impact on creating new genotypes (McDonald and Linde 2002; McDonald and McDermott 1993). Genomic studies of pathogens have shown that effectors and virulence genes are often found in rapidly evolving genomic regions, e.g. regions with a high number of retrotransposons and repetitive regions which promote repeat induced point mutations and errors during crossing over (Oliver and Solomon 2010; Rep and Kistler 2010). Such a mutation will however only become a threat when there is strong directional selection on the pathogen population caused by the widespread use of single major resistance genes, which will lead to an increase in frequency of the virulence gene in the population. Additionally, the selected mutants need to be capable of long-distance travel and successful establishment in a new environment (McDonald and Linde 2002).

Most plant pathogenic fungi have a mixed reproduction system, i.e. both sexual and asexual propagation occur in the life cycle (Giraud et al. 2008). Sexual recombination can lead to the

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combination of virulence loci by the generation of new haplotypes and therefore contributes to genetic variation. The asexual stage of fungi usually involves the production and dispersal of large numbers of clonal spores such as conidia. In fungi such as P. teres, many cycles of conidia production can occur during the season, leading to a dramatic increase in population size (see section 1.2.3). This mixed reproduction system confers to the pathogen the ability to overcome host resistance quickly, as sexual recombination can lead to the formation of genotypes with a selective advantage (virulence), which can then quickly rise to high frequency in the population via clonal propagation (McDonald and Linde 2002). The dispersal range of spores is one of the determinants of gene flow. Airborne spores of some species can travel over large distances and allow for the exchange of selective advantageous genotypes over large geographic areas (Brown and Hovmøller 2002). Another important factor that determines the exchange of pathogen genotypes is anthropogenic activity such as trade of seeds, plants and soil between regions, countries and continents, and on a small scale, the transmission of spores and mycelium between fields by contaminated machines.

The biology and the evolutionary potential of a pathogen determines which strategy to apply in resistance breeding (McDonald 2014; McDonald and Linde 2002). Pathogen populations with such properties as described above are usually genetically very diverse and consist of different strains with different pathotypes. Resistance breeding against such pathogens requires the accumulation of several quantitative resistance genes in elite cultivars since the resistance of these cultivars needs to hold up against different pathotypes. The risk of overcoming host resistance in these populations is high. Multigenic resistance is less likely to be overcome since it requires a series of mutations to occur in the pathogen population. If resistance relies on only one major resistance gene, a pathogen population with a high evolutionary potential will overcome the resistance quickly (“boom-and-bust cycle”). Clonal populations on the other hand are more stable and evolve at a much slower rate. Changes in these populations mostly occur via mutation, gene flow or a change in selection pressure.

Pathogens with a small population size, a short range of dispersal and a clonal reproduction system are usually considered low-risk pathogens. McDonald and Linde (2002) established an evolutionary risk model to classify pathogens by the threat they pose based on their biological properties. In this model, where group 1 contains pathogens with a low risk and group 9 those with a high risk, P. teres should be placed in the risk groups 5-7 if moderate gene flow occurs

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or even in the groups 7-9 where gene flow over larger distances occurs. These groups include pathogens with a mixed reproduction system, high effective population size and medium range dispersal such as Parastagonospora nodorum and Rhynchosporium commune (McDonald and Linde 2002). The effect of mutation was not considered in this model since the mutation rate is considered low and similar between pathogen species.

1.3.2. Population genetics of P. teres

The genetic structure of P. teres populations has been analyzed mostly with AFLP markers (Lehmensiek et al. 2010; Rau et al. 2003; Serenius et al. 2007; Serenius et al. 2005;

Statkeviciute et al. 2012; Stefansson et al. 2012), but also restriction fragment length polymorphisms (RFLP) (Wu et al. 2003), RAPD (Jonsson et al. 2000) and SSR markers (Akhavan et al. 2016b; Bogacki et al. 2010; Leišová-Svobodová et al. 2014) have been used. P. teres populations from different countries, e.g. Finland, Iceland, Hungary, South Africa, Canada, Australia and Czech and Slovak Republic have been studied (Akhavan et al. 2016b; Ficsor et al. 2014; Lehmensiek et al. 2010; Leišová-Svobodová et al. 2014; Serenius et al. 2005;

Stefansson et al. 2012).

The majority of population genetics studies conducted in the last years report that P. teres populations possess a great amount of variability. Usually, the genetic variation within populations is larger than between them, and genetic differentiation is usually higher between distant than between adjacent populations (Akhavan et al. 2016b; Campbell et al.

2002; Jonsson et al. 2000; Peever and Milgroom 1994; Serenius et al. 2007; Serenius et al.

2005; Stefansson et al. 2012). This suggests that only a small amount of gene flow occurs between distant populations, although exceptions exist. For example, Leišová-Svobodová et al. (2014) found high genetic variation (GST=0.29-0.31) between adjacent populations (7 m and 5 km) and low variation between populations 250 km apart, so that the relation between these two factors has not been well established and may also depend on other unknown factors.

In many studies, the ratio of the two mating types is not significantly different from 1:1, indicating that sexual recombination occurs frequently under natural conditions (Bogacki et

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al. 2010; Rau et al. 2003; Serenius et al. 2007; Stefansson et al. 2012). The percentage of individuals with unique allele combinations (multilocus genotypes) in sampled populations is usually very high (88-100%) (Akhavan et al. 2016b; Jonsson et al. 2000; Leišová-Svobodová et al. 2014; Serenius et al. 2007; Serenius et al. 2005; Statkeviciute et al. 2012; Stefansson et al.

2012) and only occasionally lower (36-68%) (Campbell et al. 2002; Rau et al. 2003). Only a few authors report that they sampled populations that only consist of one mating type (Leišová-Svobodová et al. 2014; Serenius et al. 2007). Despite a mating type ratio of 1:1, the hypothesis of random mating is often rejected based on tests of association indices, which often suggest clonal reproduction, possibly because of the presence of substructure within the population (Bogacki et al. 2010; Serenius et al. 2007; Statkeviciute et al. 2012).