Population genetics of Phytophthora infestans in Denmark reveals dominantly clonal populations and specific alleles linked to metalaxyl‐M resistance

Abstract

Control of the potato late blight pathogen Phytophthora infestans relies heavily on chemicals. The fungicide metalaxyl‐M (Mefenoxam) has played an important role in controlling the disease, but insensitivity to the fungicide in certain isolates is now of major concern. A genetic basis for resistance to metalaxyl suggests the possibility for linking resistance phenotypes to specific population genetic markers, but in order to do this, the population genetic structure and mode of reproduction in a population must first be well described. The dynamics of metalaxyl‐M resistance in the Danish population of P. infestans was characterized over the course of the 2013 growing season, as was the population genetic structure, using simple sequence repeat (SSR) genotypes and single nucleotide polymorphism (SNP)‐based mitochondrial haplotyping of over 80 isolates. Both mating types A1 and A2 were present in most fields, but tests for recombination showed that clonal reproduction dominates in Danish populations. Genotype was not linked to haplotype and no differentiation was observed at the haplotype level, but rather between fields. Resistance phenotypes were linked to specific SSR alleles, demonstrating the potential for a more precise SNP‐based marker system for predicting resistance to metalaxyl‐M.

Population genomics of an outbreak of the potato late blight pathogen, Phytophthora infestans, reveals both clonality and high genotypic diversity

“…None of the MLGs based on SNPs data were found in more than one field, even later in the season when asexual sporangia should have had sufficient time to spread across fields. This finding is in concordance with what was observed in the same potato‐growing region the previous year, where the measure for differentiation, θ , was significant between fields (Montes et al , ). Despite the field‐level subdivision, there was no significant signal of isolation by distance ( P = 0.114).…”

“…Past studies of Scandinavian populations have shown mixed results in regard to the index of association, with some showing an overall significant I A ( P < 0.001; Brurberg et al , ) and others a lack of significance for the overall population ( P = 0.73 in Denmark), but significant I A at the field level for only some fields (Sjöholm et al , ). In a 2013 analysis of the Danish population, the I A was also significant ( P < 0.001), suggesting that the population is clonal (Montes et al , ). However, these previous studies are all based on SSRs.…”

“…Six individuals collected from Denmark in 2013, and genotyped with ten SSR markers in a previous study (Montes et al , ), were whole‐genome sequenced (Table ). In order to ensure at least one sample with a high coverage, sample 13‐3‐5 was chosen to make up the largest portion ( c .…”

“…In Scandinavia, however, studies have revealed a population structure that differs from other parts of Europe. Populations with highly diverse genotypes (Brurberg et al , ; Montes et al , ; Sjöholm et al , ), the presence of two mating types (A1 and A2) in roughly equal proportion, and evidence of soil‐borne inoculum, oospores and over‐wintering in the soil have led to the general conclusion that sexual reproduction is taking place in Scandinavia (Yuen and Andersson, ). Genetic analyses for linkage disequilibrium and recombination based on SSR data have, however, led to conflicting results (Brurberg et al , ; Montes et al , ; Sjöholm et al , ), so the degree to which sexual reproduction is actually occurring is still debated and would benefit from analysis with an alternative genetic marker system with higher resolution in detecting genetic variation at fine sampling scales.…”

“…More information on these isolates can be found in Montes et al . (), where they are characterized using ten SSR markers.…”