Metalaxyl Resistance in Phytophthora infestans: Assessing Role of RPA190 Gene and Diversity Within Clonal Lineages

Abstract

Prior work has shown that the inheritance of resistance to metalaxyl, an oomycete-specific fungicide, is complex and may involve multiple genes. Recent research indicated that a single nucleotide polymorphism (SNP) in the gene encoding RPA190, the largest subunit of RNA polymerase I, confers resistance to metalaxyl (or mefenoxam) in some isolates of the potato late blight pathogen Phytophthora infestans. Using both DNA sequencing and high resolution melt assays for distinguishing RPA190 alleles, we show here that the SNP is absent from certain resistant isolates of P. infestans from North America, Europe, and Mexico. The SNP is present in some members of the US-23 and US-24 clonal lineages, but these tend to be fairly sensitive to the fungicide based on artificial media and field test data. Diversity in the level of sensitivity, RPA190 genotype, and RPA190 copy number was observed in these lineages but were uncorrelated. Controlled laboratory crosses demonstrated that RPA190 did not cosegregate with metalaxyl resistance from a Mexican and British isolate. We conclude that while metalaxyl may be used to control many contemporary strains of P. infestans, an assay based on RPA190 will not be sufficient to diagnose the sensitivity levels of isolates.

Genetic analysis of late blight resistance in Solanum pimpinellifolium accession PI 270441: Heritability and response to selection

“…Several P. infestans clonal lineages, including US‐6, 7, 8, 11 and 20, have shown resistance to Metalaxyl or Mefenoxam (Metalaxyl‐M), two of the most effective main ingredients of systemic fungicides against the pathogen. Intermediate resistance to Metalaxyl/Mefenoxam has also been observed in clonal lineages US‐21, 22, 23 (currently the most prevalent in the United States), and 24 (Chowdappa et al., ; Gevens, ; Matson, Small, Fry, & Judelson, ; Roberts, ).…”

Analysis of RPA190 revealed multiple positively selected mutations associated with metalaxyl resistance in Phytophthora infestans

“…Therefore, we believe that these three AA mutations (V1476G, P980S and F382Y) are essential for metalaxyl resistance. This may explain the previously inconsistent results in which only the role of the F382Y mutation was investigated . We checked the complete sequences from Matson's and Randall's studies and found all resistant isolates except for one in Matson et al .…”

“…None of the sensitive isolates carried any of these mutations, except for isolate 11016 in the Matson et al . study . We also checked isolates with the 1145 SNP (corresponding to F382Y) from both studies and found that all sensitive isolates carried a TT nucleotide except for one in the Randall et al .…”

“…This report showed that T1145A (the corresponding AA should be F382Y but was labeled as Y382F in the previous study) of RPA190 was associated with mefenoxam insensitivity in 86% of isolates tested . However, a later study reported that one‐third of TT homozygotes (6/18) in nucleotide position 1145 were resistant to metalaxyl, suggesting that the mutation was only loosely associated with metalaxyl resistance in P. infestans . Given the use of fungicide for P. infestans control, it is important to resolve the inconsistency in these reports.…”

In-Vitro Inhibition of Pythium ultimum, Fusarium graminearum, and Rhizoctonia solani by a Stabilized Lactoperoxidase System alone and in Combination with Synthetic Fungicides

“…All fungicides impose a selection pressure on their target pathogen populations, and some fungicides are prone to the development of resistance. This is especially true for fungicides with a single target site, as mutations in the target gene can lead to the selection of a resistant sub-population in the pathogen population with fungicide applications [4][5][6][7]. Some widely used examples of such fungicides include succinate dehydrogenase inhibitors (SDHIs), quinone outside inhibitors (QoIs), de-methylation inhibitors (DMIs), and phenylamides (PAs).…”