Sequence diversity in the large subunit of RNA polymerase I contributes to Mefenoxam insensitivity in Phytophthora infestans

Abstract

Phenylamide fungicides have been widely used for the control of oomycete-incited plant diseases for over 30 years. Insensitivity to this chemical class of fungicide was recorded early in its usage history, but the precise protein(s) conditioning insensitivity has proven difficult to determine. To determine the genetic basis of insensitivity and to inform strategies for the cloning of the gene(s) responsible, genetic crosses were established between Mefenoxam sensitive and intermediate insensitive isolates of Phytophthora infestans, the potato late blight pathogen. F1 progeny showed the expected semi-dominant phenotypes for Mefenoxam insensitivity and suggested the involvement of multiple loci, complicating the positional cloning of the gene(s) conditioning insensitivity to Mefenoxam. Instead, a candidate gene strategy was used, based on previous observations that the primary effect of phenylamide compounds is to inhibit ribosomal RNA synthesis. The subunits of RNA polymerase I (RNApolI) were sequenced from sensitive and insensitive isolates and F1 progeny. Single nucleotide polymorphisms (SNPs) specific to insensitive field isolates were identified in the gene encoding the large subunit of RNApolI. In a survey of field isolates, SNP T1145A (Y382F) showed an 86% association with Mefenoxam insensitivity. Isolates not showing this association belonged predominantly to one P. infestans genotype. The transfer of the 'insensitive' allele of RPA190 to a sensitive isolate yielded transgenic lines that were insensitive to Mefenoxam. These results demonstrate that sequence variation in RPA190 contributes to insensitivity to Mefenoxam in P. infestans.

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

“…It has been suggested that resistance to metalaxyl in P. infestans is controlled by only one or two major loci in close proximity, along with a host of minor genes. One such locus has recently been identified in the large subunit of RNA polymerase I (Randall et al ., ). This hypothesis is consistent with the pattern of resistance observed in the isolates of the present study, where most isolates fell into the two extremes of highly sensitive with an IC 50 below 1, or highly resistant with an IC 50 above 500 (Fig.…”

Efficacy of SDHI fungicides, including benzovindiflupyr, against Colletotrichum species

“…Moreover, sequence diversity in the large subunit of RNA polymerase I has been analysed recently using isolates of Phytophthora infestans (Mont.) de Bary, insensitive to the oomycete fungicide mefenoxam, and the association of one single nucleotide polymorphism in subunit RPA190 with insensitivity to this fungicide has been found . The authors pointed out the possibility that insensitivity to mefenoxam might have arisen on multiple occasions in different pathogen genotypes, leading to independent SNPs encoding changes responsible for insensitivity.…”

The Top 10 oomycete pathogens in molecular plant pathology

“…The phenylamide metalaxyl was one of the first chemicals to exhibit specificity to oomycetes. Soon after its introduction and widespread use, fully insensitive strains emerged, but only 35 years later was the molecular basis of this insensitivity uncovered (Randall et al ., ). Mining of the P. infestans genome has revealed many novel proteins with domain combinations that are unique to oomycetes (Seidl et al ., ).…”