Genomic Investigation of the Strawberry Pathogen Phytophthora fragariae Indicates Pathogenicity Is Associated With Transcriptional Variation in Three Key Races.

The oomycete Phytophthora fragariae is a highly destructive pathogen of cultivated strawberry (Fragaria × ananassa), causing the root rotting disease, "red core". The host-pathogen interaction has a well described gene-for-gene resistance relationship, but to date neither candidate avirulence nor resistance genes have been identified. We sequenced a set of American, Canadian, and United Kingdom isolates of known race type, along with three representatives of the closely related pathogen of the raspberry (Rubus idaeus), P. rubi, and found a clear population structure, with a high degree of nucleotide divergence seen between some race types and abundant private variation associated with race types 4 and 5. In contrast, between isolates defined as United Kingdom races 1, 2, and 3 (UK1-2-3) there was no evidence of gene loss or gain; or the presence of insertions/deletions (INDELs) or Single Nucleotide Polymorphisms (SNPs) within or in proximity to putative pathogenicity genes could be found associated with race variation. Transcriptomic analysis of representative UK1-2-3 isolates revealed abundant expression variation in key effector family genes associated with pathogen race; however, further long read sequencing did not reveal any long range polymorphisms to be associated with avirulence to race UK2 or UK3 resistance, suggesting either control in trans or other stable forms of epigenetic modification modulating gene expression. This work reveals the combined power of population resequencing to uncover race structure in pathosystems and in planta transcriptomic analysis to identify candidate avirulence genes. This work has implications for the identification of putative avirulence genes in the absence of associated expression data and points toward the need for detailed molecular characterisation of mechanisms of effector regulation and silencing in oomycete plant pathogens.

Induced Resistance as a Possible Means to Control Diseases of Strawberry Caused by Phytophthora spp.

Two putative elicitors of disease resistance (acibenzolar-S-methyl and chitosan) were tested for their effect on crown rot (Phytophthora cactorum) in strawberry. The effect of both compounds was enhanced when the time between treatment and inoculation was prolonged from 2 to 20 days. There were no significant differences between treatments when the concentration of acibenzolar-S-methyl was increased from 10 to 1,000 µg a.i./plant. The lowest tested concentrations of chitosan (10 and 50 µg a.i./plant) resulted in a lower disease score compared with the highest concentrations (250 or 1,000 µg a.i./plant). There were no differences in disease score between treatment with fosetyl-Al, acibenzolar-S-methyl, or chitosan when applied 5 or 15 days before inoculation. The effect of acibenzolar-S-methyl and chitosan also was tested against P. fragariae var. fragariae in alpine strawberry (Fragaria vesca var. alpina cv. Alexandria). Chitosan had no effect, whereas fosetyl-Al and all treatments with acibenzolar-S-methyl (50 or 250 µg a.i./plant; 5, 10, 20, or 40 days before inoculation) reduced the severity of the disease. There were no significant differences between acibenzolar-S-methyl and fosetyl-Al when applied at the same time. Acibenzolar-S-methyl and chitosan at concentrations of 0.5, 5, 50, and 500 µg a.i. ml-1 in V8 juice agar were tested for possible effects on P. cactorum and P. fragariae var. fragariae in vitro. Only chitosan at concentrations of 50 and 500 µg a.i. ml-1 had a growth-retarding effect on P. cactorum. Both acibenzolar-S-methyl and chitosan at a concentration of 500 µg a.i. ml-1 reduced the growth rate of P. fragariae var. fragariae.