Polymorphism of avirulence genes in potato late blight pathogen Phytophthora infestans as characterized by SSCP analysis

Fighting late blight, economically the most important of potato diseases, is greatly hampered by rapid changes in the populations of the pathogen Phytophthora infestans: new pathotypes turn up owing to pathogen evolution and migration and overcome potato varieties that were previously considered resistant. Early recognition of the changes in P. infestans populations would greatly assist potato protection against late blight. The pathogenicity of P. infestans depends on the (a)virulence genes (Avr genes), among which the best known are the genes encoding RXLR effectors. This is the first report on polymorphism of these genes when characterized by single-strand conformation polymorphism (SSCP) analysis. Highly reproducible SSCP patterns combine electrophoretic zones corresponding to the Avr alleles. Ten Avr genes were studied in two series of P. infestans samples: single cell lines obtained from the isolates collected in the potato genetic collection of the N.I. Vavilov Institute of Plant Genetic Resources (VIR), Pushkin, St. Petersburg, and the reference lines from the Western European and USA collections. The Avr3b, Avr4, and Avr8 genes were monomorphic, while in Avr1, Avr2, Avr3a, Avr9, Avr-blb1, Avr-blb2, and Avr-vnt1, we discerned two to five SSCP patterns, with their frequencies different in two series of P. infestans lines. Sequences of Avr alleles differed in synonymous and non-synonymous single nucleotide substitutions, with 93–100% identity between variants. When Avr polymorphisms were compared with the profiles of virulence factors recognized with the Mastenbroeck-Black differentials, the acceptable agreement between two independent indices was observed only for Avr1, Avr3a and Avr4.