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Development of a molecular tool for the diagnosis of the different avirulence genes of Phytophthora sojae isolates found in Canada

Chloé Dussault-Benoit: Université Laval

<div><em>Phytophthora sojae</em> is an oomycete pathogen of soybean, responsible for yearly economic losses of $1-2 billion worldwide. The most effective method to fight this pathogen is the use of resistant genes (<em>Rps</em>), counterparts of avirulence genes (<em>Avr</em>) in <em>P. sojae</em>. In Canada, a recent survey of nearly 300 <em>P. sojae</em> isolates identified many pathotypes deficient in one or several of seven <em>Avr</em> genes: <em>Avr1a, Avr1b, Avr1c, Avr1d, Avr1k, Avr3a, Avr6</em>. Currently, the identification of <em>P. sojae</em> pathotypes is often based on a phenotyping approach (hypocotyl assay) using soybean differential carrying <em>Rps</em> genes, but this method is cumbersome and imprecise. In this study, our objective was to develop a molecular tool that would lead to a rapid and precise diagnosis of the presence of <em>Avr</em> genes in <em>P. sojae</em> isolates. For this purpose, we relied on genome sequencing data of 31 isolates. Discriminant markers were identified for each <em>Avr</em> gene. Specific primers for these markers were designed to characterize the virulence profile of each isolate. Each primer amplified DNA fragments of different lengths on an agarose gel. Subsequently, the primers were pooled together in a multiplex PCR and tested against all isolates to confirm their specificity and ability to identify the exact pathotypes of each isolate. This new molecular tool will find applications in the characterization of the precise virulence profiles of <em>P. sojae</em> isolates found in expanding soybean productions in Canada and elsewhere.</div>