A rare recombination allows the redefinition of a major avirulence gene in the Phytophthora sojae genome

Significant yield losses in soybean production are imputable to Phytophthora root and stem rot (PRR) caused by Phytophthora sojae. Soybean resistance to the pathogen depends on the presence of resistance genes (Rps) that recognize key effectors from P. sojae, which are encoded by avirulence genes (Avr). A unique molecular signature associated with these genes allows the prediction of the outcome of infection with great accuracy making the interaction Rps-Avr central to reduce disease incidence. In this study, we reassessed the identity of the avirulence gene whose protein product is recognized by Rps6. Following extensive soil sampling and single-spore isolation of a large population of P. sojae, we found two salient isolates carrying a rare recombination between two effectors, Avr3c and Avr4/6. Using a PCR assay and molecular markers, we showed that only alleles at the Avr3c locus were in perfect association with the phenotypes of the isolates. Furthermore, whole-genome resequencing and de novo assembly of the two isolates revealed the full extent of this genomic rearrangement. These results bring to light an unsuspected connection between Avr3c and Rps6 and offer a more reliable target for the pathotyping of P. sojae, which ultimately leads to a better use of resistant soybean material.