Avirulence genes of Magnaporthe oryzae are a pathogen defense arsenal shaped by cognate rice resistance genes in the field.

We examined the frequency of and variation in eight avirulence (AVR) genes from 840 Magnaporthe oryzae field isolates collected from the Southern United States relative to rice resistance (R) genes deployed from 1959 to 2017. Little coding or noncoding variation was detected in AVR-Pi9, AVR-Pib, ACE1 and AVR-Pizt, which correspond to R genes not used in the United States. In the United States, AVR-Pik, corresponding to rice R gene Pi-k alleles deployed at varying levels since the late 1960s, was present in 37% of the isolates over six decades. AVR-Pita1, corresponding to Pi-ta deployed in the late 1990s, reached a low point in the 5-yr period following Pi-ta deployment and then recovered to 99% in recent years. Our results suggest a fitness penalty for M. oryzae isolates carrying nonfunctional AVR variants and provide concrete data on how changes in plant R gene composition can impact pathogen populations. These findings will inform localized strategies for R gene usage and durable control of blast disease. AVR frequencies differ over time between United States and global samples for AVR-Pik, AVR-Pi9, AVR-Pii and AVR-Pita1. Further whole genome analysis including additional US samples is necessary to confirm whether the United States is a geographically isolated population.