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

Abstract

Summary 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.