Distribution, Genetic Variation and Evolution of the <i>AVR-Pita3</i> avirulence gene in <i>Magnaporthe oryzae</i> Populations in Southwest China

The rapid variation of avirulence genes in Magnaporthe oryzae (M. oryzae) undermines the resistance function in rice varieties carrying cognate resistance genes. Monitoring the variation of these avirulence genes is crucial for deploying resistant rice cultivars in the field. AVR-Pita3 is known as a gene that lacks avirulent activity to rice carrying Pi-ta. However, its distribution, evolution, and avirulence function in M. oryzae populations remain poorly understood. In this study, we analyzed the distribution and variation of the AVR-Pita3 in M. oryzae and examined its avirulence function. Among 262 isolates collected from five hosts in rice-producing regions in Southwest China, 188 isolates of M. oryzae, including one isolate in Eleusine indica (E. indica), carried AVR-Pita3. A total of 31 nucleotide variations and 19 amino acid variations were identified, along with 5 haplotypes, the majority of isolates belonged to the haplotype H2. The isolates carrying AVR-Pita3 from rice and E. indica hosts clustered into distinct evolutionary clades, and the gene was under negative selection. Pathogenicity assays showed that a monogenic line rice carrying Pi-ta was resistant to 103 isolates, susceptible to 60 isolates, and had an unknown response to remain 25 isolates carrying AVR-Pita3. This study provides the first report on the distribution and variation of the AVR-Pita3 in M. oryzae populations across rice-growing regions in Southwest China. AVR-Pita3 is widely distributed in these populations, with a high frequency of occurrence, particularly in isolates from Guizhou. The findings indicate that Pi-ta monogenic line remains effective against most pathogen stains carrying AVR-Pita3 in these regions, which highlights its potential for disease management in rice cultivation.