The Geographic Distribution and Natural Variation of the Rice Blast Fungus Avirulence Gene AVR-Pita1 in Southern China

The avirulence (<i>AVR</i>) genes of the filamentous ascomycete fungus <i>Magnaporthe oryzae</i> (<i>M. oryzae</i>) are known to mutate rapidly under a higher selection pressure, allowing the pathogen to evade recognition by rice <i>resistance</i> (<i>R</i>) genes. Understanding the geographic distribution and natural variation of <i>AVR</i> genes is critical for the rational utilization and prolonging of the effectiveness of <i>R</i> genes. In this study, a total of 1060 <i>M. oryzae</i> strains collected from 19 rice blast nurseries in 13 provinces across southern China were subjected to presence/absence variation (PAV), genetic variation, and virulence analyses of the <i>AVR-Pita1</i> gene. PCR amplification results indicated that <i>AVR-Pita1</i> was present in only 57.45% of the blast strains, with significant geographic variation in distribution frequency. Specifically, the highest frequency (100%) was observed in strains from Chengmai, Hainan, while the lowest (1.79%) was observed in strains from Baoshan, Yunnan. A sequencing analysis identified 29 haplotypes of <i>AVR-Pita1</i>, characterized by insertions, deletions, and base substitutions. A phylogenetic analysis indicated that haplotypes of <i>AVR-Pita1</i> identified in this study were clustered into one clade. A further amino acid sequence analysis of these haplotypes led to the identification of 25 protein variants. Notably, four haplotypes of <i>AVR-Pita1</i> exhibited pathogenicity toward its corresponding rice <i>R</i> gene, <i>PtrA</i>. Additionally, we performed allele profiling of <i>Ptr</i> in a collection of elite parental lines that are widely used in rice breeding in southern China and found that the functional <i>Ptr</i> alleles (<i>PtrA</i>, <i>PtrB</i>, and <i>PtrC</i>) accounted for over 70%.