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

The avirulence () genes of the filamentous ascomycete fungus () are known to mutate rapidly under a higher selection pressure, allowing the pathogen to evade recognition by rice () genes. Understanding the geographic distribution and natural variation of genes is critical for the rational utilization and prolonging of the effectiveness of genes. In this study, a total of 1060 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 gene. PCR amplification results indicated that 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 , characterized by insertions, deletions, and base substitutions. A phylogenetic analysis indicated that haplotypes of 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 exhibited pathogenicity toward its corresponding rice gene, . Additionally, we performed allele profiling of in a collection of elite parental lines that are widely used in rice breeding in southern China and found that the functional alleles (, , and ) accounted for over 70%.