Pangenomic sequencing and gene-unit genome-wide association study insights into genome plasticity and gene functions in Magnaporthe oryzae.

INTRODUCTION: Magnaporthe oryzaeis a model pathogenic fungus that causes serious disease in the two most important staple crops, rice and wheat. Elucidating the genetic variation within natural populations ofM. oryzaeand identifying genes involved in pathogenicity and environmental adaptation are essential for sustainable disease control. OBJECTIVES: This study aimed to elucidate the mechanisms underlying genomic variation within the M. oryzae population and to develop a novel GWAS method specifically tailored to this species. METHODS: The genomes ofM. oryzaediversity population 1 (MDP1), comprising 118 strains, were sequenced andde novoassembled. In addition, a novel gene-unit GWAS (GU-GWAS) method was developed to identify associated loci. RESULTS: Phylogenetic analyses revealed three subgroups among the sequenced strains, which were associated with indica and japonica rice differentiation. We also characterized core and accessory genes in theM. oryzaepopulation through pan-genome analysis. Using GU-GWAS followed by functional validation, we cloned three new genes associated with pathogenesis (SPP1), fungicide tolerance (MoFCS1), and heavy metal tolerance (MoHMT1). CONCLUSION: This study provides new insights into the pangenome ofM. oryzaeand introduces a method for the identification of functionally important genes in fungal species.