Population Structure and Genomic Diversity of Fusarium poae Associated With Barley and Oat in Canada

Fusarium poae has emerged as a predominant Fusarium species affecting barley and oats in Canada. Despite its widespread occurrence and ability to produce multiple mycotoxins, its population genetics remain poorly understood. In this study, we used restriction site‐associated DNA sequencing (RADseq) to characterize the population structure and genomic diversity of F. poae isolates collected from four regions of Canada. A total of 1059 high‐quality single‐nucleotide polymorphisms (SNPs) were generated. Principal coordinate and phylogenetic analyses revealed a hierarchical population structure consisting of two major genetic groups (Group I and Group II), with Group II further divided into two subgroups (IIa and IIb). Subgroup IIa represented a distinct lineage marked by reduced nucleotide diversity, negative Tajima's D values and elevated genome‐wide linkage disequilibrium. Analysis of molecular variance showed that most genetic variation (63%) occurs within genetic groups, with 37% attributable to differences among groups. In contrast, when populations were partitioned by geographic region, only 3% of the variation was explained by differences among regions. Although regional differentiation was weak, it was statistically significant, reflecting shifts in the relative frequencies of genetic groups across regions. All genetic groups and regions exhibited significant multilocus linkage disequilibrium, indicating predominantly clonal reproduction in the field. Together, these findings reveal substantial genomic diversity of F. poae and highlight the emergence of a genetically distinct lineage within Group II. This study provides a genomic foundation for future investigations into the pathogenicity and mycotoxin production associated with F. poae in Canadian cereal production.