Genetic structure of <i>Botrytis cinerea</i> population from tomato in Liaoning province of China

The pronounced genetic heterogeneity of Botrytis cinerea confers adaptive advantages in fluctuating environments. Consequently, elucidating the pathogen's population structure within agricultural ecosystems is essential for developing enhanced control strategies. A total of 171 Botrytis isolates were collected from greenhouse-grown tomatoes in Liaoning province, China. Through integrated morphological characterization, restriction fragment length polymorphism analysis of the Bc-hch gene, and multi-locus phylogenetic analysis based on G3PDH, HSP60 and RPB2 sequences, the dominant species responsible for tomato gray mold in Liaoning was identified as B. cinerea. The diversity of B. cinerea isolates was assessed by characterizing transposable elements (TEs) including Boty and Flipper, determining mating types (MAT1-1 and MAT1-2), and conducting morphological and microsatellite (SSR) analyses. Based on TEs profiling, the isolates were classified into three types: Boty, Flipper, and Transposa, accounting for 19.3%, 25.7%, and 55.0% of the population, respectively. The composition of TE types differed significantly among sub-populations. The overall ratio of MAT1-1 to MAT1-2 deviated from 1:1. However, in 13 out of 14 geographic sub-populations, the mating type ratio was consistent with 1:1; only one sub-population exhibited a significant deviation. Genetic diversity was evaluated using nine SSR markers, revealing a high level of polymorphism. Most genetic variation was observed within populations. A moderate level of gene flow was detected among populations, along with a relatively high inbreeding coefficient. Significant genetic differentiation was observed among geographical populations, with the highest diversity found in Anshan and Fuxin, and the lowest in Huludao. Cluster analysis indicated a discernible phylogeographic pattern, suggesting an association between genetic relationship and geographic distance. The findings of this study enhance our understanding of the population structure and genetic diversity of B. cinerea in Liaoning province, providing valuable insights for disease management strategies.