Spatiotemporal Population Genetic Structure of Neoscytalidium dimidiatum Reveals Predominantly Clonal Expansion on Dragon Fruit in Taiwan

Since the first report of stem and fruit canker in 2012, Neoscytalidium dimidiatum has become a major pathogen affecting dragon fruit (Hylocereus spp.) production areas in Taiwan. To investigate the spatiotemporal genetic structure and the mode of reproduction of this emerging pathogen, 11 simple sequence repeat markers were developed to genotype 244 isolates, including 225 from dragon fruit, 11 from cattleya orchid, and 8 non-Taiwan isolates. Genotyping revealed limited allelic and genotypic diversity within the dragon fruit and cattleya orchid populations from Taiwan, in contrast to the higher diversity observed in the non-Taiwan population. Within the dragon fruit population, only four multilocus genotypes were identified, and a single clonal lineage predominated across sampled regions from 2011 to 2024. These results, along with significant p sex values for repeated genotypes, suggest that the N. dimidiatum population associated with dragon fruit in Taiwan is predominantly clonal. Analyses incorporating host and geographic origin indicate genetic differentiation among populations and were consistent with a possible host-associated structure. However, this pattern should be interpreted cautiously because sampling from non-dragon fruit hosts and from outside Taiwan was limited. Overall, the findings provide evidence for a predominantly asexual population structure of N. dimidiatum on dragon fruit in Taiwan and offer SSR markers that should be useful for future studies of this pathogen across broader host and geographic ranges.