Trunk rot, caused by Fomitiporia torreyae, is one of the most economically important sap rot diseases on Cryptomeria japonica, especially on a cutting cultivar ‘Sanbu-sugi’. This disease had been reported only from Chiba and Ibaraki prefectures in Japan; however, a similar trunk rot on Japanese cedars was found recently in Kyoto prefecture. We identified the causal agent of the trunk rot on Japanese cedars in Kyoto prefecture, clarified the genotype of ‘Sanbu-sugi’ (sensu stricto) using microsatellite markers, and then investigated the relatedness of these infected cedars with ‘Sanbu-sugi’. The pathogen was identified as F. torreyae by its DNA sequences and morphological characteristics of the fruiting body. The 25 ramets of ‘Sanbu-sugi’ had only one genotype based on eight microsatellite loci. Infected Japanese cedars in Kyoto were comprised of different genotypes and showed no close relatedness to ‘Sanbu-sugi’. This is the first report of trunk rot caused by F. torreyae on cultivars of Japanese cedar with no relatedness to ‘Sanbu-sugi’ outside of Chiba and Ibaraki prefectures and showed the potential for expansion of this disease to Japanese cedar plantations in other areas.
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