Triallelic SNP-mediated genotyping of regenerated protoplasts of the heterokaryotic fungus Rhizoctonia solani

► The heterokaryotic soil fungus Rhizoctonia solani has a complex nuclear genome. ► Protocol optimization increased proportion of protoplasts containing 1-4 nuclei. ► 24 triallelic SNPs were used in PCR-based genotyping assays to determine allelic loss. ► Eleven strains developed represent reduced genomic complement of the parental strain.