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Two alleles of glyceraldehyde-3-phosphate dehydrogenase gene were isolated from Auricularia auricula-judae strain Au916.Both of the genes contained five introns, but they were different in length resulted from discontinuous nucleotides insertion or deletion in the fifth intron.In this study, based on the different last intron of the alleles, an insertion-deletion length polymorphism (InDel) marker was designed;the protoplast regeneration strains were obtained from Au916.