Development of 44 Novel Polymorphic SSR Markers for Determination of Shiitake Mushroom (Lentinula edodes) Cultivars

Abstract

The shiitake mushroom (Lentinula edodes) is one of the most popular edible mushrooms in the world and has attracted attention for its value in medicinal and pharmacological uses. With recent advanced research and techniques, the agricultural cultivation of the shiitake mushroom has been greatly increased, especially in East Asia. Additionally, demand for the development of new cultivars with good agricultural traits has been greatly enhanced, but the development processes are complicated and more challenging than for other edible mushrooms. In this study, we developed 44 novel polymorphic simple sequence repeat (SSR) markers for the determination of shiitake mushroom cultivars based on a whole genome sequencing database of L. edodes. These markers were found to be polymorphic and reliable when screened in 23 shiitake mushroom cultivars. For the 44 SSR markers developed in this study, the major allele frequency ranged from 0.13 to 0.94; the number of genotypes and number of alleles were each 2–11; the observed and expected heterozygosity were 0.00–1.00 and 0.10–0.90, respectively; and the polymorphic information content value ranged from 0.10 to 0.89. These new markers can be used for molecular breeding, the determination of cultivars, and other applications.

Genetically Independent Tetranucleotide to Hexanucleotide Core Motif SSR Markers for Identifying Lentinula edodes Cultivars

“…This set of eight markers could differentiate among 20 L. edodes cultivars, with PIC values ranging from 0.269 to 0.764, with an average of 0.409 ( Table 2). Novel SSR markers for L. edodes were previously described by Lee et al [7] and Moon et al [8]. Lee et al [7] reported that the PIC values of 44 SSR markers with dinucleotide to pentanucleotide repeats ranged from 0.10 to 0.89, with an average of 0.511 and Moon et al [8] determined that the PIC values of 16 SSR markers with dinucleotide and trinucleotide repeats were between 0.07 and 0.89, with an average of 0.612.…”

“…Novel SSR markers for L. edodes were previously described by Lee et al [7] and Moon et al [8]. Lee et al [7] reported that the PIC values of 44 SSR markers with dinucleotide to pentanucleotide repeats ranged from 0.10 to 0.89, with an average of 0.511 and Moon et al [8] determined that the PIC values of 16 SSR markers with dinucleotide and trinucleotide repeats were between 0.07 and 0.89, with an average of 0.612. Our markers with tetranucleotide to hexanucleotide repeats were less useful for identifying individuals compared with the markers mainly comprising dinucleotide repeats.…”

“…In contrast, molecular techniques involving DNA analyses may be used to examine inactivated samples and can be completed relatively quickly. Several molecular techniques and markers have been developed for identifying L. edodes, including the following: amplified fragment length polymorphism analysis [1], DNA sequencing of the intergenic spacer region in nuclear ribosomal DNA [2,3], intersimple sequence repeat markers [4], random amplified polymorphic DNA markers [5], sequence characterized amplified region markers [6], and simple sequence repeat (SSR) markers [7,8]. Among these DNA markers, SSRs are useful for identifying cultivars because of co-dominant inheritance and the abundance of alleles per locus.…”

Advances in Single Molecule, Real-Time (SMRT) Sequencing

“…The pharmacological properties of medicinal mushrooms are largely conferred by secondary metabolites; these metabolites have received intense research attention [1,49,53]. Here, we used antiSMASH to search for gene clusters encoding secondary metabolites in G. incarnatum [38].…”

“…In addition, the proteomes of C. protrusum, E. weberi, T. reesei, T. virens, M. grisea, and Aspergillus nidulans were clustered into orthologous groups using OrthoFinder [52]. The multiple sequence alignments of the single-copy orthologs was used for phylogenetic analysis using the Neighbor-Joining method, which was conducted in MEGAX, to validate the relationships among C. protrusum and the other three fungi in the family Hypocreaceae [53].…”