Development and Molecular Characterization of Novel Polymorphic Genomic DNA SSR Markers inLentinula edodes

Abstract

Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3–14 and the major allele frequency was distributed from 0.17–0.96. The values of observed and expected heterozygosity ranged from 0.00–0.76 and 0.07–0.90, respectively. The polymorphic information content value ranged from 0.07–0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.

Analysis of Genetic Diversity and Population Structure of Wild Strains and Cultivars Using Genomic SSR Markers inLentinula edodes

“…The N A , H E , H O , and PIC values obtained from the study by Lee et al [23] were 4.9, 0.55, 0.31, and 0.51, respectively. Moon et al [24] reported the values of 6.8, 0.64, 0.32, and 0.61 for N A , H E , H O , and PIC, Figure 2. Clustering of distance-and model-based for 100 Lentinula edodes strains including 77 wild strains and 23 cultivars using 20 genomic SSR markers.…”

“…The 20 SSR markers used in this study were selected in our two previous studies [23,24]. The features of selected markers in higher genetic diversity values such as polymorphic information content (PIC), expected and observed heterozygous, genotypes and allele numbers are presented in Table 1.…”

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.…”