Novel microsatellite markers suitable for genetic studies in Polyporus umbellatus (Polyporales, Basidiomycota)

•The high abundance of SSRs was mined in DNA-transcribed regions of Polyporus umbellatus.•The newly developed EST-SSR marker showed high polymorphism, which may be useful for the analysis of population structure.•The geographic location patterns of P. umbellatus were affected by many factors.

Polyporus umbellatus, known as Zhuling in China, is a well-known and important medicinal fungus in Asia. Although P. umbellatus is highly valued for its medicinal properties, the expressed sequence based (genetic) markers are unknown. High-throughput transcriptome sequencing provides large amounts of transcriptome data for gene discovery and the development of molecular markers. In this study, all 38,444 unigenes were used to screen the SSR loci. A total of 1527 primer pairs were designed for marker development. Tri-nucleotide repeat motifs were the most abundant type, with a frequency of 47.4%, followed by mono- (28.5%), di- (21.1%), tetra- (0.16%), hexa- (0.1%) and penta-nucleotide repeat motifs (0.05%). A total of 50 primer pairs were synthesized, of which 31 (62%) yielded PCR amplification products. Eight individuals were used to examine amplifications and polymorphisms for all 50 loci. In eight P. umbellatus accessions, eight markers were polymorphic. To describe the genetic diversity and genetic relationship of P. umbellatus, the genotypes of 42 accessions representing diverse wild genotypes of P. umbellatus were analyzed. The number of alleles per locus varied from 7 to 13 alleles, and the genetic diversity values ranged from 0.345 to 0.785. We performed genetic diversity analysis using these 8 polymorphic markers. A UPGMA dendrogram was constructed based on Jaccard's similarity coefficients, revealing distinct clusters among the 42 accessions. This comprehensive set of genic SSR markers developed in our study is powerful and suitable for genetic analysis.