[Objective] Xianggu (Lentinulaedodes) is the second biggest edible fungi in the world. Genetic diversity and population structure analysis and reliable identification of strains are prerequisites for new cultivar breeding and the sustainable development of Xianggu mushroom industry. [Methods] Using polymorphic SSR markers to analysis the genetic diversity and population structure of the major cultivars in China, comparing their genetic pedigree and constructing the fingerprint profiles that can be used for varietal identification. [Results] In this study, 51 strains were identified with SSR markers including 24 pairs of primers and their polymorphism was 100%. According to the chustering analysis, experimental population could be divided into four clusters at the similarity of 0.69. Wild strains or cultivars derived from wild strains in cluster III and IV, and other hybrid cultivars in cluster I and II. The cultivar population can be divided into 6 genetics compositions according to the population structure analysis. Showing that several core strains are involved in others’ breeding procedure such as L808、L135, and can explain the pedigree of the cultivars used them as parents. 9SSR primer pairs delineated 45 of the cultivars based on the unique multilocus SSR fingerprint profiles. [Conclusion] The results indicated a close genetic relationship of cultivars in China, and the breeding research was always focus on several core strains such as L808、L135、9015. This research offered some references to the genetic breeding that has our own intellectual property and can adjust different cultivation mode. The fingerprint profiles could also provide safeguards for the reliable identification of Xianggu strains.
