Use of inter-simple sequence repeat markers to develop strain-specific SCAR markers for Flammulina velutipes

In this paper, we report for the first time on authentication of Flammulina velutipes cultivars by using strain-specific sequence-characterized amplified region (SCAR) markers developed from inter-simple sequence repeat (ISSR) markers. The genomic DNA polymorphism was analyzed by the ISSR technique in 7 strains of F. velutipes presently cultivated in China on a commercial scale. Eight primers selected from 20 ISSR primers amplified 104 clear and stable bands, of which 81 bands were polymorphic. Among the selected primers, primer ISSR9 can distinguish strain No. 12 from the other 6 strains by amplifying a unique and reproducible band of approximately 750 bp. According to the sequence of the strain-specific fragment, a pair of SCAR primers was designed to diagnose strain No. 12 on the molecular level. The validity of the SCAR marker was confirmed by using DNA samples from another 12 strains of F. velutipes obtained from different parts of China. Our data provided the foundation for a precise and rapid PCR-based strain-diagnostic system for F. Velutipes.