Abstract：Flammulina velutipes is an important commercial edible fungus. Exploring the genomic regions controlling important agronomic traits is helpful to the genetic improvement of F. velutipes. A total of 90 F. velutipes strains were used as tested materials, and 5 agronomic traits including primordium period, stipe diameter, stipe length, pileus diameter and yield per bottle were detected. Total 95 polymorphism simple sequence repeat(SSR) markers that developed from the whole genome sequence of F. velutipes were used to scan the genome of materials in present study. On the basis of analyzing population structure and linkage disequilibrium (LD) of the experimental materials. The association analysis between 5 agronomic traits and SSR loci were performed by using GLM (general linear model) program in TASSEL software. The results showed that the differences between the corresponding agronomic traits of the materials were highly significant(P＜0.01). A total of 582 alleles were found among 95 pairs of SSR markers with 6.13 alleles per locus. The polymorphism information content (PIC) value ranged from 0.204 to 0.818, with an average of 0.542. Through the mathematical model-based cluster in structure software, all the accessions were divided into 8 subgroups and the information on the subgroup was used for the next association analysis. A high degree of LD was detected among syntenic markers, and the loci pairs with D'＞0.5 accounting for 33.01% of the total. Twenty-eight markers were found to associate with the 5 traits, of which 7 marker associations were significantly different at P＜0.01. Thirty-one marker-trait associations were detected herein; two for primordium period with an explanation of phenotypic variation (R2) range of 13.87%~17.41%; twelve for stipe diameter with a R2 range of 7.23%~23.02%; three for stipe length with a R2 range of 13.48%~23.55%; nine for pileus diameter with a R2 range of 5.11%~17.04%; five for yield per bottle with a R2 range of 9.47%~18.94%. The present study suggested that the genetic diversity and linkage disequilibrium of the tested F. velutipes germplasm were suitable for association analysis. The marker-trait association SSR primers developed in present study provide reference for the construction of germplasm for F. velutipes germplasm and molecular marker assisted breeding.
