Assessing genetic and phenotypic diversity to advance multi-trait selection in Cyclocybe chaxingu

Cyclocybe chaxingu is a major cultivated edible mushroom in China; however, the relationship between its genetic diversity and agronomic performance remains insufficiently characterised. In this study, 100 strains were sampled, sequenced at two gene fragments (LSU and TEF1-α) and analysed for strain relationships at these loci. Ten agronomic traits were quantified under standardised cultivation conditions. Significant differences amongst strains were observed for all traits (ANOVA, p < 0.01). Amongst the ten traits, the greatest variation was found in the total number of fruiting bodies (CV 45.6%), followed by average fruiting-body weight (CV 35.0%). Principal component analysis accounted for 83.98% of the variance across three axes: PC1 (57.74%) represented a size and mass gradient (cap thickness, stipe diameter, cap diameter, gill width, average fruiting-body weight versus fruiting-body number), PC2 (15.87%) reflected stipe elongation and PC3 (10.37%) captured the timing of first harvest and earliest yield. Hierarchical clustering identified four phenotypic branches and five operational colour groups, each displaying strong differences across traits. Phylogenetic analysis at the two loci grouped strains into four distinct clusters, which partially overlapped with phenotype-based clusters. Yield was positively correlated with size-related traits and gill width and negatively correlated with fruiting-body number. Time to first harvest and earliest yield were associated with cap thickness and gill width. Stipe diameter, stipe length and gill width are proposed as practical DUS indicator traits for breeding, with size traits serving as complementary selection targets, thereby providing a quantitative breeding framework for C. chaxingu.