Objective Molecular markers closely related to the floral phenotypes of Chrysanthemum morifolium were identified to facilitate breeding selection.

Methods Based on 11 ISSR and 20 SCoT markers, 64 accessions of medicinal chrysanthemum (C. morifolium) were scanned for multiple genomic loci. On selected 9 floral phenotype traits, genetic diversity and population structure were analyzed using OriginPro 2024 and Structure 2.3 software. Association of the traits with the ISSR/SCoT markers was examined with Tassel 5.0.

Results The coefficients of variation on the 9 traits ranged from 30.67% to 82.72%. The markers generated 197 polymorphic loci with polymorphic information contents between 0.57 and 0.87, averaging 0.78. Significant or extremely significant correlation was observed between most of the traits. The 64 accessions were clustered into three primary classes by flower size, i.e., large, small, and intermediate. And, at the optimal grouping at K=4 (ΔK_max) for classifying population structure, they were divided into 4 subpopulations that covered 81.25% of all with a membership probability (Q) greater than 0.6. Out of the 31 markers, 12 loci significantly correlated with 8 flower traits (P＜0.01) explaining 11.74-29.27% of the phenotypic variations. And the association between ISSR37 and the length of ray floret was most significant.

Conclusion The collected 64 C. morifolium germplasms were genetically rich in diversity on the floral phenotypes but relatively simple in relationship. The 12 trait-related ISSR/SCoT markers identified in this study could be of value for breeding selection.