Phenotypic Characterization and Marker–Trait Association Analysis Using SCoT Markers in Chrysanthemum (Chrysanthemum morifolium Ramat.) Germplasm

Abstract

Background: Chrysanthemum is an economically important ornamental species whose genetic diversity assessment forms the foundation for effective breeding programs. Methods: Phenotypic characterization of 12 traits (7 quantitative and 5 qualitative traits) was conducted alongside SCoT marker analysis to assess genetic diversity and perform marker–trait association analysis in 65 chrysanthemum accessions. Results: Quantitative traits showed 14.81–26.43% variation (peduncle length most variable), while qualitative traits exhibited Shannon–Weiner indices of 0.23–2.28 (flower color most diverse). Phenotypic analyses consistently grouped accessions into two clusters. SCoT markers generated 160 bands (159 polymorphic; 6.957 bands/marker) with high PIC values (0.408–0.896). Molecular analyses also revealed two genetic groups, though with partial discordance to phenotypic clusters. Eight significant marker–trait associations were identified, linking SCoT28/3/30/31/35/20/14/36 to flowering duration, plant height, peduncle diameter, flower color, and pest resistance traits. Conclusions: The study revealed substantial diversity in local chrysanthemum germplasm, with SCoT markers effectively capturing genetic variation. While phenotypic and molecular groupings showed partial mismatch, identified marker–trait associations (e.g., SCoT28 linked to flowering duration) provide practical tools for marker-assisted breeding.