Genetic diversity assessment and digital labeling (QR code) of 89 marigold germplasms: A synergistic study of phenotypic traits and SSR molecular markers

Marigold ( Tagetes erecta ) is a versatile herbaceous plant widely cultivated for its ornamental value, pigment production, and industrial applications. Genetic diversity and phylogenetic relationships among 89 marigold accessions were evaluated through integrated analysis of 22 phenotypic traits and 19 SSR markers, resulting in the development of a QR code-based system for unified phenotypic and genotypic data management. Among nine qualitative characters assessed, four exhibited Shannon diversity indices ( H’ ) greater than 1.0, while six of 13 quantitative traits exhibited coefficients of variation above 30 %, indicating considerable inter-cultivar variation and rich phenotypic diversity. Correlation analysis revealed 104 significant trait associations, of with 84.6 % being highly significant ( P < 0.01), suggesting substantial synergistic regulation among phenotypic traits. Principal component analysis identified six components from the 22 traits, which together explained 77.961 % of the total variance and served as critical parameters for cultivar identification and evaluation. SSR analysis revealed high genetic diversity, with average values per locus of 3.26 for the number of alleles ( Na ), 0.92 for Shannon's index ( I ), 0.54 for Nei’s gene diversity index ( H ), and 0.57 for polymorphism information content ( PIC ). Genetic structure was evaluated using phenotypic clustering, SSR-based molecular clustering, structure analyses and principal coordinate analysis, which categorized the 89 accessions into four primary clusters, demonstrating that the genetic architecture of marigold germplasm was shaped by functional type (pigment vs. ornamental use), key ornamental trait combinations, and modern breeding lineages. A panel of eight core SSR primer pairs, covering a total of 24 loci, was used to construct molecular identification for 89 marigold accessions. Furthermore, a traceable and dynamic database was created by embedding high-resolution cultivar images, essential phenotypic data, and SSR molecular barcodes within integrated phenotypic-genotypic QR codes. This system offers a comprehensive framework supporting genetic resource evaluation, hybrid parental selection, and intellectual property protection for new marigold cultivars. • Genetic diversity and phylogenetic relationships among 89 key commercial marigold accessions. • Synergistic study of phenotypic traits and SSR molecular markers. • Genetic architecture of marigold by functional type, key ornamental trait combinations, and modern breeding lineages. • A QR code-based system of 89 marigold accessions.