Development and application of genome-derived SSR markers for genetic diversity analysis, molecular fingerprinting, and core collection construction in bougainvillea (Bougainvillea spp.)

Bougainvillea (Bougainvillea spp.) is an important ornamental shrub, yet its cultivar identification and genetic background remain poorly characterized. To address this, we developed 18 polymorphic SSR markers based on the B. glabra ‘Formosa’ genome and used them to analyze 203 Bougainvillea cultivars. These markers exhibited high discriminative power, successfully differentiating all accessions and revealing significant genetic heterogeneity. Population structure analysis indicated that the germplasm primarily derived from two ancestral groups, with most cultivars originating from bud sports. A high-resolution molecular fingerprinting system was established, enabling accurate cultivar identification. A 51-accession core germplasm collection was constructed using a 25% sampling strategy. This approach successfully maintained the original genetic diversity and minimized redundancy. This study provides a reliable SSR marker set and a representative core collection, offering practical tools for Bougainvillea cultivar identification, intellectual property protection, breeding programs, and germplasm conservation.