This study establishes Taiwan's first Phalaenopsis orchid core collection, crucial for preserving genetic diversity and key traits. It analyzed 207 cultivars using phenotypic and genotypic data, employing novel techniques like multiple imputation and weighted k-means clustering. 22 core accessions were selected using the 'P+G strategy' and MGD algorithms, showcasing effectiveness in preserving diversity. The evaluation revealed significant diversity, surpassing alternatives, supported by pedigree analysis. The study underscores the importance of rigorous evaluation for quality and effectiveness. It contributes to orchid breeding, conservation, and sustainable agriculture, offering insights into genetic landscapes and breeding advancements.

We devised a two-step ‘P+G strategy’ to capture key traits and genetic diversity in orchid germplasm. Steps include: (1) Imputing missing data using multiple imputations. (2) Exploring germplasm structure with weighted k-means clustering. (3) Estimating dissimilarity using the MGD algorithm. (4) Constructing core accessions based on MGD metric via 2-step ‘P+G strategy’.