Interspecific hybridization is a fundamental strategy in ornamental plant breeding, which enables the combination of desirable traits. In Lilium, complex hybrids, including longiflorum-Asiatic (LA) and Oriental-Trumpet (OT) cultivars, have been extensively developed via interspecific crosses between distantly related genome groups. However, the genomic structure and chromosomal behavior of these commercially important hybrids are largely uncharacterized. In this study, we applied genomic in situ hybridization (GISH) to eight triploid LA and OT lily cultivars to evaluate their chromosomal composition, assess their genome stability, and explore the utility of GISH as a practical cultivar verification tool. Flow cytometry and somatic chromosome counting confirmed the triploid status (2n = 3x = 36) of all the assessed cultivars. GISH analysis also revealed distinct parental chromosome sets in the background of each hybrid, with no evidence of intergenomic translocations or recombination. The LA cultivars exhibited 12 chromosomes derived from L. longiflorum and 24 from Asiatic parents, whereas the OT cultivars demonstrated 12 chromosomes of Oriental hybrid origin and 24 derived from Trumpet hybrids. This consistent non-recombinant genomic structure across all the cultivars strongly supports somatic polyploidization as the primary mechanism underlying their development. The suppression of homoeologous recombination underscores the cytogenetic stability of these hybrids and supports their clonal maintenance through vegetative propagation. Furthermore, these findings validate GISH as an effective tool for cultivar verification and chromosomal assessment in ornamental plant breeding and reinforce the importance of cytogenetic profiling for the development and management of interspecific hybrids.

Polyploidization, or genome doubling, has a significant impact on plant speciation and adaptation, and it is commonly used in agriculture to improve crop traits. In this study, we investigated the induction of polyploidy in three wild Allium species native to Korea: A. senescens and A. spirale Willd. and A. taquetii, using colchicine treatments tailored to meet specific experimental requirements. By avoiding tissue culture methods, we developed a more accessible, cost-effective, and scalable approach to polyploidization. Our research demonstrated that polyploid Allium plants exhibit distinct phenotypic changes, such as reduced growth rates and increased stomatal size. Flow cytometry and chromosome counting confirmed the successful induction of polyploidy, with clear peaks indicating double DNA content and stable chromosome numbers in polyploid plants. The presence of B chromosomes in A. spirale Willd. following polyploidization suggest interesting genetic dynamics. Despite the initial growth lags, polyploid plants may offer enhanced photosynthetic efficiency and resilience under optimal conditions. This study highlights the potential of polyploidization to improve ornamental traits in Allium species, thereby contributing to the diversification and sustainability of ornamental plant offerings. Future research should focus on the long-term performance and ecological adaptability of polyploid Allium species to fully harness their horticultural potential.