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New ornamental varieties of high quality can be created via artificial polyploid induction. In the present study, the first system of polyploid induction with somatic embryogenesis of Lilium distichum Nakai and Lilium cernuum Komar. was developed. Somatic embryos were cultured on MS with 0.41 μmol L −1 picloram and 1.07 μmol L −1 NAA by scales (5 mm 2 ). After 40 days, somatic embryos were transferred to MS with 2.21 μmol L −1 BA for somatic embryogenesis. As determined from observations of paraffin sections, embryonic cells of L. distichum originated from outer cells at first, and somatic embryogenesis occurred through an indirect pathway. In L. cernuum , embryonic cells originated from inner cells at first, and somatic embryogenesis occurred through a direct pathway. Polyploids were successfully formed from somatic embryos and scales by the soaking and mixed culture methods with different colchicine concentrations (0.01%, 0.05%, and 0.1%; v/v) and durations (24, 48, and 72 h). The polyploid induction rate reached 57.14% and 46.15% with 0.05% colchicine treatment in L. distichum (48 h) and L. cernuum (24 h), respectively. Tetraploids (28.57% and 23.08%) and aneuploids without chimeras among the obtained polyploid plantlets were identified by chromosome counts of root-tip tissue squashes in L. distichum and L. cernuum . Tetraploid plantlets of L. distichum exhibited broader leaves, longer guard cells, larger stomata and higher stomatal conductance than diploid plantlets. Tetraploid plantlets of L. cernuum showed 1.76 × higher chlorophyll content, significantly more leaves, longer guard cells, larger stomata and lower stomatal conductance than diploid plantlets. Key message For the first time, we established a somatic embryogenesis system for L. distichum and L. cernuum using somatic embryos and scales to induce polyploids by soaking and mixed culture. Combinations of colchicine concentrations and periods of time were compared to select the best treatment combination. Comprehensive morphological observations, stomatal observations and root-tip tissue squashes were used to identify the ploidy of doubling plants. Our results provide a foundation for improving the ornamental value of two wild lily species, creating new Lilium germplasm and improving the reproduction coefficient of these resources.

21 crossing were conducted between Asiatic Lily with different ploidy levels, the results showed that the interploidy hybridization between diploid and tetraploid lilies was not as successful as intraploidy hybridization. Regardless of male sterility, triploid lilies could be used as female parents in the hybridization which the progenies were aneuploidy. 3x×4x crosses could be cultured more successfully than 3x×2x crosses. 45S rDNA was mapped on the chromosomes of seven Lilium species and their progenies using fluorescence in situ hybridization (FISH). FISH revealed six to sixteen 45S rDNA gene loci, and normally the sites were not in pairs. The asymmetry indexes of LA (Longiflorum hybrids × Asiatic hybrids) hybrids was higher than Asiatic hybrids, the evolution degree was LA hybrids > Asiatic hybrids. 45S rDNA distributed variably on chromosome 1-10 and 12 among Asiatic hybrids. Chromosome 1 had invariable sites of 45S rDNA in all Asiatic hybrids, which could be considered as the characteristic of Asiatic hybrids. LA hybrid 'Freya' had two sites of 45S rDNA on one homologous chromosome 5, and also it could be found in the progenies. The karyotype and fluorescence in situ hybridization with 45S rDNA as probe were applied to identify the different genotypes of 9 hybrids. Typical chromosomes with parental signal sites could be observed in all the genotypes of hybrids, it was confirmed that all the hybrids were true.

, a fragrant purple-red wild lily endemic to Northeast Asia, represents both ecological significance (as a key protected species) and horticultural value. While its white variant ( var. ) exhibits distinct flower color and fragrance traits, the molecular mechanisms underlying these variations remain poorly understood. Previous studies attributed the low anthocyanin content in the white variant to LcMYB12 downregulation, yet comprehensive analyses of associated genes and metabolic pathways are lacking. This study employed integrated transcriptomics, metabolomics, and volatile metabolomics to systematically compare and its white variant. We analyzed differential gene expression in the phenylpropanoid and flavonoid biosynthesis pathways, quantified anthocyanin/flavonoid metabolites, and assessed volatile organic compound profiles. The white variant showed significant reductions in flavonoids (catechin, epicatechin) and anthocyanins (cyanidin, pelargonidin, peonidin), linked to the downregulation of 58 genes in the flavonoid pathway-including , , , and UFGT. Critically, UFGT suppression disrupted anthocyanin glycosylation, promoting degradation and vacuolar accumulation failure. Concurrently, phenylpropanoid pathway inhibition reduced p-coumaric acid synthesis, diminishing downstream anthocyanins and volatile compounds (eugenol/methyleugenol). Our multi-omics approach reveals that flower color loss in var. album results from synergistic effects of transcriptional regulation and metabolic flux redirection. The UFGT-mediated glycosylation defect provides a novel explanation for anthocyanin instability in white petals. These findings complement prior genetic studies and establish a framework for targeted breeding of ornamental traits in Lilium species.

Lilium cernuum is endangered and was listed in the category of key protected wild plants in China. In this study, we report the complete chloroplast genome of L. cernuum using Illumina paired-end sequencing. The entire chloroplast genome maps as a circular molecule of 152,604 bp built with a quadripartite organization: two inverted repeats (IRs) of 26,481 bp separated by a large single copy (LSC) sequence of 82,058 bp and a small single copy (SSC) sequence of 17,584 bp. The chloroplast genome contains the conservative structure present in most Liliaceae chloroplasts composing of 79 protein-coding genes, 30 tRNAs and 4 rRNAs. Among these genes, 15 harbor a single intron, and 2 contain a couple of introns. A maximum likelihood phylogenomic analysis showed that L. cernuum was closely related to L. tsingtauense and L. hansonii  that belonged to the family Liliaceae.