Phalaenopsis hybrids are the most popular potted flowers in flower markets worldwide because they exhibit various flower colors, including yellow, green, white and red-purple. A thorough assessment of petal color polymorphism in Phalaenopsis enables the promotion of mechanistic studies on floral coloration regulation. In this study, we collected 156 Phalaenopsis germplasms to assess their chromativity value (L*, a* and b*), and then divided them into six groups according to their petal color: white (21), green (11), yellow-orange (37), pink (40), purplish-red (25) and dark red (22). Significant correlations were detected between petal color chromaticity indices and both the total concentration and the compositional ratio of the two primary anthocyanin components: cyanidin 3,5-O-diglucoside (Cy3G5G) and delphinidin 3,5-O-diglucoside (Dp3G5G). The red petal phenotype was largely determined by high accumulations of Cy3G5G and Dp3G5G, as well as a high Cy3G5G/Dp3G5G ratio. By integrating CIELab color parameters with anthocyanin composition and gene expression analyses, a quantitative regulatory model for Phalaenopsis flower color was established. We have revealed that the phenotypic traits of high a* and low L* values are directly associated with the high expression of key structural genes (PhF3′H, PhDFR, PhF3′5′H). These results provide molecular markers and a screening basis for screening, enabling directional flower color breeding, and significantly enhancing the predictability and accuracy of breeding programs.

MADS-box transcription factors have undergone in-depth investigations regarding their function in regulating the development of plant floral organs. Flower type mutants serve as critical biological models for investigating the regulatory mechanisms of MADS-box genes in floral organ development, while simultaneously constituting essential genetic resources for molecular breeding programs. In this work, we examined a lip-like sepal of the peloric mutant in Phalaenopsis ‘Huayang’, which exhibited changes in both the morphology and color of the sepals. Our cryo-SEM investigations revealed that the mutation type belonged to a sepal labellum-like variation in Phalaenopsis ‘Huayang’. Nine glycosylated anthocyanins were identified and their contents were significantly upregulated in the Se-red of mutant flowers. Transcriptomic analysis identified 9408 differentially expressed genes, including 4934 upregulated and 4474 downregulated genes. In addition, 57 MADS-box genes were identified and classed into five groups (Mα, Mβ, Mγ, MIKC*, and MIKC^C) according to a phylogenetic comparison with Arabidopsis homologs. Furthermore, 29 MADS genes were screened from the MIKC^C group, and these genes may play a crucial role in the regulation of floral organ development. Through real-time PCR analysis and protein interaction analysis, we identified three genes that were upregulated in the mutant, which may be involved in sepal development. The subcellular localization results demonstrated that three genes were found within the nucleus. Taken together, our results elucidated the molecular mechanism of sepal variation in Phalaenopsis ‘Huayang’. Our results could enhance our comprehension of the regulatory mechanisms underlying floral patterning and promote the molecular breeding process of Phalaenopsis.