Integrated Analysis of Genetic, Spectral, Phenotypic, and Stress-Resistant Traits in Vanda × Papilionanthe Intergeneric Hybrids

Intergeneric hybridization of Vanda and Papilionanthe holds promise for pyramiding superior ornamental and stress-tolerant traits, though systematic studies on their hybrids remain scarce. Using Vanda lamellata var. Boxallii (♀), Papilionanda ‘Hetty Henderson’ (♂), and 72 progenies, we investigated parent–progeny relationships via iPBS markers, spectral phenomics, and morphology, alongside floral water balance and thermotolerance. Six iPBS primers amplified 90 bands (92.98% polymorphism), confirming high genetic diversity. Spectral reflectance (400–1000 nm) revealed organ-specific genetic differentiation. Clustering analyses consistently indicated that progenies were genetically and phenotypically closer to the female parent, with spectral/morphological patterns matching genetic groupings. Resistance evaluations showed progenies had significantly stronger floral water storage capacity than both parents, while the female parent excelled in water transport traits. Progenies developed thicker petal/sepal cuticles, though the male parent exhibited superior thermotolerance indices. This study clarifies the genetic regulation of stress resistance in these hybrids, providing critical support for precise early screening in orchid breeding.