Canalized gene regulatory networks stabilize floral polymorphism and enable modular transgressive expression

Summary Floral polymorphisms frequently persist across heterogeneous environments despite ongoing gene flow, yet the regulatory mechanisms maintaining discrete phenotypes remain unclear. We tested whether alternative flower-colour morphs in Stellera chamaejasme L. are maintained by canalized gene regulatory architectures that stabilize expression around morph-specific optima. We used a pan-transcriptomic and eco-evolutionary framework integrating genome-wide gene expression profiling, co-expression network analysis, functional enrichment, ortholog-based phylogenomics, and variance-based modeling of regulatory canalization and transgressive expression to quantify regulatory variation across morphs. Transcriptomic variation was structured primarily by morph identity rather than geography, indicating consistent morph-associated regulatory programs. Parental morphs showed reduced within-morph variance in gene co-expression modules, consistent with strong regulatory constraint at the network level. In contrast, a naturally occurring mosaic morph exhibited extensive non-additive and predominantly transgressive expression, with most genes falling outside the parental range. This transgressive signal was modular, with most networks remaining stable while a subset showed elevated variance and disrupted inheritance. Functional analyses further reveal that floral pigmentation is embedded within broader metabolic and stress-response pathways, linking color polymorphism to coordinated physiological states and ecological differentiation.