Beyond the Single Reference: Pangenomic Perspective on WRKY Structural Diversity and Its Role in Trait Adaptation across Oleaceae.

Background: WRKY transcription factors are a plant-specific family of key regulators involved in floral pigmentation, scent biosynthesis, and stress responses, and thus provide a molecular entry point for trait improvement. However, WRKY studies in Oleaceae still largely rely on single reference genomes, which incompletely capture structural variations and accession-level functional diversity.

Scope: This review summarizes recent progress in WRKY research across ornamental plants, with emphasis on the current status and resource limitations in Oleaceae. We highlight how pangenomic frameworks can uncover presence-absence variations (PAVs), copy-number variations (CNVs) and other structural variants that shape WRKY repertoires. We discuss how these resources enable the delineation of core versus variable WRKY members and support variant-to-trait hypotheses for key ornamental traits. We further propose a pangenome-driven strategy to guide the prioritization of functional WRKY candidates underlying floral coloration and scent formation, integrating comparative genomics, structural-variant profiling and multi-omics evidence.

Conclusions: Incorporating pangenomics into WRKY family analyses is expected to move Oleaceae research beyond single-reference catalogues towards trait-oriented gene discovery. A pangenome-enabled workflow significantly enhances the resolution of WRKY diversity and variant-trait hypotheses, thereby laying a foundation for functional validation and molecular breeding of cultivars that harmonize superior fragrance and coloration with enhanced environmental stress resilience.