Beyond the single reference: pangenomic perspective on WRKY structural diversity and its role in trait adaptation...

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.

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, copy-number variations 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.

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.