Independent evolution of flavour and parthenocarpy in fig, one of the earliest domesticated fruit trees

<jats:p>Domestication often modifies multiple traits in concert, but whether fruit quality and reproductive mode share a genetic basis in perennial crops has not been tested at multi-omics resolution. In fig (Ficus carica), one of the earliest domesticated fruit trees and a crop with archaeobotanical evidence of cultivation over 11,000 years ago, domestication yielded both distinctive flavour and parthenocarpy, fruit development without pollination. We integrated whole-genome resequencing, transcriptomics, volatile and metabolite profiling, and taste sensor data across a diverse accession panel, using Bayesian GWAS/TWAS and multi-omics factor analysis. Flavour emerges as an integrated sensory system led by aroma, which modulates taste through cross-modal interactions, with sugar-acid balance as a secondary axis; these quality traits map to numerous independent loci. Parthenocarpy instead traces to a single perfectly concordant chromosome 04 haplotype (Eden) centred on FcMYB101-like, carrying a selective-sweep signature and a derived allele fixed in cultivated figs but rare across the genus. Flavour and reproductive mode thus evolved along separate genomic trajectories, allowing each to be improved independently.</jats:p>