East-west divergence and metabolic differentiation in celery domestication

Celery (Apium graveolens) is a globally cultivated vegetable renowned for its health-promoting and nutraceutical benefits. Exploring its genomic and metabolic diversity can help to facilitate breeding selection. Here, by integrating genomic and metabolomic analyses of 305 globally representative accessions, we reveal pronounced east–west population structure that parallels geographical distribution and varietal differentiation, with three major variety groups showing distinct domestication trajectories. We identify key loci associated with domestication-related traits, including petiole morphology and bolting time. Metabolite profiling uncovers divergence among populations: var. dulce, predominantly consumed raw in Western culinary traditions, exhibits marked reductions in bitter coumarins and alkaloids—a metabolic signature consistent with fresh-eating preferences. Metabolite GWAS map 335,692 loci for 1552 metabolites. We develop genomic prediction models for metabolite abundance to aid breeding. Collectively, our study reveals the genomic and metabolic landscape of celery domestication, and provides hypotheses regarding how cultural practices, alongside regional environmental factors, may have jointly shaped current diversity. Celery is an economically important vegetable crop cultivated and consumed worldwide for its stems, roots, or leaves depending on botanical varieties. Here, the authors present genome assemblies of root and leaf celery and uncover genomic and metabolomic divergences that have contributed to cultivated celery diversification.