Whole-genome resequencing reveals genetic diversity and population differentiation in Gardenia jasminoides J. Ellis

Gardenia jasminoides J. Ellis, an evergreen shrub or small tree valued for ornamental horticulture and traditional Chinese medicine, has undergone millennia of cultivation and geographic expansion across China. Yet the genetic architecture underlying its population differentiation and trait variation remain largely unresolved. Here we report whole-genome resequencing of 197 G. jasminoides accessions spanning nine diverse geographic populations, yielding 7,190,745 single nucleotide polymorphisms (SNPs) and 1,865,154 insertions/deletions (InDels). Population genomic analyses showed limited divergence between wild and cultivated gene pools but revealed clear geographic structure. Among these populations, Jiangxi (JX) displays a distinctive genetic profile, characterized by the lowest nucleotide diversity, the shallowest linkage disequilibrium decay, and the highest genetic cohesion. Genome-wide scans for divergent selection identified 44 genomic regions harboring 597 candidate genes, significantly enriched in brassinosteroid biosynthesis, ascorbate and aldarate metabolism, and diterpenoid biosynthesis. These pathways plausibly modulate key agronomic and pharmacological traits. This dataset provides a foundational resource for elucidating the molecular physiology of population differentiation in this perennial medicinal shrub, with implications for marker-assisted breeding and germplasm conservation.