Graph-based pangenome reveals structural variation dynamics during cucumber breeding

Structural variants (SVs) represent an important yet underexplored component of plant genome diversity. Here we present a graph-based cucumber pangenome constructed from 39 reference-quality genomes, including 27 newly assembled and 12 previously published. The pangenome captures 171,892 high-confidence SVs, which were genotyped across 447 wild and cultivated accessions. Our analyses reveal that, during cucumber domestication, a substantial portion of mildly deleterious SNPs were retained, whereas SVs were consistently purged, highlighting their highly deleterious nature. During geographical expansion, a reduced SV burden and a younger age of SVs compared to SNPs were observed, suggesting stronger purifying selection acting on SVs. Introgressions from wild populations increased SV burden, potentially due to hitchhiking. Notably, incorporating SV burden into genomic prediction models improved prediction accuracy for several agronomically important traits. This study illuminates SV dynamics during cucumber domestication and range expansion and underscores the implications of SVs for future cucumber breeding.