Pangenome analysis uncovers large hidden structural variants underlying fruit color and bacterial wilt resistance in eggplant

Large structural variants (SVs) underlying important agronomic traits remain largely unexplored in Solanaceae crops. Eggplant (Solanum melongena L.) is a globally important horticultural crop worldwide, belonging to the Solanaceae family. Here, we first present population genomic analyses of a diversity panel of 201 eggplant accessions, largely representing genetic diversity from one of the main eggplant domestication centers, Southeast Asia. We revealed that genetic relationships are highly correlated with geographic origin. We then de novo generated the chromosome-scale genomes of nine representative accessions, plus five previously published assemblies, to construct a graph-based pangenome. With the aid of this resource in association scans, we identified a 12.4 Mb inversion at a high frequency (53.7%) within the population, which is associated with fruit color, likely the result of artificial selection favoring purple peel. We also discovered multiple mutations linked to bacterial wilt resistance, including a premature stop codon in SmCYP82D47 and copy number variations of SmEPS1 and SmRoq1 homologs. This study provides insights into the evolution and biology of large SVs in Solanaceae crops, as well as provides fundamental genomic resources accessible to genetic analyses and breeding in eggplant.