Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding

A core collection of 368 accessions representing the worldwide diversity of Solanum melongena and several wild relatives was phenotyped in multiple locations for agronomic, disease resistance and fruit metabolomic traits and resequenced. Additionally, forty chromosome-level assemblies of S. melongena, its progenitor S. insanum and the allied species S. incanum allowed the construction of two graph-based pangenomes, capturing a broad spectrum of genetic variation in the core collection. Here, we demonstrate the power of these datasets by identifying major loci associated with prickliness and resistance to Fusarium oxysporum f. sp. melongenae, driven by SVs affecting the LONELY GUY 3 gene and a resistance gene cluster, respectively, as well as a mutation in a GDSL-like esterase/lipase gene altering the levels of dicaffeoyl-quinic acids. These findings provide a cornerstone for pangenome-assisted breeding, and enable detailed analyses of genetic diversity, domestication history, and trait evolution in eggplant.