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 multiple locations for agronomic, disease resistance and fruit metabolomic traits and resequenced. Forty chromosome-level assemblies of S. melongena, its progenitor S. insanum and the allied species S. incanum were generated to construct two graph-based pangenomes, which capture a broad spectrum of structural, nucleotide, and phenotypic variation, more than doubling the size of a previously published pangenome. Pangenome-wide association analyses were conducted, identifying a total of 3,192 marker-trait associations. We demonstrate the power of these analyses through examples such as the identification of major loci associated with the prickliness and resistance to Fusarium oxysporum f. sp. melongenae, driven by SVs affecting the LONELY GUY (LOG) 3 gene and a resistance gene clusters, respectively, as well as a mutation in a GDSL-like esterase/lipase gene altering the levels of isochlorogenic acids, important compounds linked to fruit browning and antioxidant properties. These datasets provide a solid basis for pangenome-assisted breeding in eggplant, and enable detailed analyses of genetic diversity, population demography, domestication history, and trait evolution.