Graph pan-genome advances genetic discoveries and the improvement of eggplant

Eggplant is one of the most important solanaceous vegetable crops worldwide. To explore its genomic diversity, we assembled two T2T-level reference genomes from the African eggplant 'Y11' (<i>Solanum aethiopicum</i> L.) and the cultivated variety 'Gui5' (<i>Solanum melongena</i> L.) with genome sizes of 1.10 and 1.13 Gb, respectively. The contigs N50 lengths are 94.2 and 93.9 Mb, with annotations of 37 324 and 40 300 protein-coding genes correspondingly. We also sequenced 238 germplasms, primarily local and cultivated varieties from China, Southeast Asia, Europe, and Africa, identifying 7 853 531 high-quality single nucleotide polymorphisms. Phylogenetic trees and population structures suggest that the domestication of Chinese eggplants occurred later than in Southeast Asia and subsequently diverged into northern and southern groups within China, evolving relatively independently with limited genetic flow between these two groups. Their diversity is significantly lower than that of Southeast Asia and Europe. By selecting 22 representative accessions and four chromosome-level genomes, we constructed an Asian-representative eggplant pan-genome, assembling 463.94 Mb of nonreference sequences. Of these sequences, 38.3% are core genes, 46.9% are dispensable genes, and 14.9% are unique genes. Presence/absence variation genes were found to be highly associated with stress resistance in eggplants. Genome-wide association studies identified 946 SNPs and 9605 genes significantly associated with 10 important traits. Notably, genes involved in zeatin biosynthesis closely linked to plant auxins significantly impact fruit size and shape attributes, playing a crucial role in eggplant yield. This high-quality reference genome alongside the pan-genome will provide valuable insights into eggplant breeding advancement.