Recent advances in long-read sequencing enabled pangenomes and super-pangenomes that capture the full spectrum of genomic diversity within and across species. Here, we present a comprehensive resource for Solanum melongena and its wild relatives by establishing a globally representative core collection of 368 accessions, extensively phenotyped across multiple environments for agronomic performance, disease responses, and fruit metabolic traits, producing the pan-phenome of the species. We resequenced the full panel and generated chromosome-scale assemblies for 40 accessions spanning S. melongena, its wild progenitor S. insanum, and its closest sister species S. incanum, enabling the construction of two graph pangenomes. A multi-species graph (33 S. melongena, 3 S. insanum, 4 S.incanum) resolved genetic diversity, structure, and domestication trajectories. A second graph limited to S. melongena enabled pangenome-wide association studies, identifying 3,192 significant marker-trait associations and demonstrating the power of these datasets through specific examples. Structural variants affecting the LONELY GUY (LOG) 3 gene and a cluster of resistance genes were identified as key determinants of prickliness and resistance to Fusarium oxysporum f. sp. melongenae, respectively. In addition, a mutation in a GDSL-like esterase/lipase gene was linked to variation in the levels of isochlorogenic acids, important metabolites involved in fruit browning and antioxidant activity. Overall, our findings demonstrate that graph-based pangenomes, combined with pan-phenomic diversity, expose the structural basis of domestication and complex traits and provide a foundation for pangenome-informed breeding in eggplant.
Mardi 14 Avril à 11h00
Annotating the cis-regulatory space of crop pan-genomes
