Pangenome Graphs and Pan-Phenome for Exploring Diversity and Revealing Genetic Drivers of Key Traits in Eggplant

Overview & Synopsis

Advancements in sequencing technologies have facilitated the production of pangenomes and super-pangenomes that capture the entire genetic diversity of a species or higher-level taxa. In this study, a core collection of 368 accessions representing the worldwide diversity of Solanum melongena and wild relatives was extensively phenotyped across multiple environments, focusing on agronomic performance, disease resistance, and fruit metabolites. Resequencing data were produced, and chromosome-scale genome assemblies generated for 40 accessions of S. melongena, its wild progenitor S. insanum, and its closest sister species S. incanum. These resources enabled the construction of two graph-based pangenomes. The first includes 33 S. melongena, 3 S. insanum, and 4 S. incanum accessions, and was used to explore genetic diversity, population demography, and domestication events within the eggplant core collection. The second, limited to S. melongena, was exploited to carry out a pangenome-wide association analyses of the pan-phenome, identifying a total of 3,192 significant marker-trait associations. We demonstrate the power of these datasets 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 cluster, respectively. Another example is a mutation in a GDSL-like esterase/lipase gene altering the levels of isochlorogenic acids, important compounds involved in fruit browning and antioxidant activity. Overall, our findings demonstrate the potential of graph-based pangenomes for dissecting complex traits, thereby providing a cornerstone for the application of pangenome-informed strategies in eggplant breeding and genetic improvement.