Genomics of eggplant (Solanum melongena L.) for agronomic and metabolic traits improvement, as well as biotic tolerance

Solanum melongena L. (2n = 2x = 24), commonly known as eggplant, aubergine, or brinjal, is a globally significant crop of major economic and nutritional importance, with a long domestication history and considerable phenotypic and genetic diversity. Despite its economic and nutritional relevance, eggplant has historically received less attention than other solanaceous crops in genomic research. Recent advances in sequencing technologies, genotyping platforms, and pangenomic approaches have enabled deeper exploration of its genome structure and diversity. This thesis leverages these tools to dissect eggplant domestication, adaptation, and the genetic basis of key traits. The work is organized into four chapters. Chapter I provides a comprehensive review of quantitative trait loci (QTLs), and candidate genes identified in eggplant to date, highlighting the shift from biparental mapping to genome-wide association studies (GWAS) and the emerging role of pangenomics in capturing structural variants. By synthesizing data from 28 key scientific papers, this chapter offers a valuable resource for breeders and researchers aiming to implement marker-assisted selection strategies in eggplant breeding programs. Chapter II presents a large-scale genotyping effort using SPET (Single Primer Enrichment Technology) across more than 3,400 worldwide accessions of S. melongena and wild species from its primary, secondary and tertiary gene pool elucidating potential domestication history of the eggplant. This analysis revealed two independent domestication centers in India and Southeast Asia, as well as complex routes of migration and diversification. The study also addressed the challenges of managing large germplasm collections and demonstrates the value of genomic data for correcting mislabeling and duplication, optimizing conservation efforts. Chapter III, building on the diversity framework analyzed in Chapter II, investigates the genomic architecture underlying adaptation and selection. Historical GWAS and genome-environment association (GEA) analyses revealed loci shaped by both anthropic and environmental selective pressures, offering insights into the interplay between domestication and adaptation. These findings highlight candidate genes associated with climate resilience and adaptation to diverse agroecological conditions. Chapter IV describes the development a representative eggplant core collection of 368 accessions capturing the global diversity of cultivated eggplant and wild species. Using SPET date, the chapter outlines the methodology behind the selection process, ensuring a representative sampling of the species’ diversity. Subsequently, two graph-based pangenomes were constructed: one representing only S. melongena accessions and the other including its allied species, S. insanum and S. incanum. The chapter emphasizes the advantages of graph-based pangenomes over traditional linear reference genomes in describing the diversity, the population structure and dynamics of the species. Finally, it demonstrates the utility of the pangenome graphs through large-scale pan-GWAS involving more than 200 traits, spanning fruit morphology, metabolic composition, and resistance to biotic and abiotic stresses. Key results include the identification of loci linked to prickliness, resistance to Fusarium oxysporum f. sp. melongenae, and a functionally relevant mutation in a GDSL-like esterase/lipase gene affecting isochlorogenic acid levels. This represents one of the most comprehensive efforts in genotype-to-phenotype mapping in eggplant to date. Overall, the thesis significantly advances our understanding of eggplant biology, offering a genomic foundation for future breeding programs aimed at improving yield, quality, and stress resilience. It also establishes methodological frameworks that may be extended to other crops with rich wild gene pools.