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Résumé :

Within the Solanaceae family, eggplant (Solanum melongena L.) is the second most important berry-producing crop after tomato with a global production of approximately 59 Mt in 2023 (FAOSTAT). Eggplant fruits are rich in minerals, vitamins, and antioxidant compounds, such as phenolics, anthocyanins, and chlorogenic acid, which contribute to their nutritional value. In the frame of the EU G2P-SOL project (http://www.g2p-sol.eu), a core collection of 321 S. melongena accessions, as well as members of wild species belonging to its primary to tertiary gene pools, was established. The core collection was phenotyped for 46 relevant agronomic traits across three distinct geographical areas: Montanaso Lombardo (Italy), Valencia (Spain), and Antalya (Türkiye). In addition, a total of 162 semi-polar metabolites were analyzed and quantified using LC-PDA-HRMS (Q-ExactiveTM) on peel and flesh tissues sampled separately from fruit at a commercially ripe stage in two fields (Italy and Spain). The core collection was also resequenced at 20X, resulting in >51M SNPs and >1.9M structural variations (SVs), as well as a presence/absence table of >12M k-mers. After quality filtering, a genome-wide association (GWA) analysis for both agronomic and metabolic traits was carried out on 309 S. melongena accessions using >1.2M SNPs, >71k SVs, and >4M k-mers. Following a multi-environment approach, hundreds of quantitative trait loci (QTLs) for each trait class were identified, with a significant majority showing concordance across SNP-, SV-, and k-mer-based GWAS. Accessions with contrasting phenotypes for key agronomic and metabolic traits were also analyzed to identify selective sweeps (SSs) putatively involved in selection signatures. Furthermore, evidence of sinteny with other solanaceous crops has been highlighted, facilitating the identification of candidate genes associated with QTLs and SSs. High-quality chromosome-scale genomes of 40 accessions of the core collection were also used for the construction of a graph-based pangenome, providing a powerful tool for the genetic improvement of the eggplant species.

Keywords: Solanum melongena, resequencing, GWAS, selective sweeps, synteny, pangenome

Luciana Gaccione

I am a third-year PhD student at DISAFA (University of Turin, Italy) under the supervision of Prof. Lorenzo Barchi, specializing in the field of plant genomics, with a particular focus on horticultural species such as eggplant. My research primarily involves genome-wide association studies of relevant traits in eggplant. I have also conducted pangenomic analysis, involving genome assembly (using data from the latest long-read sequencing technologies, specifically Oxford Nanopore Technologies), comparative analysis for determining the best assembly strategies, structural and functional annotation, single nucleotide polymorphism analysis, and the identification of structural variants. Furthermore, I have gained valuable international experience during a research period abroad at Forschungszentrum Jülich in Germany, under the supervision of Prof. Bjorn Usadel from February to July 2023. This experience has greatly enriched my research capabilities in pangenomics, and I was also introduced to High-performance computing (HPC) data analysis.