Agronomic and fruit metabolite association studies of a worldwide eggplant core collection

Eggplant (Solanum melongena L.) is the second most important berry-producing Solanaceous crop after tomato, boasting a production of approximately 59 Mt in 2023 (FAOSTAT). Eggplant fruit has low in calorie and is considered a healthy vegetable due to its content of minerals, vitamins and bioactive compounds, such as anthocyanins in the skin and chlorogenic acid (CGA) in the flesh. Within the EU G2P-SOL project (http://www.g2p-sol.eu) a collection of more than 3400 accessions held in major worldwide genebanks, which includes both cultivated and wild species belonging to the eggplant primary, secondary and tertiary gene pools, was SPET-based genotyped. Hereafter, a core collection of 321 S.melongena accessions, which is representative of a wide spectrum of genetic diversity, was established. The core collection was phenotyped for 46 relevant agronomic traits in three environmental settings: Montanaso Lombardo (Italy), Valencia (Spain), and Antalya (Turkey). In parallel, in Italy and Spain, the LC-PDA-HRMS (Q-ExactiveTM) was used to analyze and quantify 162 semi-polar metabolites from both sampled peel and flesh tissues of commercially ripe fruits. The core collection was also resequenced at 20X, revealing > 51M SNPs and > 1.9M structural variations (SVs). In addition, a presence/absence table of 12M k-mers was created. Genome-wide association (GWA) studies were carried out on 309 accessions, on the basis of > 1.2M SNPs, > 71k SVs, and > 4M k-mers. Hundreds of quantitative trait loci (QTLs) for both agronomic and metabolic traits were identified, the majority of which showed concordance across SNP-, SV-, and k-mer-based GWAS. In some of the QTL regions identified, among which the ones related to fruit shape and size, synteny with other Solanaceous crops was highlighted, thus facilitating the identification of candidate genes.