Performance and QTL mapping of eggplant lines with Solanum insanum introgressions under contrasting nitrogen levels in substrate and hydroponic growing systems

Improving nitrogen use efficiency (NUE) is a key objective for reducing fertilizer dependence and environmental impact while maintaining productivity. In this study, a set of eggplant (Solanum melongena) introgression lines (ILs) carrying defined S. insanum genomic segments, together with their recurrent parent and the F1 hybrid, were evaluated under two nitrogen (N) levels, low (LN) and high (HN), in two growing systems: pots with substrate under greenhouse and hydroponics in a climatic chamber. Phenotyping included measurements of biomass, nitrogen and carbon contents, physiological indices and NUE components, with root architecture additionally assessed in hydroponics. Significant effects of genotype, N treatment and their interaction were observed for most traits in both growing systems. Principal component analyses (PCA) revealed a clear separation of samples by N level both for each condition and in the combined analysis. Across conditions, several ILs showed transgressive performance, outperforming the recurrent parent for traits related to biomass, root morphology, and NUE-related indices. A total of 28 QTLs (22 under LN and 4 under HN) were detected in the greenhouse and 77 (10 under LN and 67 under HN) in hydroponics, with limited overlapping. The differences observed between N levels and growing systems underlined the importance of assessing breeding materials under diverse environments and nutrient regimes to identify both stable and environment-specific beneficial alleles. This study provides the first identification of QTLs for NUE in eggplant, identifying novel loci under specific conditions and showing the significant genotype × environment interactions. These results demonstrated that S. insanum introgressions provide valuable genetic variation for improving plant growth and NUE, delivering both genomic targets and well-characterized ILs. By evaluating these materials across two distinct growing systems, new insights are provided into their performance under varying environmental conditions for the development of eggplant cultivars adapted to reduced N fertilization.