From Genetic Diversity to Genetic Gain: Molecular Approaches and Breeding Strategies in Tomato with Insights from Lithuanian Germplasm

Tomato (Solanum lycopersicum L.) is a globally important vegetable crop and a major dietary source of bioactive compounds, including lycopene, ascorbic acid, phenolics, and minerals. Modern tomato breeding has substantially improved yield, uniformity, and postharvest performance; however, these gains have often been accompanied by reduced flavor quality, lower nutritional value, and narrowing of the genetic base. This review synthesizes available evidence on Lithuanian tomato germplasm and evaluates its relevance for future breeding strategies aimed at enhancing genetic gain under Northern European conditions. The review integrates published data on genetic diversity, molecular characterization, morphological traits, fruit quality parameters, and yield performance of Lithuanian cultivars and hybrids developed in Lithuania. SSR-based studies indicate moderate genetic diversity, with mean expected heterozygosity of approximately 0.51 and mean PIC values of 0.47 in cultivars and 0.45 in hybrids, while also confirming a relatively narrow breeding pool. Lithuanian cultivars display substantial variation in fruit morphology, dry matter, soluble solids, firmness, lycopene, ascorbic acid, and yield. Traditional cultivars such as ‘Svara’, ‘Milžinai’, ‘Slapukai’, and ‘Balčiai’ show valuable nutritional and technological traits, whereas hybrids such as ‘Auksiai H’, ‘Adas H’, and ‘Ainiai H’ demonstrate improved productivity and firmness. The available evidence suggests persistent yield–quality trade-offs, particularly between productivity, soluble solids content, antioxidant accumulation, and postharvest performance. Although Lithuanian germplasm does not represent exceptionally broad genetic diversity, it contains regionally adapted material with stabilized trait combinations useful for breeding resilience, nutritional quality, and adaptation to temperate environments. Future progress will require broadening the genetic base and integrating traditional breeding with marker-assisted selection, genomic selection, GWAS, genome editing, multi-omics, and pangenomic approaches. Overall, Lithuanian tomato germplasm represents a locally adapted regional resource for translating genetic diversity into genetic gain in modern tomato breeding.