The genomic route to tomato breeding: Past, present, and future Tomato (Solanum lycopersicum L.) is an economically important vegetable crop with high nutritional value and global production of 182 million tons in 2022. Over the past 10,000 years, human selection has significantly influenced tomato genomes, enhancing traits for consumption and manufacturing. Recent advances in genome sequencing and assembly have provided valuable resources for tomato breeding, including the first published tomato genome in 2012. The reference genome of Heinz 1706 has been updated multiple times, improving genome completeness and accuracy. The closest wild species, S. pimpinellifolium, has been extensively studied for its high lycopene and nutrient content. The first tomato pan-genome was constructed from 725 accessions, revealing additional genes and highlighting gene loss during domestication. Recent pan-genome studies have identified structural variants (SVs) and their roles in genetic diversity and agronomic traits. The tomato super pan-genome includes 10 wild species and 1 cultivated species, providing a foundation for exploring genes in wild species. Genome resequencing and population genomics have enabled the identification of key genes and regulatory elements involved in fruit development, ripening, and environmental responses. GWAS has identified numerous loci associated with important agronomic traits, including fruit weight, flavor, and disease resistance. Multi-omics approaches have provided insights into the genetic basis of complex traits, such as fruit flavor and soluble solid content. DNA methylation plays a crucial role in fruit ripening and disease resistance. Genes controlling key agronomic traits, such as flowering time, fruit weight, shape, quality, and ripening, have been identified and characterized. These genes are essential for improving tomato varieties for sustainable agriculture. Genome design-based breeding, including de novo domestication, synthetic biology, and haploid induction, offers new strategies for tomato improvement. Genetic modification techniques, such as CRISPR/Cas9, have enabled the development of improved tomato varieties with enhanced traits. Male-sterility systems and haploid induction systems are important for hybrid seed production. Synthetic biology has shown potential for metabolic engineering in tomato. Heterosis and genomic selection are promising approaches for accelerating tomato breeding. Overall, genomic resources and advanced breeding strategies are crucial for improving tomato varieties to meet the demands of sustainability and evolving human societies.The genomic route to tomato breeding: Past, present, and future Tomato (Solanum lycopersicum L.) is an economically important vegetable crop with high nutritional value and global production of 182 million tons in 2022. Over the past 10,000 years, human selection has significantly influenced tomato genomes, enhancing traits for consumption and manufacturing. Recent advances in genome sequencing and assembly have provided valuable resources for tomato breeding, including the first published tomato genome in 2012. The reference genome of Heinz 1706 has been updated multiple times, improving genome completeness and accuracy. The closest wild species, S. pimpinellifolium, has been extensively studied for its high lycopene and nutrient content. The first tomato pan-genome was constructed from 725 accessions, revealing additional genes and highlighting gene loss during domestication. Recent pan-genome studies have identified structural variants (SVs) and their roles in genetic diversity and agronomic traits. The tomato super pan-genome includes 10 wild species and 1 cultivated species, providing a foundation for exploring genes in wild species. Genome resequencing and population genomics have enabled the identification of key genes and regulatory elements involved in fruit development, ripening, and environmental responses. GWAS has identified numerous loci associated with important agronomic traits, including fruit weight, flavor, and disease resistance. Multi-omics approaches have provided insights into the genetic basis of complex traits, such as fruit flavor and soluble solid content. DNA methylation plays a crucial role in fruit ripening and disease resistance. Genes controlling key agronomic traits, such as flowering time, fruit weight, shape, quality, and ripening, have been identified and characterized. These genes are essential for improving tomato varieties for sustainable agriculture. Genome design-based breeding, including de novo domestication, synthetic biology, and haploid induction, offers new strategies for tomato improvement. Genetic modification techniques, such as CRISPR/Cas9, have enabled the development of improved tomato varieties with enhanced traits. Male-sterility systems and haploid induction systems are important for hybrid seed production. Synthetic biology has shown potential for metabolic engineering in tomato. Heterosis and genomic selection are promising approaches for accelerating tomato breeding. Overall, genomic resources and advanced breeding strategies are crucial for improving tomato varieties to meet the demands of sustainability and evolving human societies.