Tomato (Solanum lycopersicum) is a premier global crop, celebrated not only for its economic importance but also as a fundamental “well-being food” that provides essential vitamins, minerals, and potent antioxidants. This review highlights the transformative impact of CRISPR/Cas9 and next-generation precision tools, such as base and prime editing, on modern tomato breeding. Beyond functional genomics, we focus on the strategic engineering of tomato to maximize productivity through fruit size optimization and the biofortification of high-value metabolites (e.g., GABA, lycopene, and vitamins). Furthermore, we examine recent advances in developing multi-stress resilience against both biotic and abiotic challenges. A significant emphasis is placed on re-designing plant architecture and developmental traits to tailor tomato varieties for future agricultural systems, particularly indoor and vertical farming. By advanced delivery methods, CRISPR technologies offer unprecedented potential to accelerate the development of “smart” tomato, ensuring sustainable agriculture and global food security in a changing climate.

Polyploid plants, such as hexaploid Solanum nigrum, present new challenges and opportunities for trait improvement due to their complex genome structures and homoeologous gene interactions. Gene editing of homoeologs provides a powerful tool to investigate the inheritance and phenotypic effects of mutations in polyploid systems. Here, we investigated the inheritance and phenotypic traits of homoeolog-edited triple and double mutants in hexaploid S. nigrum. Triple mutant genotypes (sns and snsp) were used for analyzing inheritance patterns through backcrossing and self-pollination, revealing independent segregation of homoeologous variants and consistent genotypic ratios across generations. Yield and related traits were evaluated in fixed double mutants (sns1 sns2, sns1 sns3, sns2 sns3) under greenhouse and open-field conditions. Open-field cultivation significantly enhanced yield, primarily through increased fruit weight per inflorescence, whereas greenhouse cultivation showed more modest improvements. Other traits such as plant weight and Brix values remained largely unchanged. Yield improvements were stable across F3 to F5 generations, with minimal genotype-specific variability. These findings highlight the potential of homoeolog-targeted editing in polyploid plants to achieve stable and environment-specific yield enhancements.

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Plant breeders have accumulated hybrid effects to increase food production in order to counteract the loss of arable land. Hybrids may possess novel genetic potential to increase agricultural productivity; however, the relationships between genetic resources for optimizing crop productivity remain mostly unclear. In this study, we recorded heterosis effects of genetically inherited traits by reciprocal hybridization of the Solanum lycopersicum cultivar Micro-Tom and the commercial cultivar M82, which are currently available as in silico mutant populations, to identify mutant genes which can induce heterosis. The genetic variations between M82 and Micro-Tom caused intermediate phenotypic effects with regard to flowering time, plant height, and fruit size, indicating additive interactions among variations with a hybrid background. The total yield of F1 hybrid was similar to that of cultivar M82, regardless of reduced vegetative biomass, and it revealed an overdominance effect regarding number of harvested fruits. The inheritance of the phenotypes was similar among reciprocal F1 hybrids with different paternal and maternal materials. Based on the consistency of hybrids and wild types, Micro-Tom mutants showing floral homeotic defects and large plant size can be efficiently screened for overdominant yield mutants in F1 hybrids. Therefore, we suggest that identical traits in reciprocal hybrids between Micro-Tom and M82 varieties are useful as control F1 hybrids to improve field tomato productivity by screening mutant hybrids of Micro-Tom mutants and commercial variety M82.

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