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PubMed2026

Genome-wide screening and functional analysis of protein glycosylation-related genes involved in tomato fruit ripening.

Protein glycosylation, an essential co- and post-translational modification, plays critical roles in plant growth, development, and stress responses. However, its functional role in tomato fruit ripening has not been extensively investigated. Here, key protein glycosylation-related genes involved in tomato fruit ripening were identified by genome-wide screen and subsequently functional characterization. First, a dataset comprising 242 glycosylation-related proteins was established based on Gene Ontology annotations in tomato, combined with sequence homology to protein glycosylation-related proteins from Arabidopsis thaliana and Homo sapiens. Then, Subsequently, 28 genes encoding highly expressed glycosylation-related proteins (RPKM > 30) at the breaker (BR) stage were selected for functional screening, and subsequently 6 genes were identified as regulators of fruit ripening by method of virus-induced gene silencing (VIGS). Among them, Solyc03g098600 (STT3B), Solyc01g109410 (OST48), Solyc04g082670 (RPN1), and Solyc08g076460 (DAD1) functioned as positive regulators of tomato fruit ripening, whereas Solyc04g005340 (UAM2) and Solyc08g075340 (XEG113), acted as negative regulators. The expression of these genes responded dynamically to multiple ripening-related cues, including temperature, light, ethylene, and transcription factors. Furthermore, silencing of these genes individually affected the expression of genes involved in fruit ripening, including ethylene biosynthesis genes (ACS2, ACS4, ACO1, and ACO3), ripening-associated transcription factors (RIN, NOR, NOR-LIKE1, FUL1, and FUL2), and the key gene (PSY1) of lycopene biosynthesis pathway. Collectively, these findings demonstrate that protein glycosylation plays an important role in tomato fruit ripening by modulating ethylene signaling, ripening-associated transcriptional regulation, and lycopene biosynthesis.

Fruit ripening↗
PubMed2026

Nitric oxide enhances SlSPL10-mediated transcriptional repression of carotenoid synthesis genes to delay tomato fruit carotenoid accumulation.

Nitric oxide (NO) inhibits climacteric fruit ripening, but its mechanisms remain elusive. Here, S-nitrosoglutathione (GSNO, a NO donor) reduces carotenoid accumulation in tomato fruit, confirming NO's role as carotenoid biosynthesis suppressor. Transcriptome analysis identified SlSPL10 (SQUAMOSA promoter binding protein-like 10) as a key player during this process. Genetic evidence further revealed that SlSPL10 negatively regulates carotenoid synthesis. Moreover, GSNO fails to suppress carotenoid synthesis in slspl10 mutant fruit, in contrast to wild-type fruit, highlighting the involvement of SlSPL10 in NO-inhibited carotenoid synthesis. Transcriptomic profiling of slspl10 mutant fruit showed that both NO and SlSPL10 regulate key carotenoid synthesis genes (SlGPS, SlPDS, SlZDS, SlZISO, and SlCRTISO). SlSPL10 directly binds to the promoters of these genes to repress their transcription, and NO enhances the transcriptional inhibition of SlGPS, SlZISO, and SlCRTISO. These three genes are indispensable for SlSPL10's role in NO-mediated carotenoid suppression. Collectively, NO enhances SlSPL10-mediated repression of carotenoid biosynthesis gene expression, reducing carotenoid accumulation in tomato fruit.

Solanum lycopersicum↗
PubMed2025

Chromatin accessibility analysis reveals functional cis-regulatory regions related to fruit development and domestication in tomato.

Non-coding DNA sequences harbor vast regulatory programs that ensure the precise spatiotemporal control of gene expression, which is essential for proper plant development and trait formation. Chromatin accessibility analysis could identify functional DNA regions within the extensive non-coding sequences and infer regulatory elements, serving as a crucial approach to unravel the mysteries of non-coding DNA sequences. Tomato fruit, a fleshy organ, provides a special system for studying fruit development and trait formation. However, the role of cis-accessible chromatin regions (cis-ACRs) during tomato fruit development, particularly in comparison with protein-coding DNA sequences, remains poorly understood. Here, we used ATAC-seq to define the landscape of cis-ACRs during fruit development and domestication in tomato. Temporal differential analysis revealed the dynamic opening and closing of cis-ACRs during fruit development. Comparative analysis of cis-ACRs between cultivated and wild tomatoes highlighted their significant contributions to fruit domestication. Combining analysis with genomic structural variations (SVs) suggested that SVs are likely a key factor in the formation of specific accessible cis-ACRs in cultivated tomatoes. Moreover, using gene editing, we identified a functional cis-ACR within the intron of the MBP3 gene that regulates fruit development and size traits. Overall, our findings provide a comprehensive perspective on the roles of cis-ACRs in tomato fruit development and domestication.

Solanum lycopersicum↗
PubMed2026

Phytochrome-interacting factor 1b (SlPIF1b) affects the fruit quality of tomato by regulating chloroplast development.

The increased abundance and functionality of fruit chloroplasts could promote the accumulation of nutrients and flavor in the fruit. Tomato fruit has fully developed fruit chloroplasts, whose abundance and functionality have much untapped potential in improving fruit quality by controlling fruit chloroplast development. Previous studies have identified many regulatory factors that specifically regulate fruit chloroplast development in tomatoes, but there are fewer reports on tomato phytochrome-interacting factors (SlPIFs). Arabidopsis AtPIFs have been implicated in chloroplast development and chlorophyll biosynthesis. In this study, we identified and characterized an SlPIF1b mutant in tomato, named GS, which exhibited a dark green fruit shoulder with enhanced chloroplast development. RNA-seq and genotyping analysis identified a - 21 bp (A → T) mutation in the promoter of SlPIF1b, resulting in the absence of the TATA-box core transcriptional element and inhibiting SlPIF1b transcription. The overexpression of SlPIF1b in GS inhibited chloroplast development of fruits, leading to a lighter green shoulder color, decreased chlorophyll content, reduced photosynthetic activity, diminished starch accumulation, and compromised fruit quality upon ripening. Conversely, the down expression of SlPIF1b significantly enhanced fruit chloroplast development and functionality in fruits, resulting in increased chlorophyll and carotenoid accumulation. Further analysis of expression profile and transcriptional activity indicated that SlPIF1b could bind to G/PBE-box elements present in SlGLK2, SlTKN4, SlCAO1a, SlPOR1, SlPOR3, SlCAB1 and SlCAB1b promoters, thereby inhibiting their expression. This study revealed the specific regulatory mechanism by which SlPIF1b modulates chloroplast development and chlorophyll synthesis in tomato fruit and provided valuable genetic resources and a theoretical basis for tomato quality improvement.

Solanum lycopersicum↗
PubMed2026

The durable resistance gene Tm-22 remains partially resistant to tomato brown rugose fruit virus.

The tomato Tm-22 gene is a highly effective, and durable resistance gene in agriculture that has protected tomato production against viruses of the Tobamovirus genus, such as tomato mosaic virus (ToMV) and tobacco mosaic virus (TMV) for over 60 years. This dominant R gene, originally sourced from wild tomato species (Solanum peruvianum), acts by recognizing the viral movement protein (MP) and triggering an immune response, often resulting in extreme resistance (ER). However, this durable protection is challenged by a recently emerged new tobamovirus named tomato brown rugose fruit virus (ToBRFV, Tobamovirus fructirugosum). ToBRFV-encoded MP is responsible for ER breakdown. Here, we present evidence that while ToBRFV can evade Tm-22-mediated ER, Nicotiana benthamiana and tomato plants carrying Tm-22 still remain partially resistant to ToBRFV. We show that ToBRFV MP is recognized by and interacts with Tm-22 to trigger an attenuated hypersensitive response. Moreover, we discover that overexpression of Tm-22 can enhance resistance to ToBRFV. These findings demonstrate the practical value of Tm-22 in ongoing resistance breeding programs and open a potential avenue to restore Tm-22 immunity through upregulation of Tm-22 expression.

Solanum lycopersicum↗
PubMed2025

Gene editing of clock components in Solanum lycopersicum: Effects on gene expression, development, and productivity.

The circadian clock plays a crucial role in regulating key biological processes, including growth and development. While studies in the model plant Arabidopsis thaliana have significantly advanced our understanding of circadian function, recent research has also focused on crop species for improved yield and quality. In this study, we examined the rhythmic behavior and regulatory function of circadian clock components in tomato (Solanum lycopersicum). Time course analyses of gene expression over the circadian cycle revealed robust rhythmic oscillations in tomato leaves under free-running conditions. Comparative analyses showed similar peak phases for several clock genes in Arabidopsis and tomato, suggesting functional conservation. Rhythms in tomato fruits, however, showed reduced amplitude, slight phase changes, or arrhythmia, indicating organ-specific circadian variations. By using CRISPR-Cas9 gene editing strategies (clockcrispr), we also showed that proper clock gene expression is essential for setting the phase in tomato plants. Leaf movement analyses also showed a phase change in the clockcrispr lines, correlating with shorter or longer periods. The clockcrispr lines also displayed distinct growth and developmental phenotypes that differ from those reported in the Arabidopsis clock mutant counterparts. Our transcriptomic analyses identified species-specific regulation of key target genes. The results offer mechanistic insights into the conserved and divergent molecular pathways governing circadian phenotypic variations between Arabidopsis and tomato plants.

Solanum lycopersicum↗
PubMed2026

Phosphorylation and ubiquitination coordinate homeostasis of a tomato transporter responsible for fruit sugar accumulation.

Sugar transport mediated by different transporters is essential for maintaining sugar homeostasis in plants. Here, we report that phosphorylation and ubiquitination coordinate the homeostasis of a tomato (Solanum lycopersicum) sugar transporter SlSWEET16, revealing a new aspect of plant sugar homeostasis. SlSWEET16 is localized to plasma membrane and functions as a mono- and disaccharide transporter. SlSWEET16 mediates cellular sugar efflux, and CRISPR/Cas9-mediated knockout of SlSWEET16 leads to increased fruit sugar accumulation. Strikingly, the C-terminus of SlSWEET16 is subjected to both phosphorylation and ubiquitination. Two protein kinases including SlSnRK2.3 and SlSnRK2.4 associate with the C-terminus of SlSWEET16, resulting into an increase in the stability of SlSWEET16. Meanwhile, the C-terminus of SlSWEET16 also interacts with an E3 ubiquitin ligase SlTT3.1L2, which decreases the stability of SlSWEET16. SlSnRK2.3 and SlSnRK2.4 inhibit fruit sugar accumulation, whereas SlTT3.1L2 promotes it. Mutations of phosphorylated or ubiquitinated residues in SlSWEET16's C-terminus further corroborate the contribution of phosphorylation and ubiquitination to the stability of SlSWEET16 and fruit sugar accumulation. Our results reveal a multiple-protein regulatory module that integrates different post-translational modifications to control transporter-mediated fruit sugar accumulation.

Solanum lycopersicum↗
PubMed2025

Cr3a, a candidate gene conferring fruit cracking resistance, was fine-mapped in an introgression line of Solanum lycopersicum L.

In the cultivation and production of tomato (Solanum lycopersicum L.), fruit cracking is a prevalent and detrimental issue that significantly impacts the esthetic quality and commercial value of the fruit. The complexity of the trait has resulted in a slow advancement in research aimed at identifying genes that influence tomato fruit cracking and the underlying regulatory mechanisms. In this study, a sub-introgression population for tomato crack-resistant fruit has been constructed from the cross between S. lycopersicum 1052 and Solanum pennellii LA0716, followed by 11 generations of selfing. Utilizing specifically designed InDel markers, the tomato crack-resistant gene, Cr3a, was fine-mapped, cloned, and its functionality was confirmed through transgenic and gene-knockout approaches. The precise localization of Cr3a was delineated to a 30 kb genomic region on chromosome 3, corresponding to the gene Sopen03g034650 in S. pennellii and Solyc03g115660.3 in the Heinz1706 variety. An integrated transcriptomic and metabolomic analysis of fruits with and without the Cr3a gene was finally conducted to elucidate the intricate regulatory mechanisms associated with Cr3a. The findings revealed a molecular regulatory network for tomato fruit crack resistance, characterized by 7 key metabolites, 13 pivotal genes, and 4 critical pathways: the phenylpropanoid biosynthesis pathway, the phenylalanine, tyrosine, and tryptophan biosynthesis pathway, the linolenic acid metabolism pathway, and the cysteine and methionine metabolism pathway. In summary, this research provides novel insights into the molecular underpinnings of tomato fruit crack resistance and holds substantial promise for accelerating the molecular breeding of tomatoes with enhanced fruit crack resistance.

Solanum lycopersicum↗
PubMed2026

Cis-regulatory variation in the MdCKX6 promoter is associated with allele-specific expression and fruit size in apple.

Fruit size is a key determinant of apple fruit quality and market value and is strongly influenced by phytohormone-regulated cell proliferation and expansion during early fruit development. Cytokinin oxidase/dehydrogenase (CKX) enzymes regulate cytokinin homeostasis by irreversibly degrading active cytokinins, but the contribution of natural variation in CKX genes to fruit size remains poorly understood. Here, we identified MdCKX6 as a candidate regulator of fruit growth in apple (Malus domestica). MdCKX6 exhibited pronounced allele-specific expression during fruit development in the cultivar 'Royal Gala'. Sequence analysis identified a promoter SNP associated with differential promoter activity and allele-specific expression. Genotyping of diverse apple cultivars and wild Malus accessions revealed a significant association between MdCKX6 promoter genotype and fruit size. Cultivars carrying low-expression alleles produced larger fruits, whereas high-expression alleles were associated with smaller fruits. To investigate gene function, MdCKX6 was overexpressed in tomato, resulting in reduced fruit size. Histological analyses of the transgenic tomato fruit revealed smaller pericarp cells. Transcriptome analysis of transgenic fruits revealed widespread changes in genes associated with cell-cycle regulation, cell wall modification, hormone-related processes, and transcriptional regulation. Together, these results identify MdCKX6 as a potential negative regulator of apple fruit growth and reveal an association between cis-regulatory variants, gene expression, and fruit size. This study provides new insights into the role of cytokinin metabolism in fruit development and highlights regulatory variation in MdCKX6 as a potential target for apple breeding.

Malus↗
PubMed2025

A SlEIN2-centered epigenetic network equilibrates fruit ripening and innate immunity in tomato.

Ethylene and DNA/RNA methylation serve as essential factors in controlling fruit ripening. In tomato, the mRNA N6-methyladenosine (m6A) demethylase SlALKBH2 regulates mRNA stability of the DNA 5-methylcytosine demethylase gene SlDML2 via modulating m6A modifications. However, the interplay between ethylene and these epigenetic marks remains unclear. Here, we show that SlDML2 expression is significantly inhibited in slein2 fruits, but remains unchanged in the high-order sleil mutant (sleil1 sleil2 sleil3/SlEIL3 sleil4 and sleil1 sleil2/SlEIL2 sleil3 sleil4) fruits, indicative of post-transcriptional regulation of SlDML2 expression by SlEIN2, a core ethylene signaling component acting upstream of the master transcription factors SlEILs. Interestingly, SlEIN2 preferentially regulates the asymmetric CHH methylation in promoters of several key ripening regulator genes. Mechanistically, SlEIN2 physically interacts with SlALKBH2, which promotes SlDML2 expression in a SlEIN2-dependent manner. Furthermore, SlAGO4A and SlAGO4B, components of the RNA-directed DNA methylation pathway, were upregulated in slein2 fruits. Silencing SlAGO4A/B in wild-type fruit caused precocious ripening with necrosis, indicative of hyperimmunity. Conversely, SlAGO4A/B silencing in slein2 markedly delayed this hyperimmunity. Taken together, our study reveals that ethylene, beyond transcriptional regulation, employs an elaborate epigenetic machinery mediated by the SlAGO4A/B-SlEIN2-SlALKBH2 module to balance fruit ripening and innate immunity.

Solanum lycopersicum↗
PubMed2026

The TANG cluster comprising ten nitrate transporter genes controls fruit sweetness and size in tomato.

Sucrose is a major transport form of photoassimilated carbon in tomato, Arabidopsis, and many other plant species, and plays a critical regulatory role in plant growth, development, and fruit quality. Plant vacuoles function as storage organelles, accumulating substantial quantities of metabolically inactive nitrates as a nitrogen reserve and soluble sugars as a carbon reserve. Consequently, the balance between nitrate and sucrose accumulation determines plant growth dynamics and fruit taste. In this study, we identified a gene cluster designated TANG (Total soluble solidsAccumulation viaNitrate transporterGene cluster), comprising ten nitrate transporter genes that are significantly associated with sucrose accumulation in tomato. This gene cluster mediates the transport of nitrate between the cytoplasm and vacuole, thereby influencing its storage. Functional disruption of TANG8, a member of the gene cluster, results in either enhanced sugar accumulation or increased fruit size. Selective disruption of multiple TANG cluster members yields fruits with elevated sweetness and increased fruit size in S. pimpinellifolium. The interaction between the TANG members and a tonoplast localized Sucrose Transporter 4 provides insight into the competitive accumulation of nitrate and sugar. The multiplex editing of a gene cluster provides a successful example of engineering crops with high quality and yield.

Gene cluster↗
PubMed2025

Tm-1 back in business: an allele from Solanum pennellii accessions plays a major role in ToBRFV resistance.

The Tm-1 allele from Solanum pennellii accessions together with an additional, likely recessive, locus are required for complete ToBRFV resistance. The Tobamovirus Tomato Brown Rugose Fruit Virus (ToBRFV) poses a significant threat to global tomato production. ToBRFV is a mechanically transmitted virus containing a single-stranded positive sense RNA genome. Disease symptoms include brown, rough patches on fruit surfaces, leaf mosaicism and shape abnormalities, and, in advanced stages, total collapse of infected plants. ToBRFV was first detected in the Middle East in 2014 and has rapidly spread to multiple countries across Asia, Europe, and America. In recent years, numerous studies have focused on the identification of ToBRFV resistance traits that are suitable for tomato breeding programs. In this study, we identified five ToBRFV-resistant accessions of Solanum pennellii, a wild relative of cultivated tomato. We confirmed that the major gene controlling this resistance trait is the S. pennellii allele of Tm-1. Tm-1 was previously identified in S. habrochaites as a semidominant Tomato Mosaic Virus (ToMV) resistance gene. Our results show that full resistance to ToBRFV disease requires an additional undescribed locus. These results show the potential of S. pennellii as a novel source of resistance against ToBRFV.

Disease Resistance↗
PubMed2024

Editing of SlWRKY29 by CRISPR-activation promotes somatic embryogenesis in Solanum lycopersicum cv. Micro-Tom.

At present, the development of plants with improved traits like superior quality, high yield, or stress resistance, are highly desirable in agriculture. Accelerated crop improvement, however, must capitalize on revolutionary new plant breeding technologies, like genetically modified and gene-edited crops, to heighten food crop traits. Genome editing still faces ineffective methods for the transformation and regeneration of different plant species and must surpass the genotype dependency of the transformation process. Tomato is considered an alternative plant model system to rice and Arabidopsis, and a model organism for fleshy-fruited plants. Furthermore, tomato cultivars like Micro-Tom are excellent models for tomato research due to its short life cycle, small size, and capacity to grow at high density. Therefore, we developed an indirect somatic embryo protocol from cotyledonary tomato explants and used this to generate epigenetically edited tomato plants for the SlWRKY29 gene via CRISPR-activation (CRISPRa). We found that epigenetic reprogramming for SlWRKY29 establishes a transcriptionally permissive chromatin state, as determined by an enrichment of the H3K4me3 mark. A whole transcriptome analysis of CRISPRa-edited pro-embryogenic masses and mature somatic embryos allowed us to characterize the mechanism driving somatic embryo induction in the edited tomato cv. Micro-Tom. Furthermore, we show that enhanced embryo induction and maturation are influenced by the transcriptional effector employed during CRISPRa, as well as by the medium composition and in vitro environmental conditions such as osmotic components, plant growth regulators, and light intensity.

Solanum lycopersicum↗
PubMed2026

Wastewater viromics reveals host-structured viral signals and non-human pathogens.

Wastewater represents a powerful platform for human virus surveillance. However, the entry of animal- and plant-associated viruses into sewage is heterogeneous and incompletely understood, creating uncertainty about how reliably wastewater reflects non-human virus circulation. Here, we address this by analysing monthly wastewater metagenomic data from two distinct periods (2020-2021 and 2024-2025) across five major Finnish wastewater treatment plant catchments using a targeted hybrid-capture approach to characterise the composition, host range, and spatial distribution of the non-human wastewater virome. Nearly half of the detected viral accessions were non-human, indicating substantial diversity, despite human-associated viruses accounting for 83% of normalised viral reads. Rodent-, livestock-, and bird-associated viruses showed spatial structuring consistent with regional host populations. The wastewater viromics also detected four EU-regulated plant pathogens, including tomato brown rugose fruit virus, which was highly prevalent in wastewater two years before its first official detection in Finland. Together, these results show that wastewater contains structured, host-linked viral signals, supporting its use as an ecological proxy for non-human virus circulation.

Wastewater↗
PubMed2026

Quantitative trait loci associated with improved fruit yield under heat-stress conditions in fresh-market tomato.

Rising temperatures and more frequent heat stress events pose a major challenge to global tomato production, particularly in tropical and subtropical regions such as the southern United States. High temperatures during flowering and fruit set lead to poor fruit set and reduced yield. Although several commercial cultivars and breeding lines are described as heat-tolerant, the genetic basis of yield performance under heat stress conditions in fresh-market tomato remains poorly understood. This study aimed to identify genomic regions associated with fruit yield under natural heat stress. A biparental recombinant inbred line (RIL) population developed by the UF/IFAS tomato breeding program was evaluated under natural field heat stress in the fall seasons of 2016, 2017, and 2018, with fruit yield recorded as the primary trait. Genotyping of RILs was performed with the AgriPlex commercial tomato panel. Multi-environment QTL analysis was conducted to identify loci associated with fruit yield under heat stress. A major locus on chromosome 12 was selected for validation. Backcross populations segregating for this region were evaluated in a randomized block design during the fall of 2020 at the Gulf Coast Research and Education Center (GCREC), Balm, Florida. Multi-environment QTL analysis identified several loci on chromosome 4, 5, 6, and 12 associated with fruit yield under natural heat stress conditions. Among these, a locus on chromosome 12 showed consistent effects across multiple harvests and environments and explained a relatively larger proportion of phenotypic variance. Validation using backcross populations confirmed that genotype carrying the chromosome 12 QTL produced significantly higher yield under natural heat stress than susceptible genotypes. Overall, this study identified an agronomically important region on chromosome 12 that can be targeted to improve tomato yield under heat stress. The results also highlight multiple genomic regions contributing to higher yield under heat stress. These findings provide a foundation for developing breeding strategies for developing heat-tolerant fresh-market tomato cultivars.

QTL analysis↗
PubMed2026

The transcription factor PavERF28 promotes fruit softening by regulating cell wall degradation in sweet cherry (Prunus avium L.).

Fruit softening is a critical determinant of shelf life and marketability in sweet cherry (Prunus avium L.). This process is predominantly driven by cell wall disassembly, which is tightly regulated by transcription factors. Despite evidence for ethylene's role in sweet cherry softening, how these signals are transduced to regulate the expression of cell wall-modifying genes is unclear. Here, we identified the ethylene-responsive transcription factor PavERF28 as a key regulator in this process. Overexpression of PavERF28 significantly upregulated the transcriptional levels of genes involved in pectin degradation (including genes encoding polygalacturonase, pectin methylesterase inhibitor, and pectate lyase), thus effectively enhancing fruit softening. Moreover, heterologous overexpression of PavERF28 in tomato confirmed its function in promoting fruit softening. At the molecular level, PavERF28 was shown to directly activate the expression of two polygalacturonase genes (PavPG1 and PavPL5) by binding to their promoters, which catalyze pectin depolymerization and thus drive softening. Collectively, our work provides an in-depth elucidation of the regulatory mechanism by which ERF family members control fruit softening in sweet cherry and offers potential targets for the manipulation of fruit ripening, especially softening.

Cell Wall↗
PubMed2025

Molecular breeding of tomato: Advances and challenges.

The modern cultivated tomato (Solanum lycopersicum) was domesticated from Solanum pimpinellifolium native to the Andes Mountains of South America through a "two-step domestication" process. It was introduced to Europe in the 16th century and later widely cultivated worldwide. Since the late 19th century, breeders, guided by modern genetics, breeding science, and statistical theory, have improved tomatoes into an important fruit and vegetable crop that serves both fresh consumption and processing needs, satisfying diverse consumer demands. Over the past three decades, advancements in modern crop molecular breeding technologies, represented by molecular marker technology, genome sequencing, and genome editing, have significantly transformed tomato breeding paradigms. This article reviews the research progress in the field of tomato molecular breeding, encompassing genome sequencing of germplasm resources, the identification of functional genes for agronomic traits, and the development of key molecular breeding technologies. Based on these advancements, we also discuss the major challenges and perspectives in this field.

Solanum lycopersicum↗
PubMed2026

Efficient genome editing in tomato using Cas12i3 variants.

Systematic comparison of Cas12i gene-editing tools in tomato identifies Cas-SF01 as the most efficient variant, achieving editing efficiencies comparable to conventional Cas9 at some genomic sites and providing a compact, highly specific, and versatile tool for studying gene function, engineering fruit metabolism, and developing improved tomato varieties through precision breeding.

Journal Article↗