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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↗

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↗

PubMed2025

N-glycan remodeling by α-D-mannosidase and β-D-N-acetylhexosaminidase regulates fruit softening, redox balance, and post-harvest pathogen resistance.

Post-harvest loss of fruits and vegetables poses significant challenges to food security and economic sustainability, primarily due to ripening-associated excessive softening that shortens shelf life and increases susceptibility to pathogens. N-glycans, N-glycoproteins, and their processing enzymes are integral to various plant processes, including fruit ripening. Among these, α-D-mannosidase (α-Man) and β-D-N-acetylhexosaminidase (β-Hex) are key ripening-specific enzymes that modulate fruit softening. Previously, we have shown that RNAi-mediated suppression of α-Man or β-Hex improves fruit shelf life and firmness in both climacteric and non-climacteric fruits. However, the underlying molecular and biochemical basis of fruit softening regulation by α-Man and β-Hex was not well understood. In this study, we developed transgenic tomato (Solanum lycopersicum) plants by silencing α-Man and β-Hex simultaneously using RNAi. Suppression of these enzymes reduces N-glycoprotein degradation, downregulates pectin dissolution, and inhibits ripening-related gene expression. RNAi fruits exhibited enhanced shelf life, greater firmness, reduced reactive oxygen species (ROS) accumulation and increased resistance against post-harvest pathogens without affecting plant growth, fruit development, yield, or nutritional quality. To further explore the molecular mechanism of α-Man and β-Hex function, we purified and quantified N-glycans in RNAi fruits and other ripening-impaired mutants, identifying key N-glycan species. We also carried out iTRAQ-based quantitative proteome profiling to investigate the abundance of proteins in ripened fruit affected by silencing of α-Man and β-Hex. Molecular insights revealed that N-glycan processing and degradation are key events during ripening, influencing cell wall softening, fruit redox state, and post-harvest quality attributes. This study highlights the potential of co-silencing α-Man and β-Hex as a novel approach to extending the shelf life of fruits, regardless of their climacteric behavior, without compromising quality or yield.

Fruit↗

PubMed2026

GA4+7 alleviates pear fruit semi-russeting partly by suppressing PRX-mediated lignin deposition.

Pear fruit semi-russeting is a surface disorder that frequently occurs during fruit development and significantly diminishes fruit appearance quality and commercial value. Although Gibberellin 4 + 7 (GA4+7) has been used to reduce fruit surface defects in horticultural crops, the physiological and molecular mechanisms underlying its inhibitory effect on pear fruit semi-russeting remain poorly understood. In this study, preharvest GA4+7 treatment of 'Cuiguan' pear significantly reduced russet coverage and lignin accumulation in mature fruit skin without adversely affecting fruit size, fruit shape index, or total soluble solids content. Integrated metabolomic and transcriptomic analyses revealed that GA4+7 treatment was associated with the repression of phenylpropanoid and lignin biosynthesis at both metabolic and transcriptional levels. Among the lignin-related differentially expressed genes, two class III peroxidase genes, PpyPRX22 and PpyPRX65, were strongly downregulated by both GA4+7 and bagging treatments. Both proteins localized to the cell wall, and transient expression assays in pear fruit skin supported positive roles for PpyPRX22 and PpyPRX65 in lignin deposition. Furthermore, dual-luciferase reporter assays combined with transient overexpression experiments suggested that several PpyMYB transcription factors may regulate PpyPRX expression and lignin accumulation, with PpyMYB138 and PpyMYB139 significantly activating PpyPRX22 and/or PpyPRX65 promoter activity. Taken together, these results suggest that GA4+7 alleviates pear fruit semi-russeting at least partly by reducing lignin deposition in the fruit skin, with PpyPRX22 and PpyPRX65 potentially contributing to this process.

Class III peroxidase↗

PubMed2025

Genomics insight on passion fruit viral disease complexity.

Passion fruit viral diseases pose a significant threat to Kenya's passion fruit industry. To unravel the complexity of these diseases, comprehensive virus surveys were conducted across major passion fruit-growing counties. Passion fruit woodiness disease symptoms, like fruit hardening, chlorotic mottling, and leaf distortion, were prevalent. The study unveiled the first 23 complete genomes of Ugandan passiflora virus (UPV) and two East Asian passiflora distortion virus (EAPDV) in Kenya. UPV showed 99% nucleotide (nt) match to a UPV genome from Uganda and 66% nt identity match to EAPDV. In addition, UPV variants and two partial passion fruit green spot virus sequences and partial (passiflora emaravirus) segment RNA1-5 (novel allexivirus and an emaravirus, respectively) were detected. Phylogenetic analysis revealed distinct lineages (I-III), indicating potential multiple introductions into Kenya. Recombination analysis detected no significant breakpoints. However, the study proposed the renaming of EAPDV to passiflora distortion virus (PDV) and UPV to passiflora virus (PV) for neutral nomenclature, without geographical association. Additionally, the study highlighted the role of coinfections in symptom expression, suggesting a potential synergistic relationship between PV, PDV, and other viruses. The results recommend stringent management strategies and enhanced surveillance to mitigate the economic impact of these viruses on the Kenyan passion fruit industry. The findings from this study underscore the need to strengthen nursery certification programs and pest diagnostic protocols in Kenya. Additionally, enhanced pest surveillance and import regulations are critical to preventing the introduction and spread of emerging plant viral diseases, thereby safeguarding the country's horticultural productivity and biosecurity. To our knowledge, this is the first comprehensive study of viral diseases of passion fruit in Kenya.IMPORTANCEThis study presents the first comprehensive survey of viral pathogens affecting passion fruit in Kenya, identifying Ugandan passiflora virus (UPV) and East Asian passiflora distortion virus (EAPDV) as major contributors. Through genomic sequencing, 23 complete genomes of UPV and two of EAPDV were characterized, revealing a 99% nucleotide (nt) similarity between UPV strains from Uganda and Kenya, and 66% nt match with EAPDV. Phylogenetic analysis identified distinct lineages, suggesting possible multiple viral introductions in Kenya. The study also highlights potential synergistic coinfections between UPV, EAPDV, and other viruses, leading to more severe disease symptoms. In light of these findings, the study proposes renaming EAPDV as passiflora distortion virus and UPV as passiflora virus for a more neutral name classification. The research underscores the urgent need for enhanced surveillance, stringent phytosanitary measures, and improved management strategies to mitigate the threat of viral diseases, to safeguard the Kenyan passion fruit industry, and elsewhere.

Plant Diseases↗

PubMed2026

Aggregicoccus is a myxobacterial genus inherently deficient in fruiting genes.

Myxobacteria are fascinating and important prokaryotes with remarkable multicellular behaviors, which make them a model system for studying prokaryotic development and cooperation. Although there have been sporadic discoveries of myxobacterial species unable to fruit, it is unclear whether the non-fruiting characteristic is due to taxon-specific genetic deficiency or suboptimal cultivation conditions. Aggregicoccus is a non-fruiting myxobacterial genus typified by a single validly published species, Ag. edonensis. In this study, we report five novel Aggregicoccus strains, which are classified into three novel type species, Ag. lacus, Ag. agri, and Ag. guangxiensis, based on polyphasic taxonomic analysis. All the Aggregicoccus strains are unable to produce fruiting bodies, but can still sporulate. We compared the genome differences between Aggregicoccus and Myxococcus; both genera belong to the Myxococcaceae family, and all the genomes are of similar sizes. The results showed that the Aggregicoccus strains are inherently deficient in the fruiting body-associated genomic information (FAGI). We propose an assessment of FAGI for the classification of non-fruiting myxobacterial species.IMPORTANCEFruiting body formation is traditionally regarded as a defining trait of myxobacteria. Here, we report that Aggregicoccus spp., including six strains of four species, can sporulate but are deficient in the fruiting body-associated genomic information (FAGI). This demonstrates that the non-fruiting characteristic in Aggregicoccus stems from inherent genetic deficiencies rather than suboptimal cultivation. Our findings highlight the need to assess FAGI presence in classifying non-fruiting lineages, innovate the isolation method, and refine our understanding of the diversity and evolution of the myxobacteria.

Aggregicoccus↗

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↗

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↗

PubMed2025

Development of recombinant inbred lines and QTL analysis of plant height and fruit shape-related traits in Cucurbita pepo L.

UNLABELLED: Zucchini (Cucurbita pepo subsp. pepo) stands as an economically vital crop in China. In zucchini breeding, plant architectural patterns and fruit morphological characteristics serve as pivotal traits. In this study, we employed quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) derived from two distinct inbred lines, JinGL (subsp. ovifera) and HM-S2 (subsp. pepo), in conjunction with a high-density genetic map. Our investigation focused on ten QTLs associated with six horticulturally significant traits, including hypocotyl length (HL), plant height (PH), and four fruit-related traits: fruit length (FL), fruit diameter (FD), fruit shape index (FSI), and fruit weight (FW). The QTLs governing HL and PH were mapped to Chr03/LG10 and named qhl3.1 and qph3.1, respectively. The candidate gene Cp4.1LG10g05910/CpDw for qph3.1 was successfully identified. Additionally, three novel QTLs related to fruit size and shape were discovered. Among them, qfsi8.1/qfl8.1, demarcated by Marker238258 and Marker240069 on Chromosome 08/Linkage group 17 (Chr08/LG17), is a new major QTL regulating the fruit shape of zucchini. Through genomic insertion-deletion (InDel) and qRT-PCR analyses, we predicted genes within the qfsi8.1/qfl8.1 candidate interval, uncovering Cp4.1LG17g02030/CpIAA12 and Cp4.1LG17g02010/CpCalB as potential candidate genes. We developed molecular markers tightly linked to qph3.1 and qfl8.1 and validated them in 171 and 224 Cucurbita pepo germplasms, achieving accuracy rates of 96% and 100%, respectively. This study deepens our understanding of the genetic basis of key traits and provides valuable references for molecular breeding in Cucurbita pepo. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-025-01592-y.

Cucurbita pepo↗

PubMed2024

Transcriptional landscape and dynamics involved in sugar and acid accumulation during apple fruit development.

In fleshy fruit, sugars and acids are central components of fruit flavor and quality. To date, the mechanisms underlying transcriptional regulation of sugar and acid during fruit development remain largely unknown. Here, we combined ATAC-seq with RNA-seq to investigate the genome-wide chromatin accessibility and to identify putative transcription factors related to sugar and acid accumulation during apple (Malus domestica) fruit development. By integrating the differentially accessible regions and differentially expressed genes, we generated a global data set of promoter-accessibility and expression-increased genes. Using this strategy, we constructed a transcriptional regulatory network enabling screening for key transcription factors and target genes involved in sugar and acid accumulation. Among these transcription factors, 5 fruit-specific DNA binding with one finger genes were selected to confirm their regulatory effects, and our results showed that they could affect sugar or acid concentration by regulating the expression of sugar or acid metabolism-related genes in apple fruits. Our transcriptional regulatory network provides a suitable platform to identify candidate genes that control sugar and acid accumulation. Meanwhile, our data set will aid in analyzing other characteristics of apple fruit that have not been illuminated previously. Overall, these findings support a better understanding of the regulatory dynamics during apple fruit development and lay a foundation for quality improvement of apple.

Malus↗

PubMed2026

Post-exercise rehydration: a randomized cross-over trial comparing a 100% fruit juice, a glucose-based sports drink, and water.

BACKGROUND: Previous studies indicate that sports drinks may improve rehydration, compared to water, an effect likely achieved by manufacturing sports drinks to contain carbohydrates and sodium. However, there is a growing preference for natural products and a "food first" approach to sports nutrition. Fruit juices naturally contain similar concentrations of carbohydrates to sports drinks, but fruit juices may produce a more stable blood glucose profile. Fruit juices also naturally contain electrolytes, particularly potassium, but their potential as effective rehydration alternatives to sports drinks, which have higher sodium concentrations, is not well understood. This study compared the rehydration efficacy and glucose responses following consumption of a 100% fruit juice (Raw Hydrate®; FRU), a glucose-based sports drink (SPO), and water (WAT) after exercise-induced hypohydration. Importantly, rehydration beverages were matched for water volume, rather than total volume, to ensure that any potential differences in water balance were not due to unequal water volumes between trials, a limitation affecting previous rehydration research. METHODS: After familiarization, 17 adults (age: 28 ± 8  years; BMI: 23.8 ± 2.9 kg/m2) completed three trials in a randomized cross-over design. The participants cycled in the heat (~35°C) to induce ~2% body mass loss (BML), then rehydrated over a 1 h period in a laboratory (~21°C) with a water volume equivalent to 150% of BML from either FRU, SPO, or WAT. This was followed by an additional 4 h of seated rest (5 h rehydration period), when blood glucose was measured (0, 0.25, 0.5, 0.75, 1, 1.5, and 2 h after beverage consumption), and all urine produced was collected. RESULTS: During the 5 h rehydration period, there was no effect of trial on total urine volume (FRU: 1266 ± 403 mL, SPO: 1338 ± 361 mL, WAT: 1394 ± 360 mL; P = 0.156) or water retention (FRU: 42 ± 12%, SPO: 37 ± 10%, WAT: 35 ± 11%; P = 0.059). The blood glucose area under the curve differed by trial (P < 0.001), with all beverages significantly different from each other (FRU: 10.12 ± 0.72 mmol/L/2h, SPO: 12.48 ± 1.34 mmol/L/2h, WAT: 7.90 ± 0.47 mmol/L/2h; P < 0.003). CONCLUSION: Rehydration efficacy was similar between all beverages, but each elicited a distinct glycemic response. For sports drink consumers seeking a natural alternative or implementing a "food first" nutritional strategy, switching to a 100% fruit juice will not compromise rehydration effectiveness, but may elicit a lower blood glucose response. Although, it should be noted that an additional three participants were withdrawn from the study because of gastrointestinal issues after consuming the 100% fruit juice. This was likely a product of the present study's design, where a large volume of 100% fruit juice (average ~2,300 mL) was consumed in a short period of time (1 h). Whilst this is a commonly used study design to robustly assess the rehydration efficacy of different beverages, future studies should distribute fluid intake over a longer duration, in order to improve ecological validity and reduce the risk of gastrointestinal issues.

Humans↗

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

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↗

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

Natural variants of CsSHN1 orchestrate a temporal regulatory cascade driving fruit skin netting in cucumber.

Fruit skin netting (russeting, Rs) forms when epidermal microcracks are sealed by a suberized periderm, reducing marketability. We previously identified the Rs locus (CsSHN1), which encodes an AP2/ERF transcription factor, as a major determinant of cucumber skin netting, but how fruit growth is temporally coupled to periderm formation remains unclear. Here, we integrated population genomics, time-series multiomics, DNA affinity purification sequencing (DAP-seq), and transgenic assays to decode the CsSHN1-mediated regulatory network. Six functionally relevant CsSHN1 variants were identified across 325 cucumber accessions. Allele distribution and selective sweep analyses revealed breeding-driven selection for smooth fruit skin. Overexpression of a netted allele in a smooth background induced epidermal fissures, altered cell geometry, and increased fruit size, demonstrating a dosage-sensitive effect. Time-series transcriptomics and metabolomics of near-isogenic lines (NILs) defined 3 developmental phases of netting: early suppression of lignin and trehalose genes preceding cracks, growth-driven fissuring accompanied by cell-wall remodeling and defense activation, and maturation-stage cell-wall degradation with strong induction of ligno-suberin biosynthesis. Across the cucumber genome, DAP-seq identified approximately 8,000 in vitro CsSHN1 binding sites. These binding sites were significantly enriched for the GCC-box motif and included genes involved in cutin and suberin biosynthesis. Together, these results show that CsSHN1 orchestrates fruit skin netting through a growth-coupled temporal regulatory cascade, providing a mechanistic framework for manipulating fruit epidermal properties.

Cucumis sativus↗

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

Genome-Wide Identification of the R2R3-MYB Gene Family in Solanum americanum and Functional Analysis of Its Role in Fruit Coloration.

Anthocyanins are key secondary metabolites responsible for fruit coloration in plants, and their biosynthesis is largely regulated by R2R3-MYB transcription factors. However, the R2R3-MYB regulators controlling fruit anthocyanin accumulation in wild Solanum species remain poorly understood. Here, Solanum americanum was used to identify candidate R2R3-MYB genes associated with fruit coloration through genome-wide identification, phylogenetic analysis, synteny analysis, expression profiling, and virus-induced gene silencing (VIGS). A total of 122 SaMYB genes were identified, and phylogenetic analysis revealed that SaMYB proteins clustered with Arabidopsis thaliana R2R3-MYB members in conserved subgroups, suggesting evolutionary conservation of this family. Synteny analysis identified 37 syntenic gene pairs among SaMYB genes, and the Ka/Ks values of all analyzable gene pairs were below 1, indicating that these duplicated genes are subject to functional constraint. Integrated analysis of phylogenetic relationships, protein structures, promoter cis-elements, and fruit developmental expression patterns identified SaMYB59 and SaMYB106 as candidate regulators of anthocyanin accumulation. VIGS analysis demonstrated that silencing SaMYB106 reduced purple coloration, decreased anthocyanin content, and downregulated the expression of the structural gene DFR. These results indicate that SaMYB106 functions as a positive regulator of fruit anthocyanin accumulation in S. americanum. This study provides insights into the molecular basis of fruit coloration in wild Solanum species.

Solanum americanum↗

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↗