MADS-box transcription factors are key regulators of plant development and environmental responses. Here, we performed an integrated phylogenomic and expression analysis of the MADS-box gene family in Capsicum annuum, identifying 97 members that fall into 52 Type I and 45 Type II genes. Comparative phylogeny, exon–intron organization, conserved motifs, and chromosomal mapping allowed classification into 15 subfamilies. Gene duplication analysis revealed that segmental duplication has been a major driver of family expansion. Expression profiling across multiple tissues, together with promoter cis-element prediction and stress-responsive transcriptome data, demonstrated that Type II genes exhibit broad and dynamic expression patterns, particularly under ABA treatment and temperature stress. A key finding of this study is the complete absence of the Mβ lineage, a Type I subfamily typically associated with gametophyte and endosperm development in other angiosperms. No Mβ-like sequences were detected in the pepper genome, and Type I genes overall showed extremely low expression, suggesting that the Mβ lineage has undergone lineage-specific evolutionary loss and that its functions may be compensated by other Type I members or by expanded Type II regulatory modules. Together, this study provides the first evidence for the evolutionary disappearance of the Mβ subfamily in Capsicum and offers a comprehensive resource for dissecting the developmental and stress-responsive roles of MADS-box genes in pepper.

Small tomatoes are an important economic fruit crop. Strategies to rapidly and stably improve their taste and nutritional quality are of significant economic value. This study evaluated grafting tomato scion ZheYingFen1 (ZYF1) onto eggplant rootstocks (ZheQie117 or ZheQie10). Comprehensive metabolomics and targeted assays demonstrated that grafting substantially increased fructose and glucose levels, thereby enhancing sweetness compared with self-rooted controls. Lycopene content rose significantly, particularly with the ZQ117 rootstock, without elevating key organic acids linked to sourness. Conversely, most free amino acids decreased, including umami-associated glutamate. Energy metabolite profiling showed graft-specific shifts, with pronounced enrichment in sulfur-containing glucosinolate biosynthesis pathways, suggesting modified defense responses and flavor profiles. These results demonstrate that compatible eggplant rootstocks provide a practical horticultural strategy to directly improve tomato sweetness and nutritional value without compromising acidity. This work provides evidence that eggplant rootstocks can effectively improve both the sweetness and nutritional value of tomatoes through metabolic reprogramming, offering a practical and sustainable approach for quality enhancement in commercial tomato production while maintaining a favorable acidity balance.

Nucleotide-binding site leucine-rich repeat (NLR, historically termed NBS-LRR) proteins are among the most rapidly evolving components of plant innate immunity, yet comparative analyses of NLR subfamily diversification between wild and cultivated accessions of tomato (Solanum lycopersicum) have remained limited. Here, we compared the NLR gene family across three representative tomato accessions—the wild species S. chilense and the cultivated tomatoes S. lycopersicum Heinz1706 (large-fruited) and S. lycopersicum LA1464 (cherry tomato)—by integrating genome-wide identification, phylogenetic reconstruction, motif analysis, orthologous clustering, selection-pressure assessment, and expression profiling. We identified 220, 223, and 245 candidate NLR genes in S. chilense, Heinz1706, and LA1464, respectively, and classified them into TIR-type (TNL) and coiled-coil-type (CNL) subfamilies at a consistent ratio of approximately 1:5 across all three accessions. Motif analysis revealed pronounced structural divergence between TNL and CNL proteins, most notably in the region corresponding to the second conserved motif of the NB-ARC domain. Orthologous clustering identified 67 gene clusters shared among the three accessions; within these, TNL genes showed greater sequence divergence (higher Ka and Ks values) than CNL genes but significantly lower Ka/Ks ratios (ω), indicating stronger purifying selection despite their greater raw divergence. Expression profiling further showed that CNL genes were more broadly expressed across tissues and were induced by multiple pathogen-associated molecular patterns, whereas TNL gene expression was more spatially restricted and preferentially induced by effector-related treatments. These results indicate that the TNL and CNL subfamilies of the tomato NLR repertoire have followed distinct evolutionary trajectories and regulatory strategies. As these conclusions are based on comparative genomic and transcriptomic evidence from three accessions rather than on functional validation, they should be regarded as hypotheses; nonetheless, they offer candidate genomic resources and a comparative framework that may inform future disease-resistance breeding in tomato.

Background/Objectives: Nucleotide-binding leucine-rich repeat (NLR) proteins are major intracellular immune receptors involved in effector-triggered immunity. However, the evolutionary diversity and genomic organization of NLR repertoires remain incompletely characterized in Solanaceae crops and their wild relatives. This study aimed to investigate the pan-NLRome landscape and evolutionary patterns of tomato and related species. Methods: A comparative pan-NLRome analysis was performed across five angiosperms, including cultivated tomato (Solanum lycopersicum) and four related species (Solanum chilense, Solanum lycopersicoides, Solanum pimpinellifolium, and Arabidopsis thaliana). NLR genes were identified using an integrated HMMER- and BLASTp-based pipeline, followed by chromosome anchoring, orthogroup (OG) classification, phylogenetic analysis, spatial organization analysis, and evaluation of associations with long terminal repeat (LTR) retrotransposons. Results: A total of 1566 chromosome-anchored NLR genes were assigned to 150 OGs. Core OGs represented 25.3% of total OG diversity but contained a large proportion of NLR genes. Rarefaction analysis indicated continuous accumulation of novel OGs with increasing species sampling, supporting an open pan-NLRome structure. Phylogenetic analysis identified 18 NLR subfamilies, with SF_03 and SF_01 together accounting for approximately 79% of NLR genes. Dispersed homologs represented the predominant spatial arrangement pattern, accounting for 85.1% of NLR gene pairs across Solanaceae species. Conclusions: This study provides a comparative genomic framework for understanding NLR diversity and evolution in tomato and related Solanum species, highlighting the dynamic expansion and spatial organization of plant immune receptor repertoires and providing valuable resources for resistance gene discovery.

High temperatures compromise crop productivity worldwide, but breeding bottlenecks slow the delivery of climate-resilient crops. By investigating tomato fruit set under high temperatures, we discover a module comprising two linked genes, THERMOSENSITIVE PARTHENOCARPY 4a (TSP4a) and TSP4b, which encode the transcriptional regulators IAA9 and AINTEGUMENTA (ANT), respectively, to control thermosensitive parthenocarpy. TSP4a and TSP4b form a positive feedback loop upon heat stress to repress auxin signaling in ovaries. Natural TSP4a and TSP4b alleles bear regulatory-region polymorphisms and are differentially expressed to overcome the trade-off between fruit set and wider plant development. Gene editing of the TSP4a promoter and TSP4b 3' UTR in open-chromatin regions results in expression down-regulation, increased parthenocarpy without yield penalties and maintenance of fruit-sugar levels without broad auxin-related pleiotropic defects in greenhouse-grown plants. These mechanistic insights into heat-induced parthenocarpy and auxin signaling in reproductive organs demonstrate breeding utility to safeguard tomato yield under warming scenarios.

Glycosylation, a crucial posttranslational modification of proteins, profoundly impacts protein folding, enzymatic activity, and protein stability. The soil-borne pathogen Ralstonia solanacearum (R. solanacearum) poses a severe threat to global tomato production. However, the underlying molecular mechanisms of glycosylation-mediated immunity to R. solanacearum in tomato have not been fully elucidated. This study successfully revealed the N-glycosylate variation in tomato after R. solanacearum infection or non-infection. A total of 806 N-glycoproteins were identified, among which 222 exhibited infection-responsive alterations. Motifs analysis revealed that highlighted a preference for glycosylation in random coil regions (72.14 %) and identified rare noncanonical N-X-C motifs (1.90 %). Subcellular localization showed enrichment in plasma membranes (29.28 %) and chloroplasts (23.87 %), with 57.66 % of glycoproteins harboring endoplasmic reticulum-targeting signal peptides. Functional enrichment and protein interaction network analysis revealed that brassinosteroid (BR) receptor complex BRI1/BAK1 as a potential core regulators. Gene silencing experiments confirmed that SlBRI1 and SlBAK1 positively regulate tomato resistance to R. solanacearum infection. Further studies showed that glycosylation at BRI1N235 and BAK1N83/N107 reduced protein stability, impairing BR-mediated immune signalling. Phylogenetic analysis confirmed evolutionary conservation of BRI1/BAK1 in Solanaceae, underscoring glycosylation's role in immune adaptation. Collectively, these findings offer viable targets for breeding R. solanacearum-resistant cultivars via N-glycosylation strategies.

Cherry tomato is a notable dietary source of metabolites associated with antioxidant functions. However, how ripening reshapes primary, specialized, and volatile metabolites remains incompletely resolved. Green-ripe and red-ripe fruits were comparatively analyzed using targeted HPLC assays for quality indices and vitamins, UPLC–MS/MS for non-volatile metabolites, and HS-SPME–GC–MS for volatiles. Ripening was accompanied by a pronounced accumulation of lycopene and an increase in soluble solids, reflecting a shift of sugars toward glucose and fructose while sucrose remained low. Organic acids declined overall, with citric acid remaining predominant. The free-amino-acid pool expanded, with redistribution from GABA toward glutamate and aspartate. Vitamins exhibited stage-dependent patterns; antioxidant-related vitamins (A, E, and C) were higher at the red-ripe stage, indicating a compositional enhancement relevant to nutritional quality. Non-volatile metabolomics revealed 618 differentially accumulated metabolites, with phenolic acids, flavonoids, alkaloids, amino acids, and lipids as major classes. Phenolic acids and flavonols, dominated by hydroxycinnamoyl-quinic acids and quercetin/kaempferol glycosides, accumulated at the red-ripe stage, whereas steroidal glycoalkaloids decreased, suggesting conversion away from bitter or anti-nutritional constituents. GC–MS profiling identified 788 volatiles, with esters, terpenoids, and ketones contributing more than half of the volatilome. Ripening favored fruity–floral odorants such as β-ionone and (5Z)-octa-1,5-dien-3-one, while reducing green-leaf aldehydes. These stage-specific shifts in metabolite composition jointly define the sensory and nutritional maturation of cherry tomato. The identified metabolite markers provide a foundation for evaluating fruit maturity and guiding breeding toward improved quality attributes.

Background: Phospholipase A (PLA) enzymes catalyze the hydrolysis of glycerophospholipids, releasing free fatty acids and lysophospholipids that play vital roles in plant growth, development, and stress responses. Methods: This study identified and analyzed SlPLA genes through bioinformatics and further explored the function of PLA genes under cold stress through virus-induced gene silencing (VIGS) experiments. Results: This study systematically characterized the SlPLA gene family in tomato, identifying 80 genes distributed across 12 chromosomes. Phylogenetic analysis categorized these genes into three groups: pPLA, PLA1, and PLA2. Conserved motifs and gene structure analysis revealed distinct patterns, with some genes lacking untranslated regions (UTRs), which suggests functional diversification. Promoter analysis indicated that SlPLA genes are regulated by light, hormones, and stress-related elements, particularly cold stress. RNA-seq data and qRT-PCR results indicated the differential expression of SlPLA genes across various tissues in tomato cultivars (Heinz and Micro-Tom). Under cold stress, certain SlPLA genes, especially SlPLA1-2, were up-regulated, suggesting their involvement in cold tolerance. Silencing SlPLA1-2 resulted in increased membrane damage, elevated malondialdehyde (MDA) levels, higher electrolyte leakage, and a lower expression of cold-responsive genes within the ICE1-CBF-COR pathway and jasmonic acid (JA) biosynthesis. Conclusions: This study discovered 80 SlPLA genes in tomato across 12 chromosomes, categorizing them into pPLA, PLA1, and PLA2 via phylogenetic analysis. The qRT-PCR analysis identified that SlPLA1-2 was strongly induced by cold stress, and further experiments regarding genetics and physiology revealed that SlPLA1-2 boosts the cold tolerance of tomato by affecting the CBF signaling pathway and JA biosynthesis, offering insights for future stress-resilience breeding.

This study aimed to identify and compare the flavor substances in mature tomato and pepper fruits using flavoromics based on GC×GC-TOF-MS. A total of 1560 volatile substances were identified, including 627 tomato specific substances and 534 pepper specific substances. Esters were identified as the distinguishing factor in the aroma profiles of the two. ROAV, an effective flavor evaluation criterion, can help identify the main contributors to flavor that can be detected by the taste buds. VOCs with ROAV > 1 are typically regarded as the key flavor contributors. Interestingly, it was found that tomato and pepper shared three common VOCs (2-nonenal, (E)-; 2-octenal, (E)-; and furan, 2-pentyl-.), which exhibited higher ROAV in both. Except for the three common VOCs, heptanal; 2-dodecenal, (E)-; 1-octen-3-one; 2-undecanone in tomato and pyrazine, 2-methoxy-3-(2-methylpropyl)- in pepper were identified to be contributive to their corresponding aromatic flavor (ROVA > 1), respectively. The contents of 138 volatile metabolites differ between tomato and pepper. Among them, acetoin, dodecanal and 1-decanol demonstrated highest fold change (Log2FC > 10). The flavor wheel shows the most obvious flavor characteristic of both tomato and pepper is sweet flavor. In addition, green, fruity, herbal, woody and apple flavors are prominent in pepper, while waxy, citrus and fatty flavors are prominent in tomato.

Histone methylation plays important roles in plant development and adaptation to multiple stresses. SET domain group (SDG) proteins are identified as plant histone lysine methyltransferases in Arabidopsis and other crops. However, the SDG gene family and its functional roles in tomato remain unknown. In this research, 48 tomato SDG (SlSDG) gene family members were identified, and their chromosomal locations and conserved motifs were determined. According to phylogenetic analysis, the SlSDGs are divided into seven groups, which is consistent with Arabidopsis and rice. Promoter analysis indicated that the SlSDGs may be associated with biotic and abiotic stress responses. The expression pattern of SlSDGs illustrates that heat and cold stress significantly influence the transcript abundance of SDG14/19/21/23/48. The results of a VIGS assay showed that silencing SlSDG19 and SlSDG48 decreases tomato heat tolerance, while silencing SlSDG14 improves the heat tolerance of tomato plants. The analysis of downstream regulating genes indicated that heat shock proteins (HSPs), especially HSP70 and HSP90, act as critical effectors. Similarly, the experimental assay and expression analysis suggest that SDG21 and SDG23 positively and negatively regulate tomato cold tolerance through the CBF-COR pathway, respectively. These findings clarify the function of tomato SDG proteins and provide insight for the genetic improvement of tomato for temperature stress tolerance.

Acid invertases (Ac-Invs) are crucial enzymes in plant physiology, regulating sucrose metabolism and hydrolyzing sucrose into glucose and fructose. These sugars serve not only as energy sources and structural components but also as signaling molecules, influencing diverse developmental processes, including seed and fruit growth, flowering, and stress responses. Ac-Invs are classified into cell wall invertases (CWINs) and vacuolar invertases (VINs) based on their subcellular localization, with both playing distinct roles in sucrose unloading, osmotic regulation, and sugar accumulation. Recent studies have also highlighted their involvement in abiotic stress adaptation and hormonal regulation, emphasizing their central role in plant resilience and productivity. However, gaps remain in understanding their regulatory mechanisms, particularly their interactions with plant hormones, defective invertases, and responses to environmental stresses. This review summarizes the biochemical characteristics, functions, and regulatory mechanisms of Ac-Invs, providing insights into their evolutionary significance and potential applications in crop improvement. Future research directions are proposed to elucidate unresolved questions and leverage Ac-Invs for enhancing agricultural sustainability.

Tomato is one of the highest-value fruit and vegetable crop worldwide, serving as an important source of micro-nutrients in the human diet. Understanding the spatial distribution changes of critical metabolites during fruit maturation is essential for investigating the physiological roles, nutritional value, and potential functional values of phytochemicals in tomato fruit. However, information on their spatial distribution remains limited. This study aimed to visualize the distribution differences of endogenous metabolites in tomatoes across four maturity stages (from green to red) using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Relative quantification results showed that as the fruit ripened, levels of soluble sugars, amino acids and volatile organic compounds (VOCs) increased significantly at the red ripening stage, while L-hydroxysuccinic acid exhibited an opposite trend, and citric acid initially decreased, then increased. Mass spectrometry imaging revealed that soluble sugars, organic acids, and amino acids were evenly distributed throughout the fruit across all maturity stages. During maturation, nine VOCs transitioned from a widespread distribution in the flesh tissue to concentrating near the peel, suggesting that aromatic compounds predominantly localize in the fruit's outer regions at full maturity. Additionally, a colocalization phylogenetic tree was constructed based on the spatial distribution imaging of each metabolite. These findings provide a deeper understanding of the changes and distribution of phytochemicals during tomato fruit development, offering a scientific basis for breeding, utilization, and production strategies.

The tomato, a widely cultivated vegetable crop, is prized by consumers for its distinctive flavor. Fruit color and flavor are important quality characters of cherry tomatoes. In this study, HS-SPME-GC-MS was utilized to analyze the metabolomic profiles of cherry tomatoes in different colors, including pink, red, brown, and yellow. A total of 585 volatile flavor compounds were identified, with 435 being common metabolites. Terpenoids and heterocyclic compounds were found to be the dominant metabolites in cherry tomatoes. PCA and total ion current mapping effectively distinguished the seven cherry tomato varieties. Using the ROAV method, 90 key VOCs were identified. Among them, benzenemethanethiol, 2-thiophenemethanethiol, (Z)-6-nonenal, dimethyl trisulfide, (Z,Z)-3,6-nonadienal, and 5-methyl-(E)-2-hepten-4-one were found to be the primary VOCs contributing to the flavor of cherry tomatoes. A total of 270 DAMs were detected across all comparisons. The yellow and brown varieties exhibited the greatest metabolite diversity, while the brown and pink varieties showed the least variability. KEGG pathway analysis indicated that the terpenoid synthesis, alpha-linolenic acid, and phenylalanine pathways were the most significant metabolic routes influencing flavor. In conclusion, this study provides a comprehensive comparison of VOCs across cherry tomatoes of different colors and a systematic analysis of the chemical composition underlying flavor differences, ultimately identifying the main factors contributing to flavor differentiation.

Neutral/alkaline invertases (N/A-Invs) are crucial enzymes in sucrose metabolism, playing essential roles in plant growth, development, and stress responses. Unlike acidic invertases, N/A-Invs are localized in various subcellular compartments, including the cytoplasm, mitochondria, chloroplasts, and plastids, with distinct functions in each organelle. These enzymes regulate sugar homeostasis and are involved in key processes such as root development, carbon partitioning, and osmotic stress responses. Recent studies have identified two subfamilies of N/A-Invs, α and β, with the β subfamily being more conserved and primarily localized in the cytoplasm, whereas the α subfamily is associated with mitochondria and plastids. Despite significant advances, many aspects of N/A-Invs remain unclear, particularly their interaction with signaling pathways and their differential roles across plant species. Future research should focus on understanding the molecular mechanisms underlying N/A-Invs' regulation, their evolutionary history, and their potential applications in improving crop resilience and productivity. This growing body of knowledge promises to enhance our understanding of plant physiology and offer insights into agricultural biotechnology.

ABSTRACT Pepper ( Capsicum annuum L.) is a widely cultivated vegetable crop globally. This study aimed to investigate the effects of different cooking methods on the flavor (taste and aroma) and nutritional composition (amino acids, vitamins, etc.) of “HJ008” pepper fruits. We utilized ultra‐high performance liquid chromatography‐tandem mass spectrometry (UPLC‐MS/MS) and gas chromatography–mass spectrometry (GC–MS) to analyze and compare the nonvolatile and volatile flavor compounds (VOCs), as well as nutrient components, in fresh peppers (Fresh), pan‐frying peppers without oil (PWOO), and pan‐frying peppers with oil (PWO). A total of 797 nonvolatile primary metabolites and 610 VOCs were identified across three different groups of samples. The comparative analysis revealed that PWOO treatment increased the content of most nonvolatile primary metabolites (including lipids, organic acids, and amino acids), whereas the PWO treatment led to a significant decrease in certain VOCs (such as terpenoids, esters, and aldehydes). In general, from the perspective of actual cooking practice and healthy diet, PWOO has more advantages than PWO, which can better retain the nutritional value of pepper fruit to a certain extent, and also help to maintain its unique aroma characteristics.

The comprehensive analysis of NBS-LRR resistance genes in the pepper (Capsicum annuum L.) genome reveals their structural diversity, evolutionary history, and functional importance in plant immunity. A total of 252 NBS-LRR genes were identified, distributed unevenly across all chromosomes, with 54% forming 47 gene clusters. These clusters, driven by tandem duplications and genomic rearrangements, underscore the dynamic evolution of resistance genes. Phylogenetic analysis demonstrated the dominance of the nTNL subfamily over the TNL subfamily, reflecting lineage-specific adaptations and evolutionary pressures. Structural analyses identified six conserved motifs (P-loop, RNBS-A, kinase-2, RNBS-B, RNBS-C, and GLPL) essential for ATP/GTP binding and resistance signaling. Subfamily-specific differences in motif composition and sequence similarity highlight their functional divergence and specialization. Comparative analyses across species further revealed a greater prevalence of nTNL genes in angiosperms, with significant losses of TNL genes in monocots. This study enhances our understanding of the evolution and diversification of plant-resistance genes and provides a foundation for developing disease-resistant crops through targeted breeding strategies.

Pepper is a globally cultivated vegetable known for its distinct pungent flavor, which is derived from the presence of capsaicinoids, a class of unique secondary metabolites that accumulate specifically in pepper fruits. Since the accumulation of capsaicinoids is influenced by various factors, it is imperative to comprehend the metabolic regulatory mechanisms governing capsaicinoids production. This review offers a thorough examination of the factors that govern the metabolism of capsaicinoids in pepper fruit, with a specific focus on three primary facets: (1) the impact of genotype and developmental stage on capsaicinoids metabolism, (2) the influence of environmental factors on capsaicinoids metabolism, and (3) exogenous substances like methyl jasmonate, chlorophenoxyacetic acid, gibberellic acid, and salicylic acid regulate capsaicinoid metabolism. The findings of this study are expected to enhance comprehension of capsaicinoids metabolism and aid in the improvement of breeding and cultivation practices for high-quality pepper in the future.

Chili pepper ( Capsicum annuum L.) is highly preferred by consumers owing to its distinctive flavor. Volatile organic compounds (VOCs) significantly influences the aromatic characteristics of chili peppers, thereby impacting their overall fruit quality. The study of chili pepper aroma remains at a nascent stage, with a notable gap in the literature regarding the composition and metabolic regulation of volatile flavor compounds in fresh chili peppers. This study focuses on the pepper cultivar var 'Qujiao 5' with rich fruit aroma, using headspace solid-phase microextraction full two-dimensional gas chromatography time of flight mass spectrometry (HS-SPME-GC x GC-TOFMS) and headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) detection technology platforms to analyze the VOCs present in green ripe pepper. A total of 1,558 VOCs were successfully identified. Utilizing the HS-SPME-GC x GC-TOFMS method pinpointed 933 substances, whereas the HS-SPME-GC-MS approach detected 773 compounds. Moreover, the two methods together identified 150 substances. Through the meticulous analysis of relative odor activity values (ROAV), it was conclusively determined that Pyrazine, 2-methoxy-3-(2-methylpropyl)- and 2Nonenal, (E)- serve as pivotal volatile flavor compounds in chili fruit. Through the analysis of sensory flavor characteristics of chili peppers, it was found that fresh chili peppers have the main aroma characteristics of fatty, green bell pepper, and green, while also possessing modified odors such as floral and sweet. This research undertook a thorough comparative analysis of two different detection methods. It also meticulously examined the compositional and sensory attributes of the pepper VOCs, providing an essential reference for subsequent studies on the development of pepper fruit flavor quality.