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.

Individual biochemical indicators are insufficient for comprehensive tomato food flavor quality assessment, necessitating multi-parameter models of the core soluble taste matrix. We hypothesized that age stratification of trained sensory assessors would expose differential biochemical variable importance profiles in flavor quality prediction. Accordingly, this study aimed to: (1) construct and compare multiple regression models linking eight biochemical indicators to sensory scores, (2) identify key quality drivers via feature selection, and (3) examine whether age stratification alters the identified sensory drivers. Eight baseline taste indicators across 62 tomato cultivars were evaluated by 30 age-stratified trained sensory panelists (<40 and ≥40 years), using cross-validation to ensure model robustness against small-sample constraints. Partial least squares regression (PLSR), support vector regression (SVR), random forest (RF), and Boruta were applied. Random forest achieved the best performance (R2 = 0.82). In the full panel model, key variables were fructose, total free amino acids, and vitamin C. After age stratification, the under-40 group retained these variables, whereas the ≥40 group replaced vitamin C with soluble solids. Fructose and total free amino acids were consistently robust drivers, while total acidity remained least important. Deploying the RF-Boruta framework within an age-stratified context provides a structured analytical framework for investigating flavor perception from biochemical data. These findings suggest that fructose and total free amino acids represent highly robust candidate indicators for flavor quality prediction, while age-stratified variances suggest the utility of integrating demographic-specific metrics into precision breeding frameworks.

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.

To decipher the metabolic regulation of pepper fruit (Capsicum annuum L.) quality, tissue-scale matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) was employed to systematically map 19 key metabolites across four developmental stages at a spatial resolution of 50 μm. Imaging revealed distinct spatiotemporal dynamics: capsaicinoids exhibited a localized "bimodal accumulation" in the placenta, while capsanthin precursors shifted from a uniform distribution to specific enrichment in the pericarp. Notably, a synthesis-distribution decoupling was observed in ascorbic acid metabolism, suggesting potential inter-tissue redistribution. Integration with high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) for the absolute quantification of four core metabolites (n = 3) provided complementary insights, distinguishing continuous bulk accumulation from dynamic, non-linear local metabolic activity. This study constructs a tissue-scale spatial metabolomic atlas, highlighting the synergistic value of combining spatial imaging with bulk quantification to unravel metabolic heterogeneity in food matrices.

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.

Abiotic stresses such as heat and drought lead to oxidative damage in plants by inducing excessive accumulation of reactive oxygen species (ROS). Aldehyde dehydrogenases (ALDHs), which detoxify reactive aldehydes, play critical roles in stress responses, but their functions in pepper (Capsicum annuum) remain largely unexplored. In this study, 28 CaALDH genes were identified and categorized into nine families. Phylogenetic and synteny analyses revealed strong evolutionary conservation, highlighting CaALDH2B4 and CaALDH7B1 as key members. Expression profiling showed distinct tissue-specific patterns and robust induction under heat and drought stress. Functional analysis via virus-induced gene silencing (VIGS) confirmed that CaALDH7B1 enhances stress tolerance by limiting ROS accumulation, promoting antioxidant enzyme activity (SOD, CAT, APX, POD), and maintaining NADPH/NADP+ homeostasis. Comparative genomics and structural modeling further revealed that CaALDH7B1 is evolutionarily conserved, with critical NADP+-binding residues retained across plant species. These findings underscore the pivotal role of CaALDH7B1 in oxidative stress regulation and provide new insights into the functional evolution of the ALDH gene family in pepper.

Significant losses of vegetables and fruits occur at multiple stages, including harvest, sorting, storage, and transportation, primarily due to mechanical damage, pathogen invasion, and the natural process of senescence. To mitigate postharvest decay and maintain superior quality of produce, conventional techniques such as low temperature storage and synthetic fungicide treatment are widely employed. Acibenzolar-S-methyl (ASM), an effective plant resistance inducers, has demonstrated its efficacy in protecting against a diverse range of fungal and bacterial pathogens. The present review primarily concludes that exogenous application of ASM effectively maintains postharvest quality, delays senescence, and controls decay of postharvest fruits and vegetables through the following mechanisms: (1) modulation of signal transduction pathways including Ca2+ signal, H2O2, and mitogen-activated protein kinase cascades; (2) regulation of reactive oxygen species metabolism; (3) accumulation of pathogenesis-related proteins; (4) activation of the phenylpropanoid pathway; (5) regulation of energy metabolism; and (6) mediation of fatty acid metabolism. Taken together, ASM is a potent activator that enhances resistance against a wide range of postharvest pathogens and effectively preserves the storage quality of horticultural products.

Flavonoids are important secondary metabolites that regulate plant growth and development and confer resistance against biotic and abiotic stress. As natural polyphenol substances, flavonoids determine the quality traits of commercial fruits, such as color, flavor, and nutrition. In the past few decades, research on the regulation of flavonoid biosynthesis in plants has made significant progress. However, a deep understanding of this aspect in flavonoid-rich horticultural crops is lacking. This review aims to systematically summarize the current knowledge in the regulation of flavonoid biosynthesis in fruits, including the transcriptional, post-transcriptional, epigenetic, and post-translational regulation mechanisms as well as the composite regulation cascades. Our analysis shows that direct transcriptional regulation involves the actions of different transcription factor families, such as MYB, WRKY, bZIP, AP2/ERF, and MADS, by directly targeting the key synthase genes in flavonoid biosynthetic pathway. Indirect regulation involves specific transcription factors and microRNAs that target the downstream regulators, as well as the regulation modules triggered for degradation of activators or repressors in response to environmental signals or plant hormones. In addition, epigenetic regulation, associated with methylation level in the gene promoter regions or the insertion or deletion of specific sequences therein, plays an important role in controlling anthocyanin accumulation. Based on the diverse regulation mechanisms of the flavonoid biosynthetic pathway, more molecular design targets can be applied in the future, facilitating the production of more stress-tolerant and quality-elevated crop varieties.

4-Chlorophenoxyacetic acid (4-CPA) is an auxin-type plant growth regulator widely used in fruit and vegetable production. However, its influence on the nutritional and sensory qualities of horticultural crops remains insufficiently characterized. This study investigated the influence of 4-CPA application and oscillator-mediated pollination on the metabolic composition of fully ripe fruits of Solanum lycopersicum var. cerasiforme cv. ‘Zheyingfen No. 1’. Two concentrations of 4-CPA (16 mg/L and 8 mg/L) were applied during flowering, and their effects on amino acids, soluble sugars, organic acids, and volatile compounds (VOCs) were comparatively analyzed. The results indicated that treatment with 8 mg/L 4-CPA treatment significantly increased the total amino acid content in ripe fruits compared with the control and the 16 mg/L treatment. Among the 17 amino acids identified, the contents of umami-related amino acids, including glutamic acid (Glu) and aspartic acid (Asp), were markedly enhanced. In particular, Glu content in the C8 treatment was the highest and accounted for more than 50% of the total amino acid content. The accumulation of sugars was not significantly affected by 4-CPA treatment, while the C8 treatment resulted in the lowest level of total organic acids, which are crucial for flavor development at the ripening stage. A 29.35% increase in VOCs was observed” for conciseness in 4-CPA-treated fruits compared with the control. Analysis of relative odor activity values (rOAVs) showed that although 4-CPA treatment reduced the number of aroma-active compounds, it promoted the accumulation of β-ionone, thereby shifting the tomato fruit aroma profile toward floral, woody, sweet, and fruity notes. In summary, 4-CPA treatment regulated the nutritional and flavor quality of ripe cherry tomato fruits by increasing the content of Glu and other amino acids, enhancing the diversity of VOCs, and promoting the formation of key aroma-active substances such as β-ionone.

L-Cysteine desulfhydrase (DES1), a key enzyme in eukaryotes, catalyzes the synthesis of hydrogen sulfide (H2S), which is a gaseous signaling molecule. However, the genes encoding DES1 enzymes in wheat, one of the world's most important crop species, have yet to be fully characterized. This study offers a comprehensive analysis of the wheat TaDES1 gene family and delves into its potential functions. We identified a total of 18 TaDES1 genes, located across 13 chromosomes, categorized them into four subfamilies, and comprehensively analyzed their physicochemical properties. Furthermore, three DES1 gene families (HvDES1, OsDES1, and ZmDES1) were identified in three Poaceae species to explore the evolutionary relationships of TaDES1 and its homologs. The results indicated that segmental duplication drove the expansion of the TaDES1 family, which experienced strong purifying selection. Promoter cis-elements and gene ontology (GO) enrichment analysis revealed the significant roles of this gene in the stress response, phytohormone regulation, and plant growth. miRNA target prediction analysis further explored the regulatory relationships. Transcriptomic data revealed that TaDES1 members are responsive to abiotic stresses, biotic stresses, and exogenous abscisic acid (ABA) treatment. The qPCR (RT-qPCR) results also demonstrated that the TaDES1 gene is responsive to multiple stresses. Co-expression network analysis emphasized the importance of key TaDES1 genes in stress responses. Finally, simple sequence repeats (SSRs) within the TaDES1 family were predicted, and variation analysis of three key TaDES1 genes and their homologs across ten wheat cultivars was performed to explore their potential in wheat breeding.

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.

Genetic transfers are pervasive across both prokaryotes and eukaryotes, primarily involving canonical genomic introgression between species or genera and horizontal gene transfer (HGT) across kingdoms. However, DNA transfer between phylogenetically distant species, which differs from canonical introgression and HGT in certain aspects of its temporal scale and mechanistic features, here defined as remote introgression (RI), has received less attention in evolutionary genomics. In this study, we present RIFinder, a novel phylogeny-based method for the detection of RI events, and apply it to a comprehensive dataset of 122 grass genomes. Our analysis identifies 622 RI events originating from 543 distinct homologous genes, revealing distinct characteristics among grass subfamilies. Specifically, the subfamily Pooideae contains the largest number of introgressed genes, whereas Bambusoideae contains the fewest. Comparisons among the accepted genes, their donor copies, and native homologs demonstrate that introgressed genes undergo post-transfer localized adaptation and show significant functional enrichment in stress-response pathways. Notably, we identify a large Triticeae-derived segment in the Chloridoideae species Cleistogenes songorica, which is potentially associated with its exceptional drought tolerance. Furthermore, we provide compelling evidence that RI has contributed to the origin and diversification of biosynthetic gene clusters for gramine, a defensive alkaloid chemical, across grass species. Our study establishes a robust method for RI detection and highlights its critical role in adaptive evolution. The Python implementation of RIFinder is publicly available at https://github.com/Ne0tea/RIFinder.

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.

Nondestructive measurement of physical and chemical indicators (PCIs) in fruits and vegetables is essential for quality control in agriculture. However, existing techniques such as hyperspectral and near-infrared (NIR) spectroscopy face limitations in terms of high costs, noise sensitivity, low efficiency, and reduced accuracy under real-world conditions. In this work, we propose a novel approach using magnetic induction tomography (MIT) to address these issues, offering enhanced accuracy, noise resistance, and cost-effectiveness. Specifically, we design and implement a PCIs measurement system based on MIT, which is previously unexplored in this article. In addition, we develop an efficient, portable system with customized regression models that map MIT conductivity data to quantitative PCI values, enabling practical field applications. Both controlled and real-world experiments show that our MIT system achieves an accuracy of 97% and 81% in predicting the freshness of tomatoes and grapes, respectively, and improves the ${R}<^>{{2}}$ value in tomato acidity prediction by 32.9% over NIR methods, demonstrating its effectiveness for nondestructive agricultural quality assessments.