Tomato (Solanum lycopersicum) is an important vegetable crop, whose growth and development are frequently subjected to drought stress, which severely limits its growth and yield. Identifying key drought-resistance genes in tomato is crucial for elucidating the mechanisms of drought resistance and improving tomato's drought tolerance, which has practical implications for agricultural production. The results of this study demonstrate that silencing SlSLAC1-6 (Slow anion channel associated 1-6) reduces tomato's drought tolerance. SnRK2.6/OST1 (Open stomata 1) protein kinase is a key component in plants' resistance to abiotic stress. Interactions between SlOST1 and SlSLAC1-6 were confirmed through Y2H, BiFC, LCI, Co-IP, and Pull-down assays. Simultaneously, overexpression and knockout of SlOST1 proved that it positively regulates tomato's drought tolerance by influencing reactive oxygen species (ROS) homeostasis, photosynthetic capacity, stomatal closure, and other mechanisms. Silencing SlSLAC1-6 in SlOST1 knockout plants further reduced tomato's drought tolerance. The regulation of tomato drought tolerance by SlOST1 and SlSLAC1-6 highlights the complexity of plant adaptation to drought. These findings provide new insights into the regulatory network of the SlOST1-SlSLAC1 protein module in tomato drought tolerance and offer gene resources for future tomato drought-resistance breeding.

Fruit are an important source of human dietary nutrition, in which carotenoids are crucial for their appearance and nutritional quality. However, the regulatory network of carotenoid biosynthesis in the fruit of horticultural crops remains obscure. Here, a natural tomato mutant, yellowing mutant (ym), ym ), in the genetic background of Solanum lycopersicum cultivar 'Zhongshu 4' (ZS4) was investigated. Phenotypic analysis showed that the coloring of ym fruit was delayed compared to their wild type, and carotenoid content in ym fruit was significantly lower than that of ZS4 fruit. Integrative metabolome and transcriptome profiling was used to analyze the dynamic changes of carotenoid metabolite content and gene expression in ZS4 and ym fruit during ripening, and differences in carotenoid metabolite content and gene expression between ZS4 and ym fruit were compared. In contrast to ZS4 fruit, the content of carotenes dramatically decreased in ym fruit, of which phytoene and lycopene levels were down-regulated in ym throughout fruit ripening. In the process of fruit ripening, the transcriptome fluctuation of ym was obviously stronger than that of ZS4. Differences in gene expression between ZS4 and ym gradually reduced with fruit ripening. Furthermore, 105 consistently up-regulated and 113 consistently down-regulated genes were found in ym fruit during ripening. KEGG pathway enrichment analyses indicated that differentially expressed genes between ZS4 and ym were implicated in the carotenoid biosynthesis pathway. Correlation analysis showed that 28 genes were positively correlated with phytoene and lycopene content, including SlNF-YA3b (Solyc12G000315) encoding an NF-YA subunit of nuclear factor Y (NF-Y) transcription factors. Expression analysis exhibited that SlNF-YA3b presented a ripening-related expression pattern. Virus- induced gene silencing demonstrated that SlNF-YA3b positively regulated carotenoid accumulation in tomato fruit. . Yeast-one hybrid and transcriptional activity assays showed that SlNF-YA3b could bind to the promoter of the carotenogenic gene SlPDS (Solyc03G003570) and promote its transcription. These data suggest that SlNFYA3b may participate in the regulation of carotenoid biosynthesis in tomato fruit by directly activating the expression of SlPDS. . Our findings not only achieve deeper insights into the regulatory mechanisms of carotenoid biosynthesis in the fruit of horticultural crops but also provide better guidance for the improvement of fruit quality maintenance technologies.

KCS, an endogenous cellular enzyme, catalyzes the elongation of fatty acid chains and plays a crucial role in the biosynthesis of plant epidermal wax. Through processes such as transfer, decarboxylation, and fixation, it contributes to plant growth and adaptation to abiotic and biotic stresses. However, the mechanism by which KCS genes participate in the response of tomato plants to driught remains unclear. In this study, 15 SlKCS gene family members were identified in tomato using bioinformatics methods. Comprehensive analyses were conducted on their amino acid sequences, conserved motifs, cis-elements, phylogenetic relationships, duplication events, and collinearity. Transcriptome and qRT-PCR analysis revealed diverse expression patterns of SlKCS genes under abiotic stresses, with SlKCS8 and SlKCS10 displaying significant upregulation during drought conditions. The two genes were localized to the plasma membrane and exhibit tissue-specific expression. Functional studies demonstrated that silencing SlKCS8 and SlKCS10 reduced drought tolerance in tomato by disrupting stomatal closure. Further analysis revealed that the silencing of KCS compromised the drought tolerance of tomato by reducing its capacity to scavenge reactive oxygen species. These findings provide critical insights into the regulatory functions of SlKCS genes, particularly SlKCS8 and SlKCS10, in drought resistance. Additionally, this research offers important genetic resources for developing drought-tolerant tomato cultivars.

The indole-3-acetic acid (IAA) signaling pathway plays a critical role in plant growth, development, and stress responses. Botrytis cinerea is a major biotic stress factor affecting tomato production. However, the mechanism by which small auxin up-regulated RNA (SAUR) genes participate in the response of tomato plants to B. cinerea remains unclear. In this study, the high-quality tomato genome SL4.0 was used to conduct a comprehensive genome-wide identification of 114 SlSAUR genes. We performed an integrative analysis of phylogenetic relationships, gene structure, cis-acting elements, gene duplications, and stress- and hormone-responsive expression patterns. Among the SAUR genes, SlSAUR50 was identified as a promising candidate because of its significant response to both B. cinerea infection and IAA treatment. Subcellular localization analysis revealed that SlSAUR50 was ubiquitously localized in protoplasts. Functional characterization showed that SlSAUR50 knockout aggravated B. cinerea infection in tomato leaves, whereas its overexpression significantly mitigated infection. Further analysis demonstrated that SlSAUR50 enhanced resistance to B. cinerea by promoting reactive oxygen species scavenging. In summary, this study provides a comprehensive analysis of the SAUR gene family in tomato and offers a theoretical basis for understanding the roles of SlSAUR genes, particularly SlSAUR50, in tomato's defense against B. cinerea infection.

When under drought stress, plants experience hindrances in photosynthesis and cell division, which consequently leads to a decrease in their growth rates. Abscisic acid (ABA) regulates the exchange of water and gases between plants and the external environment by controlling stomatal opening and closing. This hormone plays a significant role in enhancing plant resistance to stressful conditions. Pivotal rate-limiting enzymes involved in the biosynthesis of plant ABA are encoded by genes belonging to the NCED (9-cis-epoxy-carotenoid dioxygenase) family. Therefore, the present study investigated the functions and mechanisms of the tomato NCED gene family in drought resistance. Bioinformatic analysis revealed that the promoters of most SlNCED genes harbored cis-acting elements associated with stress responses. The quantitative reverse transcription-polymerase chain reaction (qRT-PCR) results showed that SlNCED2 may be a key gene in drought stress resistance in this family. After drought treatment, the SlNCED2 silenced tomato plants had significantly diminished ABA and Pro-levels compared to the control plants, the stomatal opening proportion was significantly higher, oxidative stress was more intensive, and drought tolerance was significantly diminished. In addition, SlNCED2 interacted with loxC, a key protein in plant resistance to stress responses. Therefore, the SlNCED2 gene serves as a crucial enhancer of drought tolerance in tomatoes. In summary, this study elucidated the evolutionary patterns and functional distinctions within the NCED family of tomato genes, providing a deeper understanding of the regulatory mechanisms governing plant resistance to drought stress.

Glycosyltransferases (GTs) are a diverse superfamily of enzymes involved in glycosylation reactions, with the GT8 (glycosyltransferase 8) playing a crucial role in plant growth, development, and abiotic stress responses. Tomato, widely cultivated and is a thermophilic plant. So it is significant to study how GT8 regulates cold resistance in tomato for plant growth. In this study, we screened the whole genome of tomato by using bioinformatics methods and identified 40 members of the GT8 gene family. Analysis of cold stress transcriptome data and qRT-PCR experiments revealed the potential significance of SlGolS1 in responding to cold stress. SlGolS1 was highly expressed in the stems and flowers of tomato, with its mature protein localized in the chloroplast. Used the VIGS method to transiently silence the SlGolS1 gene, the SlGolS1-silenced plants (pTRV2-SlGolS1) SlGolS1 ) rendered tomato more sensitive to cold stress compared with the control (pTRV2) tomato plant phenotype after cold treatment; enzyme activity assays showed that oxidative damage was more severe in the pTRV2-SlGolS1. SlGolS1 . In summary, SlGolS1 positively regulates cold resistance in tomato.

Environmental stress significantly affects plant growth and productivity. The effects of drought stress on plants are reflected primarily in enzyme activity, membrane systems, and cell-water loss. Here, the Kelch repeat F-box (KFB) protein family in tomato was systematically identified and analysed. Using bioinformatics, we identified 37 SlKFB family members in the tomato genome and analysed their protein structure, phylogenetic relationships, chromosome distribution, and expression under drought or biotic-stress conditions. Transcriptome data revealed that SlKFB members exhibit differential responses to drought stress, with significant differences in SlKFB16 and SlKFB34 expression. Functional analysis revealed that SlKFB16 functions in the cytoplasm and SlKFB34 in the nucleus and cytoplasm. Under drought stress, SlKFB16 and SlKFB34-silencing significantly reduced reactive oxygen species scavenging and resistance to drought stress. These findings provide a reference for further studies of the mechanisms of SlKFB16 and SlKFB34 in drought stress in tomato as well as a foundation for enhancing their resistance to drought stress.

Ascorbate peroxidase (APX) is a crucial enzyme involved in cellular antioxidant defense and plays a pivotal role in modulating reactive oxygen species (ROS) levels under various environmental stresses in plants. This study utilized bioinformatics methods to identify and analyze the APX gene family of pomelo, while quantitative real-time PCR (qRT-PCR) was employed to validate and analyze the expression of CmAPXs at different stages of fruit postharvest. This study identified 96 members of the CmAPX family in the entire pomelo genome, with uneven distribution across nine chromosomes and occurrences of gene fragment replication. The subcellular localization includes peroxisome, cytoplasm, chloroplasts, and mitochondria. The CmAPX family exhibits a similar gene structure, predominantly consisting of two exons. An analysis of the upstream promoter regions revealed a significant presence of cis-acting elements associated with light (Box 4, G-Box), hormones (ABRE, TCA-element), and stress-related (MBS, LTR, ARE) responses. Phylogenetic and collinearity analyses revealed that the CmAPX gene family can be classified into three subclasses, with seven collinear gene pairs. Furthermore, CmAPXs are closely related to citrus, pomelo, and lemon, followed by Arabidopsis, and exhibit low homology with rice. Additionally, the transcriptomic heat map and qPCR results revealed that the expression levels of CmAPX57, CmAPX34, CmAPX50, CmAPX4, CmAPX5, and CmAPX81 were positively correlated with granulation degree, indicating the activation of the endogenous stress resistance system in pomelo cells by these genes, thereby conferring resistance to ROS. This finding is consistent with the results of GO enrichment analysis. Furthermore, 38 miRNAs were identified as potential regulators targeting the CmAPX family for post-transcriptional regulation. Thus, this study has preliminarily characterized members of the APX gene family in pomelo and provided valuable insights for further research on their antioxidant function and molecular mechanism.

When plants under salt stress, the intracellular ion concentration and osmotic pressure increase, which inhibits normal growth, development and life processes, and even leads to plant wilting and death. CLC (chloride channel protein) is a kind of anion channel protein that widely exists in plant cell membrane or organelle membrane. CLC proteins participate in the transmembrane transport of anions and plays an active role in plant tolerance to salt stress. In this study, we analysed the response and function of tomato CLC family genes in salt stress tolerance. Bioinformatics analysis showed that the promoter of SlCLC gene contained the most cis-acting elements related to abiotic stress response. Transcriptome data analysis and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) results showed that SlCLC8 may be the key gene for salt stress resistance in this family. After salt stress treatment, the SlCLC8-silenced tomato plants showed higher wilting and oxidative stress, and significantly reduced salt tolerance compared with the control plants. Therefore, SlCLC8 is a positive regulator of tomato salt tolerance. In summary, this study elucidated the evolutionary patterns and functional differences of the tomato CLC gene family, and deepened the understanding of the regulatory mechanisms of salt stress tolerance in plants.

In green plants, the chloroplast is responsible for light energy transition and organic assimilation. However, the molecular mechanisms underlying chloroplast development in horticultural crops remain unclear. Here, four-dimensional data-independent acquisition-based proteomic profiling identified 1,727 differentially expressed proteins between "Zhongshu 4" (ZS4) and yellowing mutant (ym) leaves, a considerable proportion of which were down-regulated chloroplast proteins. Functional analysis revealed that light harvesting and chlorophyll biosynthesis were correlated with ym leaf yellowing, validated by RNA sequencing. Quantitative PCR confirmed that chlorophyll a/b-binding protein 3C (CAB3C) related to light harvesting and NADPH:protochlorophyllide oxidoreductase 3 (POR3) involved in chlorophyll biosynthesis were repressed in ym leaves. Virus-induced gene silencing showed that suppressing CAB3C and POR3 decreased the net photosynthetic rate and chlorophyll content. Additionally, the F-box protein Slym1 negatively regulated the expression of CAB3C by depressing transcription factor SlFHY3 levels. Our findings offer insights into the regulatory mechanisms of chloroplast development in tomato.

The effects of cold stress on plants are mainly reflected in enzyme activity, membrane system, cell water loss, etc., leading to cell metabolism disorder, and even death. The SLAC1 gene family encodes S-type anionic channel proteins, which play an essential role in plant response to environmental stimuli by regulating stomatal opening and closure of guard cells. Therefore, the tomato SLAC1 gene family was used as the object of this study to explore its function and mechanism in tomato cold resistance. Firstly, bioinformatics analysis showed that most of the promoter regions of the SLAC1 gene family members contained stress-related cis-acting elements. Tran-scriptomic data and qRT-PCR experiments result show that SlSLAC1-6 might be a key gene in the resistance of the family. After cold treatment, the increase of antioxidant enzymes in SLAC1-6 silenced plants resulted in the inability of plants to maintain normal osmotic pressure of cells and significantly reduced the cold tolerance of tomato plants compared with the control (pTRV2:00) tomato plants. In addition, the stomatal aperture of the SLAC1-6 silenced plant was significantly more extensive than that of the pTRV2:00 tomato plants. The results showed that SlSLAC1-6 was a positive regulator of tomato cold resistance. In conclusion, our study provides a more extensive analysis of the tomato SLAC1 gene family and will provide a reference for future research on the mechanism of the SlSLAC1-6 gene in tomato cold resistance.

Drought, one of the most important abiotic factors affecting plant growth, causes a large reduction in tomato production every year. Tomato, a berry fruit and vegetable that can be eaten fresh or cooked, has rich nutritional value. However, most of ripe fruits show softening of pericarp, which leads to damage easily during transportation, and shorten the shelf life. Fruit mechanical strength is important to the texture, transport resistance and shelf life of tomato fruit. We found a natural tomato mutant in the field, which showed excellent drought resistance ability and late ripening characteristics. The target gene Solyc09g075360 (SlGH9-21) was obtained through transcriptome data screening. After the gene was silenced, tomatoes improved their drought resistance by reducing stomatal aperture and increasing stem vessel diameter. We also found that silencing of the SlGH9-21 gene delayed the ripening of tomato fruit and improved fruit firmness. Compared with the control, the ripening of the fruit of SlGH9-21 gene-silenced plants was delayed by approximately 10 days, which increased the fruit firmness and storage tolerance and reduced the water loss rate of fruit. Overall, the study of tomato stress response mechanisms and the identification of key genes regulating fruit hardness are beneficial to the improvement of tomato resistance. It is also conducive to the improvement of tomato quality. The research results can lay a foundation for the enhancement of fruit storage tolerance and stress resistance.

Grey mould (Botrytis cinerea) is a common disease in tomato (Solanum lycopersicum L.), which can cause a severe reduction in production. Clonostachys rosea (C. rosea) is an effective biological control agent that can inhibit the growth and establishment of B. cinerea and significantly improve tomato resistance to B. cinerea. However, the molecular basis of B. cinerea resistance mechanisms induced by C. rosea is still unknown. In this study, integration of proteomic and transcriptomic approaches was used to analyse B. cinerea resistance induced by C. rosea in tomatoes. The results revealed that C. rosea treatment resulted in the overexpression of several genes and proteins associated with oxidation-reduction (REDOX) reactions and defense-related enzymes. In this regard, we recorded greater levels of expression in peroxisome-related enzymes, the ascorbate–glutathione (AsA–GSH) cycle and the phenylpropane pathways. The results showed that the activation of peroxisome-related proteins and proteins associated with the AsA-GSH cycle pathways could enhance B. cinerea resistance in plants by scavenging ROS accumulated due to disease infection and maintaining the ROS balance in cells. In addition, the activation of the enzymes associated with the phenylpropanoid pathway can contribute to enhanced B. cinerea resistance by synthesizing primary and secondary metabolites that can inhibit the establishment of invading pathogens in the host. Overall, the results of this study shed some light on the molecular basis of the mechanism of B. cinerea resistance induced by C. rosea and provided a deeper understanding of detailed regulatory pathways associated with resistance.

Leaf color mutants are ideal materials for studying mechanisms of plant such as photosynthesis, photorespiration, the pigment biosynthesis, and some other agronomic traits. Meanwhile, leaf color mutants are widely used in the screening of the offspring of cross breeding. The molecular mechanisms of yellow leaf and REDOX balance of tomatoes have not been explored. Here we obtain a naturally yellow leaf tomato mutant (ym). In order to further understand the role of REDOX, a series of experiments are conducted to assess the physiological and molecular reactions of two tomato lines, ym and zs4. The results showed that the ym mutant cells accumulated excessive H2O2. The chlorophyll content of the mutant decreased greatly. The chloroplast structure of the mutant is observed by transmission electron microscope (TEM). The results showed that mutant's chloroplast membrane structure is seriously damaged. A transcriptomic approach is used to analyze the gene regulate etiolation traits in ym mutant tomato plants. Many genes are enriched in oxidation-reduction (REDOX). Kyoto encyclopedia of genes and genomes (KEGG) revealed that DEGs are involved in pathways such as plant hormone signal transduction, carotenoid biosynthesis, MAPK signaling pathway, phenols and flavonoids synthesis, and pentose and glucuronate interconversions, which further confirmed the role of yellow trait. Overall, the damage of chloroplast structure, low pigment content and low level ROS scavenging capability are the main factors leading to yellow leaf. Main Conclusion Damage of chloroplast structure lead to the low level of the chlorophyll and the REDOX imbalance cause tomato yellow leaf color.

NAC proteins in plants respond to stress and play an important role in plant growth regulation. This regulation occurs through a variety of downstream effects mediated by plant hormones in response to stress. In this study, we performed a systematic genome-wide analysis of the NAC gene family in tomato based on genome version SL4.0. We identified 99 SlNAC genes by abiotic stress analysis of conserved motifs and gene structure, phylogenetic analysis, cis-element analysis, chromosome localization analysis, synteny relationship and expression pattern analysis. These 99 SlNAC genes were distributed on all 12 chromosomes. Except for genes without introns, there was no significant correlation between gene structures and phylogenetic relationships. Most of the cis-elements identified were associated with plant hormones and environmental responses. There were 77 SlNAC genes that showed no homogeneity between tomato and wild rice, suggesting that these homologous genes arose after the differentiation of dicotyledonous and monocotyledonous plants. The comprehensive analysis of the SlNAC gene family provides a valuable resource for studying this gene family in tomato and a foundation for further study of the functional characteristics of these genes.

Drought stress will lead to a decrease in tomato yield and poor flavour, yield and quality, resulting in economic losses in agricultural production. Mining the key genes regulating tomato drought resistance is of great significance to improve the drought resistance of tomato plants. The cell wall can directly participate in the plant drought stress response as one of the main components of the cell wall, and the regulation of pectin content in plant drought resistance is still unclear. Here, the candidate gene Solyc08g006690 (Slpmei27) was obtained by fine mapping based on genome sequencing technology (BSA-seq) of late-maturing stress-resistant tomato mutants found in the field. Slpmei27 is expressed in the cell wall. The transient silencing of Slpmei27 by VIGS significantly improved the drought resistance of tomato. Meanwhile, Slpmei27 silencing could significantly change the cell wall structure of plants, change the stomatal pass rate, reduce the water loss rate of plants, improve the scavenging ability of reactive oxygen species, change the redox balance in plants, and thus improve the drought resistance of tomato. The promoter region of this gene contains a large number of hormone-response and stress-response binding sites. The promoter region of the Slpmei27 gene in the mutant could lower the expression of downstream genes. Through this study, the mechanism by which Slpmei27 improves tomato drought resistance was revealed, and the relationship between pectin methyl ester metabolism and plant drought resistance was established, providing a theoretical basis for the production of high-quality tomato materials with high drought resistance.

Photosynthesis, as an important biological process of plants, produces organic substances for plant growth and development. Although the molecular mechanisms of photosynthesis had been well investigated, the relationship between chlorophyll synthesis and photosynthesis remains largely unknown. The leaf-color mutant was an ideal material for studying photosynthesis and chlorophyll synthesis, which had been seldom investigated in tomato. Here, we obtained a yellow leaf tomato mutant ym (The mutant plants from the line of zs4) in field. Transmission electron microscopy (TEM) and photosynthetic parameters results demonstrated that chloroplast’s structure was obviously destroyed and photosynthetic capacity gets weak. The mutant was hybridized with the control to construct the F2 segregation population for sequencing. Slym1 gene, controlling yellow mutant trait, was identified using Bulked Segregation Analysis. Slym1 was up-regulated in the mutant and Slym1 was located in the nucleus. The genes associated with photosynthesis and chlorophyll synthesis were down-regulated in Slym1-OE transgenic tomato plants. The results suggested that Slym1 negatively regulate photosynthesis. Photosynthetic pigment synthesis related genes HEMA, HEMB1, CHLG and CAO were up-regulated in Slym1 silencing plants. The redundant Slym1 binding the intermediate proteins MP resulting in hindering the interaction between MP and HY5 due to the Slym1 with a high expression level in ym mutant, lead to lots of the HY5 with unbound state accumulates in cells, that could accelerate the decomposition of chlorophyll. Therefore, the yellow leaf-color mutant ym could be used as an ideal material for further exploring the relationship between leaf color mutant and photosynthesis and the specific mechanism.

番茄是一种世界性蔬菜,BZR基因在植物生长发育中发挥重要作用,但目前有关番茄BZR基因响应非生物胁迫研究较少.为更好研究BZR基因在番茄中分布与功能,研究共鉴定9个SlBZR基因家族成员,并利用生物信息学技术分析其基本信息、保守基序、染色体定位、系统进化、顺式作用元件及非生物胁迫下表达模式.结果表明,9个SlBZR基因成员分布在番茄8条染色体上.qRT-PCR分析表明,SlBZR基因在植物逆境或激素响应方面具有重要作用.SlBZR3和SlBZR8在非生物胁迫中明显上调表达,说明其可能在番茄响应非生物胁迫中发挥重要作用.研究为进一步探索番茄BZR基因功能提供理论依据.

YUCCA基因是植物在合成生长素过程中限速酶的编码基因,植物在生长发育过程中离不开生长素,也同样也离不开YUCCA基因.为深入研究番茄中的YUCCA基因,本研究利用生物信息学方法,在番茄全基因组范围内共鉴定出了17个YUCCA基因,并对17个YUCCA基因的基本信息、转录本结构、保守基序、顺式元件、染色体定位、系统发育以及表达模式进行了分析.结果 表明,17个YUCCA基因分布在7条染色体上,并且可以分为三大类A、B、C.YUCCA基因的内含子在O～7之间分布.系统发育分析表明,同一条染色体上的YUCCA基因有明显的进化关系.通过以上分析,对后续深入研究番茄YUCCA基因家族提供了参考.

Yellow mutant is an important material for studying chlorophyll biosynthesis, degradation and the genetics and development of chloroplasts. The chlorophyll biosynthesis and degradation pathways of tomato (Solanum lycopersicum) mutant ym (Yellow mutant) and control ZS4 (Zhongshu 4) were studied. Photosynthetic parameters and chlorophyll fluorescence parameters of the variety ym and ZS4 were measured. The results showed that ym was more sensitive than the variety ZS4, while the variety ym has more tolerant to low light. The chloroplasts in ym exhibited onset of degradation compared with ZS4 under the transmission electron microscopy (TEM). The lack of chlorophyll-protecting material or the chloroplast grana degradation causes the leaf fade.