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Mitochondrial transcription termination factor (mTERF) is a DNA-binding protein that is encoded by nuclear genes, ultimately functions in mitochondria and can affect gene expression. By combining with mitochondrial nucleic acids, mTERF regulates the replication, transcription and translation of mitochondrial genes and plays an important role in the response of plants to abiotic stress. However, there are few studies on mTERF genes in tomato, which limits the in-depth study and utilization of mTERF family genes in tomato stress resistance regulation. In this study, a total of 28 mTERF gene family members were obtained through genome-wide mining and identification of the tomato mTERF gene family. Bioinformatics analysis showed that all members of the family contained environmental stress or hormone response elements. Gene expression pattern analysis showed that the selected genes had different responses to drought, high salt and low temperature stress. Most of the genes played key roles under drought and salt stress, and the response patterns were more similar. The VIGS method was used to silence the SLmTERF13 gene, which was significantly upregulated under drought and salt stress, and it was found that the resistance ability of silenced plants was decreased under both kinds of stress, indicating that the SLmTERF13 gene was involved in the regulation of the tomato abiotic stress response. These results provide important insights for further evolutionary studies and contribute to a better understanding of the role of the mTERF genes in tomato growth and development and abiotic stress response, which will ultimately play a role in future studies of tomato gene function. [ABSTRACT FROM AUTHOR]

The PEBP gene family is crucial for the growth and development of plants, the transition between vegetative and reproductive growth, the response to light, the production of florigen, and the reaction to several abiotic stressors. The PEBP gene family has been found in numerous species, but the SLPEBP gene family has not yet received a thorough bioinformatics investigation, and the members of this gene family are currently unknown. In this study, bioinformatics was used to identify 12 members of the SLPEBP gene family in tomato and localize them on the chromosomes. The physicochemical characteristics of the proteins encoded by members of the SLPEBP gene family were also examined, along with their intraspecific collinearity, gene structure, conserved motifs, and cis-acting elements. In parallel, a phylogenetic tree was built and the collinear relationships of the PEBP gene family among tomato, potato, pepper, and Arabidopsis were examined. The expression of 12 genes in different tissues and organs of tomato was analyzed using transcriptomic data. It was also hypothesized that SLPEBP3, SLPEBP5, SLPEBP6, SLPEBP8, SLPEBP9, and SLPEBP10 might be related to tomato flowering and that SLPEBP2, SLPEBP3, SLPEBP7, and SLPEBP11 might be related to ovary development based on the tissue-specific expression analysis of SLPEBP gene family members at five different stages during flower bud formation to fruit set. This article's goal is to offer suggestions and research directions for further study of tomato PEBP gene family members. [ABSTRACT FROM AUTHOR]

The cysteine-rich polycomb-like protein (CPP) gene family is a class of transcription factors containing conserved cysteine-rich CRC structural domains that is involved in the regulation of plant growth and stress tolerance to adversity. Relative to other gene families, the CPP gene family has not received sufficient attention. In this study, six SlCPPs were identified for the first time using the most recent genome-wide identification data of tomato. Subsequently, a phylogenetic analysis classified SlCPPs into four subfamilies. The analysis of cis-acting elements in the promoter indicates that SlCPPs are involved in plant growth and development and also stress response. We present for the first time the prediction of the tertiary structure of these SlCPPs proteins using the AlphaFold2 artificial intelligence system developed by the DeepMind team. Transcriptome data analysis showed that SlCPPs were differentially expressed in different tissues. Gene expression profiling showed that all SlCPPs except SlCPP5 were up-regulated under drought stress; SlCPP2, SlCPP3 and SlCPP4 were up-regulated under cold stress; SlCPP2 and SlCPP5 were up-regulated under salt stress; all SlCPPs were up-regulated under inoculation with Cladosporium fulvum; and SlCPP1, SlCPP3, and SlCPP4 were up-regulated under inoculation with Stemphylium lycopersici. We performed a virus-induced gene silencing experiment on SlCPP3, and the results indicated that SlCPP3 was involved in the response to drought stress. Finally, we predicted the interaction network of the key gene SlCPP3, and there was an interaction relationship between SlCPP3 and 10 genes, such as RBR1 and MSI1. The positive outcome showed that SlCPPs responded to environmental stress. This study provides a theoretical and empirical basis for the response mechanisms of tomato in abiotic stresses. [ABSTRACT FROM AUTHOR]

Flower development is not only an important way for tomato reproduction but also an important guarantee for tomato fruit production. Although more and more attention has been paid to the study of flower development, there are few studies on the molecular mechanism and gene expression level of tomato flower development. In this study, RNA-seq analysis was performed on two stages of tomato flower development using the Illumina sequencing platform. A total of 8536 DEGs were obtained by sequencing, including 3873 upregulated DEGs and 4663 down-regulated DEGs. These differentially expressed genes are related to plant hormone signaling, starch and sucrose metabolism. The pathways such as pentose, glucuronate interconversion, and Phenylpropanoid biosynthesis are closely related and mainly involved in plant cellular and metabolic processes. According to the enrichment analysis results of DEGs, active energy metabolism can be inferred during flower development, indicating that flower development requires a large amount of energy and material supply. In addition, some plant hormones, such as GA, may also have effects on flower development. Combined with previous studies, the expression levels of Solyc02g087860 and three of bZIPs were significantly increased in the full flowering stage compared with the flower bud stage, indicating that these genes may be closely related to flower development. These genes were previously reported in Arabidopsis but not in tomatoes. Our next work will conduct a detailed functional analysis of the identified bZIP family genes to characterize their association with tomato flower size. This study will provide new genetic resources for flower formation and provide a basis for tomato yield breeding. [ABSTRACT FROM AUTHOR]

Tomato (Solanum lycopersicum) is one of the highest-value vegetable crops worldwide, but tomato planting can be easily affected by leaf mold. Tomato leaf mold disease is caused by Cladosporium fulvum, and plants carrying the Cf genes have effective resistance to C. fulvum. To identify leaf mold resistant varieties and screen for specific cDNA amplified fragment length polymorphism (cDNA-AFLP) molecular markers, tomato plants harbouring genes Cf-5, Cf-11, Cf-19, and the moneymaker (MM) tomato line (without Cf gene) were used as plant materials. The changes in reactive oxygen species (ROS) levels and antioxidant activities of plant leaves after inoculation of C. fulvum were measured. Ethylene (ETH), abscisic acid (ABA) and salicylic acid (SA) contents were also determined. The results revealed that the ROS levels in Cf-19 tomato were the most sensitive to C. fulvum inoculation, while in MM they were the least. The antioxidant enzymes of Cf-carrying plants exhibited different activities as compared to those of MM. In the cDNA-AFLP analysis data, the expression of ERF109, sedoheptulose-1,7-bisphosphatase (SBPase), L-ascorbic acid oxidase (AAO) and Thioredoxin H2 (TRX2) were different between Cf-gene carriers and MM plants. In summary, in the process of leaf–mold interaction, the outbreak of ROS and development of systemic acquired resistance (SAR) are tightly combined with antioxidant enzymes, including thioredoxin. Tomato plants carrying the Cf-19 gene appear to have stronger C. fulvum resistance. [ABSTRACT FROM AUTHOR]

GATA transcription factors (TFs) are widely distributed in eukaryotes. Some GATA TFs have been shown to be related to photosynthesis, germination, circadian rhythm, and other functions in plants. Our previous study found that some members of this family have obvious responses when tomato plants are subjected to drought stress, in which the SlGATA17 gene is significantly upregulated. To further verify the function of this gene under drought stress, we constructed tomato lines with this gene overexpressed. Phenotypic and physiological indicators indicated that the SlGATA17- overexpressing plants were more drought tolerant than the wild-type plants. Transcriptomic sequencing results showed that the overexpression of the SlGATA17 gene improved the activity of the phenylpropanoid biosynthesis pathway. The PAL enzyme activity assay results confirmed that the initial activity of this pathway was enhanced in transgenic plants, especially in the initial response stage, indicating that the SlGATA17 gene regulates the drought resistance of tomato plants by regulating the activity of the phenylpropanoid biosynthesis pathway. [ABSTRACT FROM AUTHOR]

Drought seriously threatens tomato production worldwide. Despite much research on exogenous salicylic acid (SA) and Ca2+ improving plant resistance to biotic and abiotic stress, the molecular mechanisms of exogenous SA- and Ca2+-mediated drought resistance response in tomato remain unclear. In this study, we analyzed SA- and Ca2+ -induced differentially expressed transcripts under drought in tomato plants using cDNA-amplified fragment length polymorphism (cDNA-AFLP). In total, 34 transcript derived fragments (TDFs) were differentially expressed. The functions identified through NCBI BLAST alignment mainly involved signal transduction, amino acid metabolism, transcription factors, transfer transport and stress response. The quantitative real-time polymerase chain reaction results of 12 TDFs associated with drought response were consistent with the patterns of changes observed with cDNA-AFLP analysis. These differentially expressed transcripts may be used for functional verification, transgenic research and breeding of drought-resistant tomato varieties. [ABSTRACT FROM AUTHOR]

C2H2-type zinc finger proteins are classic and extensively studied members of the zinc finger family. C2H2-type zinc finger proteins participate in plant growth, development and stress responses. In this study, 99 C2H2-type zinc finger protein genes were identified and classified into four groups, and many functionally related cis -elements were identified. Differential C2H2-ZFP gene expression and specific responses were analyzed under drought, cold, salt, and pathogen stresses based on RNA-Seq data. Thirty-two C2H2 genes were identified in response to multiple stresses. Seven, 3, 5, and 8 genes were specifically expressed under drought, cold, salt, and pathogenic stresses, respectively. Five glycometabolism and sphingolipid-related pathways and the endocytosis pathway were enriched by KEGG analysis. The results of this study represent a foundation for further study of the function of C2H2-type zinc finger proteins and will provide us with genetic resources for stress tolerance breeding. [ABSTRACT FROM AUTHOR]

Inflorescences are the main factor affecting fruit yield. The quantity and quality of inflorescences are closely related to fruit quality and yield. The presence of compound inflorescences in cherry tomatoes is well established, and it has been discovered by chance that compound racemes also exist in tomatoes. To explore the formation of compound inflorescences in tomato, transcriptome sequencing was performed on Moneymaker (MM) and Compound Inflorescence (CI) plants. In-florescences were collected in three periods (early, middle and late) in three replicates, for a total of 18 samples. Data analysis showed that the DEGs were most enriched in metabolic pathways and plant hormone signal transduction pathways. The DEGs were also enriched in the cell cycle pathway, photosynthesis pathway, carbon metabolism pathway and circadian rhythm pathway. We found that the FALSIFLORA (FA), COMPOUND INFLORESCENCE (S) and ANANTHA (AN) genes were involved in compound inflorescence development, not only revealing novel genes but also providing a rich theoretical basis for compound inflorescence development. [ABSTRACT FROM AUTHOR]

Flowering is a morphogenetic process in which angiosperms shift from vegetative growth to reproductive growth. Flowering time has a strong influence on fruit growth, which is closely related to productivity. Therefore, research on crop flowering time is particularly important. To better understand the flowering period of the tomato, we performed transcriptome sequencing of early flower buds and flowers during the extension period in the later-flowering "Moneymaker" material and the earlier-flowering "20965" homozygous inbred line, and we analyzed the obtained data. At least 43.92 million clean reads were obtained from 12 datasets, and the similarity with the tomato internal reference genome was 92.86–94.57%. Based on gene expression and background annotations, 49 candidate genes related to flowering time and flower development were initially screened, among which the greatest number belong to the photoperiod pathway. According to the expression pattern of candidate genes, the cause of early flowering of "20965" is predicted. The modes of action of the differentially expressed genes were classified, and the results show that they are closely related to hormone regulation and participated in a variety of life activities in crops. The candidate genes we screened and the analysis of their expression patterns provide a basis for future functional verification, helping to explore the molecular mechanism of tomato flowering time more comprehensively. [ABSTRACT FROM AUTHOR]

Previous studies have shown that WRKY transcription factors play important roles in abiotic stress responses. Thus, virus-induced gene silencing (VIGS) was used to identify the function of SlWRKY79 in the salt tolerance of tomato plants by downregulating the expression of the SlWRKY79 gene. Under the same salt treatment conditions, the SlWRKY79-silenced plants showed faster stem wilting and more severe leaf shrinkage than the control plants, and the bending degree of the stem of the SlWRKY79-silenced plants was also greater than that of the control plants. Physiological analyses showed that considerably higher levels of hydrogen peroxide (H2O2), superoxide anion (O2−), and abscisic acid (ABA) accumulated in the leaves of the SlWRKY79-silenced plants than in those of the controls after salt treatment. Taken together, our results suggested that SlWRKY79 plays a positive regulatory role in salt tolerance in tomato plants. [ABSTRACT FROM AUTHOR]

Heterosis and combining ability are two important considerations in the utilization of heterosis, which can be used to generate excellent hybrid resource candidates and is very important in conventional hybrid breeding. In this study, the combining ability, heritability, and heterosis of eight major agronomic traits were analyzed in 10 tomato parents and 45 crosses between them. As well as TY-301, a recognized and official excellent variety that is currently selling well on the market was used as a control to conduct a control heterosis analysis, with the goal of selecting ideal parents with high combining ability and new hybrids with commodity value, high yield, early maturity, and high quality. The results showed that both additive and nonadditive genetic effects are involved in the expression of the traits and that the additive genetic effect is dominant in trait inheritance. Although general combining ability (GCA) and specific combining ability (SCA) were not correlated, and the strength of heterosis depends on SCA, the sum of the parental GCA values (GCAsum) did predict heterosis for some traits with higher predictive accuracy than did SCA. Compared with heterosis, GCAsum can better predict hybrid performance. Finally, the parent 17,969 was the breeding material with the best comprehensive trait performance, especially in yield. We screened a high-yielding candidate combination 17,927 × 17,969 and a precocious and good taste candidate combination 17,666 × 17,927. This information may play an important role in the selection of superior parents and hybrid combinations based on combining ability and heterosis analysis. [ABSTRACT FROM AUTHOR]

Tomato (Solanum lycopersicum) is one of the most widely cultivated vegetable crop species in the world. Tomato late blight caused by Phytophthora infestans is a severe disease, which can cause serious losses in tomato production. In this study, tomato SlbZIP68 was identified as a transcription factor that can be induced by P. infestans , salicylic acid (SA) and jasmonic acid (JA). Knockout of SlbZIP68 via clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) technology revealed a significant decrease in tomato resistance to P. infestans. Furthermore, knockout of SlbZIP68 reduced the activity of defense enzymes and increased the accumulation of reactive oxygen species (ROS). Our findings also indicated that SlbZIP68 can activate the expression of the PR genes and enhance resistance to P. infestans. In addition, SlbZIP68 can bind to the PR3 and PR5 promoters and induce gene expression, as revealed by yeast one-hybrid (Y1H) and dual-luciferase (LUC) assays. These findings not only elucidate the mechanisms of response to P. infestans but also enable targeted breeding strategies for tomato resistance to P. infestans. • To identify tomato SlbZIP68 as a transcription factor that can be induced by P. infestans, SA and JA. • Knockout of SlbZIP68 using CRISPR-Cas9 technology resulted in a significant decrease in tomato resistance to P. infestans. • SlbZIP68 was found to play a positive regulatory role in tomato resistance to late blight. • The mechanism model of slbzip68 regulating tomato late blight immunity was proposed from an innovative perspective. [ABSTRACT FROM AUTHOR]

In a previous study, when resistant tomato plants (cv. Motelle) carrying the Sm gene were challenged with S. lycopersici , the SLNLC1 gene was significantly upregulated. In this study, to verify the function of the SLNLC1 gene response to disease resistance against S. lycopersici , virus-induced gene silencing (VIGS) was used to downregulate the expression level of the SLNLC1 gene in resistant tomato plants inoculated with S. lycopersici . After inoculation with S. lycopersici , a susceptible phenotype was observed in the silenced SLNLC1 -resistant plants. Through microscopy, impaired hypersensitive response (HR) and decreased ROS accumulation were also observed in the silenced SLNLC1 plants. In addition, the production of lignin and callose were decreased in the silenced SLNLC1 plants. Taken together, these results indicated that silencing the SLNLC1 gene attenuated the resistance of tomato plants resistant to S. lycopersici. [ABSTRACT FROM AUTHOR]

S-adenosylmethionine decarboxylase (SAMDC) is a key enzyme in polyamine (PA) biosynthesis, and overexpression of SAMDC in plants can increase the PA level and enhance tolerance to multiple abiotic and biotic stresses. In our previous study, this gene was significantly up-regulated during Cladosporium fulvum resistance gene ( Cf )/ Avirulence ( Avr ) interaction in tomato. In this study, to further understand the role that the SAMDC gene plays in Cf / Avr interaction, the virus-induced gene silencing (VIGS) method was applied to down-regulate SAMDC expression in CGN18423, a line carrying the Cf-19 gene for resistance to C. fulvum . Then, these plants were infected with C. fulvum to analyze changes in resistance. The silencing of SAMDC was confirmed by quantitative real-time PCR (qRT-PCR) analysis and PA quantification. The resistance levels of SAMDC -silenced plants were lower than those of untreated CGN18423 plants. No visible signs of infection were observed on the leaves of untreated CGN18423 plants, while some small chlorotic spots were observed on parts of the leaf margins of SAMDC -silenced plants, and hyphae inside the chlorotic spots were observed late in the hypersensitive response (HR) process. These changes suggested that silencing of the SAMDC gene affected the process of Cf/Avr interaction and decreased the resistance of CGN18423 to C. fulvum . [ABSTRACT FROM AUTHOR]

• We focused on the effects of salicylic acid and jasmonic acid on the resistance of Mi-3 in high temperature soils. • We observed the endogenous levels of SA and JA in the plants treated with different soil temperatures after inoculation. • We explored the roles of ROS in the process of the resistance. • Key genes involved in above signal pathways were validated to be specially expressed. Genes that are resistant to Meloidogyne incognita in tomato are mainly members of the Mi gene family. The Mi-3 gene is a heat-stable R gene that retains resistance under high-temperature soil conditions (below 32 °C). The findings of a preliminary investigation of the signaling pathway of Mi-3 -mediated resistance combined with that of a previous transcriptome analysis showed that Mi-3 -mediated resistance mainly occurred in the early stages of nematode infection. An coexpression analysis of key differentially expressed genes (DEGs) related to disease resistance at 3 dpi filtered 7 DEGs as the hub genes that encoded key proteins, including CPKs, RBOHs, HSP, EDS1, and SAPK7. An analysis of the key resistant signal plant hormone pathways, namely, salicylic acid (SA) and jasmonic acid (JA) showed that both external sprays could alleviate the pathogenicity caused by inactivation of Mi-3 at high temperature (34 °C). Additionally, in the early stage of nematodes inoculation, the initial synthesis of SA and JA in the plant under a state of disease resistance (25 °C) was high. The levels of DEGs (LOXs and PALs) involved in the biosynthesis of both plant hormones were up-regulated in the 25 °C assay. Additionally, after inoculation with nematodes, the high expression of the active oxygen synthesis genes (RBOHs) at 25 °C and the activity determination of antioxidant enzymes (superoxide dismutase (SOD), POD, and catalase (CAT)) indicated that the instantaneous accumulation of reactive oxygen species (ROS) was likely to play a positive role in Mi-3 -mediated disease resistance. [ABSTRACT FROM AUTHOR]