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Leaves are the main site of photosynthesis in plants, and leaf color plays a major role in crop quality, yield, resistance, as well as other aspects. Although the genes related to photosynthesis have been well characterized in plants in general, yellow-green leaf mutants have not yet been fully studied in tomatoes. In the present study, a dark green leaf (GL) mutant was isolated from yellow-leaf tomato (wild-type). The dark GL displays a distinct yellow-green phenotype, and has a greater chlorophyll content and higher photosynthetic rate. Furthermore, the lamellae were clear, and the stroma and grana were orderly, with more stacking and larger starch grains according to the ultrastructure analysis of chloroplasts in GL leaves. Comparative transcriptome analysis of GL and wild-type plants was performed to identify the pathways and genes related to photosynthesis. In this work, a total of 292 differentially expressed genes (DEGs) between GL plants and WT plants were identified, of which 131 genes were upregulated and 161 genes were downregulated. The diterpenoid biosynthesis and photosynthesis antenna proteins were the two most significantly enriched in the first 20 pathways according to KEGG analysis. Most of the DEGs involved in diterpenoid biosynthesis and photosynthesis were antenna proteins. The photosynthesis antenna protein Solyc02g071030 (LHCB1) and the diterpenoid biosynthesis-related genes, Solyc08g005710 and Solyc09g059240, were significantly upregulated in GL leaves compared with WT leaves. The expression patterns of the DEGs were similar to those determined by qRT-PCR. Overall, our research not only revealed the diterpenoid biosynthesis and photosynthesis pathways involving in leaf color variation, but also identified the putative target genes for genetic manipulation in the future. [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]

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]