Soluble solids content (SSC) plays an important role in determining the flavor of tomato fruits. Tomato fruit SSC is transcriptionally regulated via sugar metabolism. Previous studies have predominantly focused on the role of C2H2-type zinc finger proteins in tomato growth and development. However, the specific regulatory mechanisms of C2H2 in the accumulation of soluble solids in tomato fruits are not fully understood. This study used eight tomato accessions with varying levels of SSC to study the expression of SlC2H2 family genes in red ripe fruits. The levels of SlC2H2-71 expression were found to be significantly reduced in high-SSC accessions compared to low-SSC accessions. Several Slc2h2-71 mutant lines were developed using the CRISPR-Cas9 system, which led to elevated levels of soluble solids, fructose, glucose, malic acid, and citric acid in mature red ripe fruits. However, the sucrose content in the edited Slc2h2-71 mutant lines was generally lower. RNA-seq analysis revealed that fruits from the mutant lines had altered expression of genes related to the sugar and acid metabolic pathways, which was further confirmed by quantitative real-time PCR. Specifically, the expression of SlLIN5 encoding the cell wall invertase (CWIN) was elevated. The yeast one-hybrid (Y1H) assay, 35S::UAS-GUS, dual-luciferase reporter systems and electrophoretic mobility shift assay (EMSA) demonstrated that C2H2-71 regulates tomato sugar metabolism by directly binding to the promoter region of SlLIN5, culminating in the repression of its transcriptional activity. The activity of acid invertase exhibited a significantly higher level in the SlC2H2-71 knock-out lines compared to the control lines. In summary, the regulation of tomato fruit SSC by C2H2-71 involves the inhibition of SlLIN5 expression.

Enhancing crop production and yield is necessary to feed an increasing population, but cadmium (Cd) accumulation in crops poses a serious threat to human health. It is found that a trend during domestication is for the co-selection of improved tomato yield and reduced Cd accumulation. A genome-wide association study (GWAS) of 506 tomato accessions identifies a natural allele, LCT1AA, which confers low Cd accumulation in the shoots and fruits of tomato. The linkage disequilibrium (LD) analysis reveals a tight linkage between LCT1A and a large fruit allele fw3.2T. Evolution analysis shows that fw3.2 and LCT1 experience similar selection pressure. Grafting experiments using tomato hypocotyls as the junction point further demonstrate that LCT1 reduces Cd accumulation primarily through regulation in the root rather than the shoot of the plant. These findings collectively highlight the importance of LCT1 in regulating Cd accumulation and indicate that the widespread presence of low Cd accumulating types in cultivated tomato is due to genetic hitchhiking and co-selection of LCT1A with fw3.2T during yield breeding.

Citric acid (CA) plays a crucial role as a fruit flavor enhancer and serves as a mediator in multiple metabolic pathways in tomato fruit development. Understanding factors influencing CA metabolism is essential for enhancing fruit flavor and CA-mediated biological processes. The accumulation of CA, however, is influenced by a complex interplay of genetic and environmental factors, leading to challenges in accurately predicting and regulating its levels. In this study, we conducted a genome-wide association study (GWAS) on CA, employing six landmark models based on genome-wide variations including structural variants, insertions and deletions, and single nucleotide polymorphisms. The identification of 11 high-confidence candidate genes was further facilitated by leveraging linkage disequilibrium and causal variants associated with CA. The transcriptome data from candidate genes were examined, revealing higher correlations between the expression of certain candidate genes and changes in CA metabolism. Three CA-associated genes exerted a positive regulatory effect on CA accumulation, while the remaining genes exhibited negative impacts based on gene cluster and correlation analyses. The CA content of tomatoes is primarily influenced by improvement sweeps with minimal influence from domestication sweeps in the long-term breeding history, as evidenced by population differentiation and variants distribution. The presence of various causal variants within candidate genes is implicated in the heterogeneity of CA content observed among the tomato accessions. This observation suggests a potential correlation between the number of alternative alleles and CA content. This study offers significant function-based markers that can be utilized in marker-assisted breeding, thereby enhancing their value and applicability.

Sticky nightshade (Solanum sisymbriifolium Lam.) is a spiny species with a variety of disease resistance characteristics found worldwide within the Solanum genus. However, its low germination rate and long germination period pose obstacles to the effective use of this species. Here, we treated Sticky nightshade with different concentrations of gibberellin (GA3) and observed paraffin sections of Sticky nightshade seeds treated with different GA3 concentrations over different time ranges. The results showed that a 400 mg/L exogenous GA3 concentration at room temperature could improve the germination rate of Sticky nightshade the most effectively. Exogenous GA3 treatment can significantly accelerate the hydrolysis of starch granules and increase the germination rate of seeds. Subsequently, we also measured the MDA content of Sticky nightshade seeds treated with different GA3 concentrations over different time ranges. The result reveals that GA3 treatment can steadily decrease Sticky nightshade seeds’ MDA content during germination, indicating that exogenous GA3 treatment also reduces membrane peroxidation and maintains the stability of the plasma membrane. In this paper, we identified an optimal GA3-treated concentration of Sticky nightshade to improve seed germination at room temperature and explored the reason why the exogenous GA3 treatment of Sticky nightshade seed increased the germination rate.

Tomato, a vegetable of considerable global significance, has been the subject of extensive breeding efforts primarily aimed at achieving high yields and resistance to multiple stressors. However, despite these endeavors, the quality of fruits still cannot fully satisfy the diverse preferences of the majority of consumers. The elucidation of genetic determinants underlying fruit quality traits, coupled with the advancement of gene editing techniques, has significantly contributed to the enhancement of tomato quality. Combining with gene editing technology to improve tomato fruit quality traits represents a viable approach for maximizing the utilization of essential genes in breeding programs. This review provides a comprehensive summary of the significant genes associated with tomato fruit quality traits, as well as an overview of the current advancements and potential avenues for enhancing tomato quality through gene editing technology. Four important aspects of fruit quality—appearance, flavor, nutritional profiles and postharvest properties form the basis of the review, providing a thorough update on the state of research in tomato fruit quality improvement via new gene editing techniques.

High temperature stress is one of the major environmental factors that affect the growth and development of plants. Although WRKY transcription factors play a critical role in stress responses, there are few studies on the regulation of heat stress by WRKY transcription factors, especially in tomato. Here, we identified a group I WRKY transcription factor, SlWRKY3, involved in thermotolerance in tomato. First, SlWRKY3 was induced and upregulated under heat stress. Accordingly, overexpression of SlWRKY3 led to an increase, whereas knock-out of SlWRKY3 resulted in decreased tolerance to heat stress. Overexpression of SlWRKY3 accumulated less reactive oxygen species (ROS), whereas knock-out of SlWRKY3 accumulated more ROS under heat stress. This indicated that SlWRKY3 positively regulates heat stress in tomato. In addition, SlWRKY3 activated the expression of a range of abiotic stress-responsive genes involved in ROS scavenging, such as a SlGRXS1 gene cluster. Further analysis showed that SlWRKY3 can bind to the promoters of the SlGRXS1 gene cluster and activate their expression. Collectively, these results imply that SlWRKY3 is a positive regulator of thermotolerance through direct binding to the promoters of the SlGRXS1 gene cluster and activating their expression and ROS scavenging.

Photosynthesis is one the most important chemical reaction in plants, and it is the ultimate energy source of any living organisms. The light and dark reactions are two essential phases of photosynthesis. Light reaction harvests light energy to synthesize ATP and NADPH through an electron transport chain, and as well as giving out O2; dark reaction fixes CO2 into six carbon sugars by utilizing NADPH and energy from ATP. Subsequently, plants convert optical energy into chemical energy for maintaining growth and development through absorbing light energy. Here, firstly, we highlighted the biological importance of photosynthesis, and hormones and metabolites, photosynthetic and regulating enzymes, and signaling components that collectively regulate photosynthesis in tomato. Next, we reviewed the advances in tomato photosynthesis, including two aspects of genetic basis and genetic improvement. Numerous genes regulating tomato photosynthesis are gradually uncovered, and the interaction network among those genes remains to be constructed. Finally, the photosynthesis occurring in fruit of tomato and the relationship between photosynthesis in leaf and fruit were discussed. Leaves and fruits are photosynthate sources and sinks of tomato respectively, and interaction between photosynthesis in leaf and fruit exists. Additionally, future perspectives that needs to be addressed on tomato photosynthesis were proposed.

Domestication and improvement are important processes that generate the variation in genome and phonotypes underlying crop improvement.Unfortunately,during selection for certain attributes,other valuable traits may be inadvertently discarded.One example is the decline in fruit soluble solids content(SSC)during tomato breeding.Several genetic loci for SSC have been identified,but few reports on the underlying mechanisms are available.In this study we performed a genome-wide association study(GWAS)for SSC of the red-ripe fruits in a population consisting of 481 tomato accessions with large natural variations and found a new quantitative trait locus,STP1,encoding a sugar transporter protein.The causal variation of STP1,a 21-bp InDel located in the promoter region 1124 bp upstream of the start codon,alters its expression.STP1 Insertion accessions with an 21-bp insertion have higher SSC than STP1Deletion accessions with the 21-bp deletion.Knockout of STP1 in TS-23 with high SSC using CRISPR/Cas9 greatly decreased SSC in fruits.In vivo and in vitro assays demonstrated that ZAT10-LIKE,a zinc finger protein transcription factor(ZFP TF),can specifically bind to the promoter of STP1Insertion to enhance STP1 expression,but not to the promoter of STP1Deletion,leading to lower fruit SSC in modern tomatoes.Diversity analysis revealed that STP1 was selected during tomato improvement.Taking these results together,we identified a naturally occurring causal variation underlying SSC in tomato,and a new role for ZFP TFs in regulating sugar transporters.The findings enrich our understanding of tomato evolution and domestication,and provide a genetic basis for genome design for improving fruit taste.

Tomato (Solanum lycopersicum) is widely cultivated and is one of the most important vegetable crops in the world, with great economic significance [...]

Malic acid (MA) is an important flavor acid in fruits and acts as a mediator in a series of metabolic pathways. It is important to understand the factors affecting MA metabolism for fruit flavor improvement and to understand MA-mediated biological processes. However, the metabolic accumulation of MA is controlled by complex heredity and environmental factors, making it difficult to predict and regulate the metabolism of MA. In this study, we carried out a genome-wide association study (GWAS) on MA using eight milestone models with two-environment repeats. A series of associated SNP variations were identified from the GWAS, and 15 high-confidence annotated genes were further predicted based on linkage disequilibrium and lead SNPs. The transcriptome data of candidate genes were explored within different tomato organs as well as various fruit tissues, and suggested specific expression patterns in fruit pericarp. Based on the genetic parameters of population differentiation and SNP distribution, tomato MA content has been more influenced by domestication sweeps and less affected by improvement sweeps in the long-term history of tomato breeding. In addition, genotype x environment interaction might contribute to the difference in domestication phenotypic data under different environments. This study provides new genetic insights into how tomato changed its MA content during breeding and makes available function-based markers for breeding by marker-assisted selection.

Flowering time is of great agricultural importance and the timing and extent of flowering usually determines yield and availability of flowers, fruits and seeds. Identification of genes determining flowering has important practical applications for tomato breeding. Here we demonstrate the roles of the FANTASTIC FOUR (FAF) gene family in regulating tomato flowering time. In this plant-specific gene family, SlFAF1/2a shows a constitutive expression pattern during the transition of the shoot apical meristem (SAM) from vegetative to reproductive growth and significantly influences flowering time. Overexpressing SlFAF1/2a causes earlier flowering compared with the transformations of other genes in the FAF family. SlFAF1/2c also positively regulates tomato flowering, although to a lesser extent. The other members of the SlFAF gene family, SlFAF1/2b, SlFAF3/4a and SlFAF3/4b, are negative regulators of tomato flowering and faf1/2b, faf3/4a and faf3/4b single mutants all display early flowering. We generated a series of early flowering mutants using the CRISPR/Cas9 editing system, and the faf1/2b faf3/4a faf3/4b triple mutant flowering earliest compared with other mutants. More importantly, these mutants show no adverse effect on yield. Our results have uncovered the role of the FAF gene family in regulating tomato flowering time and generated early flowering germplasms for molecular breeding.

BRs (Brassinosteroids) regulate many essential pathways related to growth, cell elongation, cell expansion, plant architecture, and fruit development. The potential exogenous application of BR-derivatives has been proven to stimulate plant growth and development, including quality attributes of fruits, whereas its biosynthesis inhibition has shown the opposite effect. In this study, BR-insensitive tomato mutants were used to reveal the potential function of BR signaling in the regulation of fruit development to elaborate the regulatory mechanism of BR signaling in tomato fruits. The BR-signaling mutant exhibited a typical dwarf phenotype and reduced vegetative growth, fruit size, and weight. Microscopic and transcriptional evaluation of the abs1 mutant fruits implies that reduced cell size and number are responsible for the phenotypic variations. Additionally, we also found that the altered content of phytohormones, such as auxin, gibberellin, cytokinin, and ethylene levels, contributed to altered fruit development. Moreover, fruit growth and cell development-specific gene expression levels were downregulated in BR-insensitive plants; culminating in reduced cell size, cell number, and cell layers. These findings provide insight into physio-chemical changes during fruit development in response to BR-insensitivity.

In plants, chloroplasts are the sites at which photosynthesis occurs, and an increased abundance of chloroplasts increases the nutritional quality of plants and the resultant color of fruits. However, the molecular mechanisms underlying chlorophyll synthesis and chloroplast development in tomato fruits remain unknown. In this study, we isolated a chlorophyll-deficient mutant, reduced chlorophyll mutant 1 (rcm1), by ethylmethanesulfonate mutagenesis; this mutant produced yellowish fruits with altered chloroplast development. MutMap revealed that Solyc08g005010 is the causal gene underlying the rcm1 mutant phenotype. A single-nucleotide base substitution in the second exon of SlRCM1 results in premature termination of its translated protein. SlRCM1 encodes a chloroplast-targeted metalloendopeptidase that is orthologous to the BCM1 protein of Arabidopsis and the stay-green G protein of soybean (Glycine max L. Merr.). Notably, the yellowish phenotype of the lutescent1 mutant can be restored with the allele of SlRCM1 from wild-type tomato. In contrast, knockout of SlRCM1 by the CRISPR/Cas9 system in Alisa Craig yielded yellowish fruits at the mature green stage, as was the case for lutescent1. Amino acid sequence alignment and functional complementation assays showed that SlRCM1 is indeed Lutescent1. These findings provide new insights into the regulation of chloroplast development in tomato fruits.

Fruit development involves chloroplast development, carotenoid accumulation and fruit coloration. Although genetic regulation of fruit development has been extensively investigated, epigenetic regulation of fruit coloration remains largely unexplored. Here, we report a naturally occurring epigenetic regulation ofTAGL1, and its impact on chloroplast development and fruit coloration. We used a genome-wide association study in combination with map-based cloning to identify theGREEN STRIPE(GS) locus, a methylated isoform ofTAGL1regulating diversified chloroplast development and carotenoid accumulation. Nonuniform pigmentation of fruit produced byGSwas highly associated with methylation of theTAGL1promoter, which is linked to a SNP at SL2.50ch07_63842838. High degrees of methylation of theTAGL1promoter downregulated its expression, leading to green stripes. By contrast, low degrees of methylation led to light green stripes ings. RNA-seq and ChIP collectively showed that the expression of genes involved with Chl synthesis and chloroplast development were significantly upregulated in green stripes relative to light green stripes. Quantitative PCR and dual luciferase assay confirmed that TAGL1 downregulates expression ofSlMPEC,SlPsbQ, andSlCAB, and upregulates expression ofPSY1- genes which are associated with chloroplast development and carotenoid accumulation. Altogether, our findings regarding theGSlocus demonstrate that naturally occurring methylation ofTAGL1has diverse effects on plastid development in fruit.

Radish is a crucial vegetable crop of the Brassicaceae family with many varieties and large cultivated area in China. Radish is a cool season crop, and there are only a few heat tolerant radish varieties in practical production with little information concerning the related genes in response to heat stress. In this work, some physiological parameter changes of young leaves under short-term heat stress were detected. Furthermore, we acquired 1802 differentially expressed mRNAs (including encoding some heat shock proteins, heat shock factor and heat shock-related transcription factors), 169 differentially expressed lncRNAs and three differentially expressed circRNAs (novel_circ_0000265, novel_circ_0000325 and novel_circ_0000315) through strand-specific RNA sequencing technology. We also found 10 differentially expressed miRNAs (ath-miR159b-3p, athmiR159c, ath-miR398a-3p, athmiR398b-3p, ath-miR165a-5p, ath-miR169g-3p, novel_86, novel_107, novel_21 and ath-miR171b-3p) by small RNA sequencing technology. Through function prediction and enrichment analysis, our results suggested that the significantly possible pathways/complexes related to heat stress in radish leaves were circadian rhythm-plant, photosynthesis—antenna proteins, photosynthesis, carbon fixation in photosynthetic organisms, arginine and proline metabolism, oxidative phosphorylation, peroxisome and plant hormone signal transduction. Besides, we identified one lncRNA–miRNA–mRNAs combination responsive to heat stress. These results will be helpful for further illustration of molecular regulation networks of how radish responds to heat stress.