Identification of key gene networks controlling organic acid and sugar metabolism during watermelon fruit development by integrating metabolic phenotypes and gene expression profiles

Transcriptomic and metabolomic analyses reveal the importance of ethylene networks in mulberry fruit ripening

Mulberry (Morus alba L.) is a climacteric and highly perishable fruit. Ethylene has been considered to be an important trigger of fruit ripening process. However, the role of ethylene in the mulberry fruit ripening process remains unclear. In this study, we performed a comprehensive analysis of metabolomic and transcriptomic data of mulberry fruit and the physiological changes accompanying the fruit ripening process. Our study revealed that changes in the accumulation of specific metabolites at different stages of fruit development and ripening were closely correlated to transcriptional changes as well as underlying physiological changes and the development of taste biomolecules. The ripening of mulberry fruits was highly associated with the production of endogenous ethylene, and further application of exogenous ethylene assisted the ripening process. Transcriptomic analysis revealed that differential expression of diverse ripening-related genes was involved in sugar metabolism, anthocyanin biosynthesis, and cell wall modification pathways. Network analysis of transcriptomics and metabolomics data revealed that many transcription factors and ripening-related genes were involved, among which ethylene-responsive transcription factor 3 (MaERF3) plays a crucial role in the ripening process. The role of MaERF3 in ripening was experimentally proven in a transient overexpression assay in apples. Our study indicates that ethylene plays a vital role in modulating mulberry fruit ripening. The results provide a basis for guiding the genetic manipulation of mulberry fruits towards sustainable agricultural practices and improve post-harvest management, potentially enhancing the quality and shelf life of mulberry fruits for sustainable agriculture and forestry.

Chemical diversity, traditional uses, and bioactivities of Rosa roxburghii Tratt: A comprehensive review

Rosa roxburghii Tratt (RRT), known as chestnut rose, has been a subject of growing interest because of its diverse chemical composition and wide range of traditional uses. This comprehensive review aimed to thoroughly examine RRT, including its traditional applications, chemical diversity, and various bioactivities. The chemical profile of this plant is characterized by the presence of essential nutrients such as vitamin C (ascorbic acid), flavonoids, triterpenes, organic acids, tannins, phenolic compounds, polysaccharides, carotenoids, triterpenoids, volatile compounds, amino acids, and essential oils. These constituents contribute to the medicinal and nutritional value. Additionally, we explore the multifaceted bioactivities of RRT, including its potential as an anticancer agent, antioxidant, antiaging agent, antiatherogenic agent, hypoglycemic agent, immunoregulatory modulator, radioprotective agent, antimutagenic agent, digestive system regulator, anti-inflammatory agent, cardioprotective agent, and antibacterial agent, and its intriguing role in modulating the gut microbiota. Furthermore, we discuss the geographical distribution and genetic diversity of this plant species and shed light on its ecological significance. This comprehensive review provides a holistic understanding of RRT, bridges traditional knowledge with contemporary scientific research, and highlights its potential applications in medicine, nutrition, and pharmacology.

Improving grape fruit quality through soil conditioner: Insights from RNA-seq analysis of Cabernet Sauvignon roots

The application of fertilizers and soil quality are crucial for grape fruit quality. However, the molecular data linking different fertilizer (or soil conditioner [SC]) treatments with grape fruit quality is still lacking. In this study, we investigated three soil treatments, namely inorganic fertilizer (NPK, 343.5 kg/hm2 urea [N ≥ 46%]; 166.5 kg/hm2 P2O5 [P2O5 ≥ 64%]; 318 kg/hm2 K2O [K2O ≥ 50%]), organic fertilizer (Org, 9 t/hm2 [organic matter content ≥ 35%, N + P2O5 + K2O ≥ 13%]), and SC (SC, 3 t/hm2 [humic acid ≥ 38.5%; C, 56.1%; H, 3.7%; N, 1.5%; O, 38%; S, 0.6%]), on 4-year-old Cabernet Sauvignon grapevines. Compared with the NPK- and Org-treated groups, the SC significantly improved the levels of soluble solids, tannins, anthocyanins, and total phenols in the grape berries, which are important biochemical indicators that affect wine quality. Furthermore, we conducted RNA-seq analysis on the grapevine roots from each of the three treatments and used weighted gene co-expression network analysis to identify five hub genes that were associated with the biochemical indicators of the grape berries. Furthermore, we validated the expression levels of three hub genes (ERF, JP, and SF3B) and five selected genes related to anthocyanin biosynthesis (UFGT1, UFGT2, UFGT3, GST, and AT) by using quantitative reverse transcription-polymerase chain reaction. Compared to the NPK and Org treatment groups, the SC treatment resulted in a significant increase in the transcription levels of three hub genes as well as VvUFGT1, VvUFGT3, VvGST, and VvAT. These results suggest that the SC can improve grape fruit quality by altering gene transcription patterns in grapevine roots and further influence the biochemical indices of grape fruits, particularly anthocyanin content. This study reveals that the application of SC can serve as an important measure for enhancing vineyard SC and elevating grape quality.

Joint transcriptomic and metabolomic analysis provides new insights into drought resistance in watermelon (Citrullus lanatus)

Introduction

Watermelon is an annual vine of the family Cucurbitaceae. Watermelon plants produce a fruit that people love and have important nutritional and economic value. With global warming and deterioration of the ecological environment, abiotic stresses, including drought, have become important factors that impact the yield and quality of watermelon plants. Previous research on watermelon drought resistance has included analyzing homologous genes based on known drought-responsive genes and pathways in other species.

Methods

However, identifying key pathways and genes involved in watermelon drought resistance through high-throughput omics methods is particularly important. In this study, RNA-seq and metabolomic analysis were performed on watermelon plants at five time points (0 h, 1 h, 6 h, 12 h and 24 h) before and after drought stress.

Results

Transcriptomic analysis revealed 7829 differentially expressed genes (DEGs) at the five time points. The DEGs were grouped into five clusters using the k-means clustering algorithm. The functional category for each cluster was annotated based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database; different clusters were associated with different time points after stress. A total of 949 metabolites were divided into 10 categories, with lipids and lipid-like molecules accounting for the most metabolites. Differential expression analysis revealed 22 differentially regulated metabolites (DRMs) among the five time points. Through joint analysis of RNA-seq and metabolome data, the 6-h period was identified as the critical period for watermelon drought resistance, and the starch and sucrose metabolism, plant hormone signal transduction and photosynthesis pathways were identified as important regulatory pathways involved in watermelon drought resistance. In addition, 15 candidate genes associated with watermelon drought resistance were identified through joint RNA-seq and metabolome analysis combined with weighted correlation network analysis (WGCNA). Four of these genes encode transcription factors, including bHLH (Cla97C03G068160), MYB (Cla97C01G002440), HSP (Cla97C02G033390) and GRF (Cla97C02G042620), one key gene in the ABA pathway, SnRK2-4 (Cla97C10G186750), and the GP-2 gene (Cla97C05G105810), which is involved in the starch and sucrose metabolism pathway.

Discussion

In summary, our study provides a theoretical basis for elucidating the molecular mechanisms underlying drought resistance in watermelon plants and provides new genetic resources for the study of drought resistance in this crop.

Multi-omics analysis reveals key regulatory defense pathways and genes involved in salt tolerance of rose plants

Salinity stress causes serious damage to crops worldwide, limiting plant production. However, the metabolic and molecular mechanisms underlying the response to salt stress in rose (Rosa spp.) remain poorly studied. We therefore performed a multi-omics investigation of Rosa hybrida cv. Jardin de Granville (JDG) and Rosa damascena Mill. (DMS) under salt stress to determine the mechanisms underlying rose adaptability to salinity stress. Salt treatment of both JDG and DMS led to the buildup of reactive oxygen species (H2O2). Palisade tissue was more severely damaged in DMS than in JDG, while the relative electrolyte permeability was lower and the soluble protein content was higher in JDG than in DMS. Metabolome profiling revealed significant alterations in phenolic acid, lipids, and flavonoid metabolite levels in JDG and DMS under salt stress. Proteome analysis identified enrichment of flavone and flavonol pathways in JDG under salt stress. RNA sequencing showed that salt stress influenced primary metabolism in DMS, whereas it substantially affected secondary metabolism in JDG. Integrating these datasets revealed that the phenylpropane pathway, especially the flavonoid pathway, is strongly enhanced in rose under salt stress. Consistent with this, weighted gene coexpression network analysis (WGCNA) identified the key regulatory gene chalcone synthase 1 (CHS1), which is important in the phenylpropane pathway. Moreover, luciferase assays indicated that the bHLH74 transcription factor binds to the CHS1 promoter to block its transcription. These results clarify the role of the phenylpropane pathway, especially flavonoid and flavonol metabolism, in the response to salt stress in rose.

Prohexadione-calcium improves grape quality by regulating endogenous hormones, sugar and acid metabolism and related enzyme activities in grape berries

Prohexadione-Calcium (Pro-Ca) plays key roles in improving fruit quality and yield by regulating various aspects of plant growth. However, the effects of how Pro-Ca regulates the regulation of sugar and acid balance and its impact on the production of volatile aroma substances during fruit growth and development are poorly understood. In this study, the Pro-Ca solutions developed at concentrations of 200, 400, 600 and 800 mg·L-1 were sprayed on the entire "Chardonnay" grape tree 22, 42, 62 and 82 days after initial flowering. The values of endogenous hormones, sugar and acid content, enzyme activities and flavor content were then measured in grapes 45, 65, 85 and 105 days (ripeness stage) after the initial flowering. The results showed that Pro-Ca had significant effects on fruits during development, including reducing ABA content, increasing ZT, GA3 and IAA levels, promoting fruit ripening and enhancing enzymes, which are involved in sugar and acid synthesis. Consequently, these effects led to an increase in sugar and acid content in the berries. Particularly during the ripening phase, the application of 600 mg L-1 Pro-Ca resulted in an increase in soluble sugar content of 11.28% and a significant increase in citric acid and malic acid content of 97.80% and 68.86%, respectively. Additionally, Pro-Ca treatment enhanced both the variety and quantity of aroma compounds present in the berries, with the 600 mg·L-1 Pro-Ca treatment showcasing the most favorable impact on volatile aroma compounds in 'Chardonnay' grapes. The levels of aldehydes, esters, alcohols, phenols, acids, ketones, and terpenes were significantly higher under the 600 mg·L-1 Pro-Ca treatment compared to those of control with 51.46 - 423.85% increase. In conclusion, Pro-Ca can regulate the content of endogenous hormones and the activities of enzymes related to sugar and acid metabolism in fruit, thereby increasing the content of soluble sugar and organic acid in fruit and the diversity and concentration of fruit aroma substances. Among them, foliar spraying 600 mg · L-1 Pro-Ca has the best effect. In the future, we need to further understand the molecular mechanism of Pro-Ca in grape fruit to lay a solid foundation for quality improvement breeding.

Transcriptome Analysis Reveals Fruit Quality Formation in Actinidia eriantha Benth

Actinidia chinensis Planch. is a fruit tree originating from China that is abundant in the wild. Actinidia eriantha Benth. is a type of A. chinensis that has emerged in recent years. The shape of A. eriantha is an elongated oval, and the skin is covered with dense, non-shedding milk-white hairs. The mature fruit has flesh that is bright green in colour, and the fruit has a strong flavour and a grass-like smell. It is appreciated for its rich nutrient content and unique flavour. Vitamin C, sugar, and organic acids are key factors in the quality and flavour composition of A. eriantha but have not yet been systematically analysed. Therefore, we sequenced the transcriptome of A. eriantha at three developmental stages and labelled them S1, S2, and S3, and comparisons of S1 vs. S2, S1 vs. S3, and S2 vs. S3 revealed 1218, 4019, and 3759 upregulated differentially expressed genes and 1823, 3415, and 2226 downregulated differentially expressed genes, respectively. Furthermore, the upregulated differentially expressed genes included 213 core genes, and Gene Ontology enrichment analysis showed that they were enriched in hormones, sugars, organic acids, and many organic metabolic pathways. The downregulated differentially expressed genes included 207 core genes, which were enriched in the light signalling pathway. We further constructed the metabolic pathways of sugars, organic acids, and vitamin C in A. eriantha and identified the genes involved in vitamin C, sugar, and organic acid synthesis in A. eriantha fruits at different stages. During fruit development, the vitamin C content decreased, the carbohydrate compound content increased, and the organic acid content decreased. The gene expression patterns were closely related to the accumulation patterns of vitamin C, sugars, and organic acids in A. eriantha. The above results lay the foundation for the accumulation of vitamin C, sugars, and organic acids in A. eriantha and for understanding flavour formation in A. eriantha.

Effects of Vine Water Status on Malate Metabolism and γ-Aminobutyric Acid (GABA) Pathway-Related Amino Acids in Marselan (Vitis vinifera L.) Grape Berries

Malic acid is the predominant organic acid in grape berries, and its content is affected by abiotic factors such as temperature (fruit zone microclimate) and water (vine water status). The objectives of this study were to explore the potential mechanisms behind the effects of vine water status on the biosynthesis and degradation of berry malic acid and the potential downstream effects on berry metabolism. This study was conducted over two growing seasons in 2021 and 2022, comprising three watering regimes: no water stress (CK), light water stress (LWS), and moderate water stress (MWS). Compared to CK, a significantly higher level of malic acid was found in berries from the MWS treatment when the berry was still hard and green (E-L 33) in both years. However, water stress reduced the malic acid content at the ripe berry harvest (E-L 38) stage. The activities of NAD-malate dehydrogenase (NAD-MDH) and pyruvate kinase (PK) were enhanced by water stress. Except for the E-L 33 stage, the activity of phosphoenolpyruvate carboxylase (PEPC) was reduced by water stress. The highest phosphoenolpyruvate carboxykinase (PEPCK) activity was observed at the berry veraison (E-L 35) stage and coincided with the onset of a decrease in the malate content. Meanwhile, the expression of VvPEPCK was consistent with its enzyme activity. This study showed that water stress changed the content of some free amino acids (GABA, proline, leucine, aspartate, and glutamate), two of which (glutamate and GABA) are primary metabolites of the GABA pathway.

GIFTdb: a useful gene database for plant fruit traits improving

Fruit traits are critical determinants of plant fitness, resource diversity, productive and quality. Gene regulatory networks in plants play an essential role in determining fruit traits, such as fruit size, yield, firmness, aroma and other important features. Many research studies have focused on elucidating the associated signaling pathways and gene interaction mechanism to better utilize gene resources for regulating fruit traits. However, the availability of specific database of genes related to fruit traits for use by the plant research community remains limited. To address this limitation, we developed the Gene Improvements for Fruit Trait Database (GIFTdb, http://giftdb.agroda.cn). GIFTdb contains 35 365 genes, including 896 derived from the FR database 1.0, 305 derived from 30 882 articles from 2014 to 2021, 236 derived from the Universal Protein Resource (UniProt) database, and 33 928 identified through homology analysis. The database supports several aided analysis tools, including signal transduction pathways, gene ontology terms, protein-protein interactions, DNAWorks, Basic Local Alignment Search Tool (BLAST), and Protein Subcellular Localization Prediction (WoLF PSORT). To provide information about genes currently unsupported in GIFTdb, potential fruit trait-related genes can be searched based on homology with the supported genes. GIFTdb can provide valuable assistance in determining the function of fruit trait-related genes, such as MYB306-like, by conducting a straightforward search. We believe that GIFTdb will be a valuable resource for researchers working on gene function annotation and molecular breeding to improve fruit traits.

Main flavor compounds and molecular regulation mechanisms in fruits and vegetables

Fruits and vegetables (F&V) are an indispensable part of a healthy diet. The volatile and nonvolatile compounds present in F&V constitute unique flavor substances. This paper reviews the main flavor substances present in F&V, as well as the biosynthetic pathways and molecular regulation mechanisms of these compounds. A series of compounds introduced include aromatic substances, soluble sugars and organic acids, which constitute the key flavor substances of F&V. Esters, phenols, alcohols, amino acids and terpenes are the main volatile aromatic substances, and nonvolatile substances are represented by amino acids, fatty acids and carbohydrates; The combination of these ingredients is the cause of the sour, sweet, bitter, astringent and spicy taste of these foods. This provides a theoretical basis for the study of the interaction between volatile and nonvolatile substances in F&V, and also provides a research direction for the healthy development of food in the future.

Sugar composition and transcriptome analysis in developing 'Fengtang' plum (Prunus salicina Lindl.) reveal candidate genes regulating sugar accumulation

Sweetness is an important attribute of fruit quality, which directly affects consumers' preference for fresh fruit and is mostly determined by carbohydrate composition. 'Fengtang' plum (Prunus salicina Lindl.) is recognized for its high soluble sugar content, but the sugar composition and the molecular mechanisms underlying sugar overproduction are not fully understood. In this work, the sugar components were analyzed using gas chromatography-mass spectrometry combined with transcription profiles from RNA-sequencing and Quantitative Real-time PCR during fruit development. The target metabolic group showed that sucrose was the dominant sugar component in mature fruit, followed by glucose, fructose, and sorbitol. Based on the transcriptome data and qRT-PCR validation, we identified 12 key structural genes that significantly responded to corresponding component accumulation: sucrose synthase (PsSUS4), sucrose phosphate synthase (PsSPS2), neutral invertase (PsNINV1/3/4), phosphoglucomutase (PsPGM1), UTP-glucose-1-phosphate uridylyl transferase (PsUGP1/2), hexose kinase (PsHXK1/3), sugar transport protein (PsSTP1), and Sugars Will Eventually be Exported Transporter (PsSWEET4). In which PsSUS4 and PsSPS2, whose encoding proteins immediately catalyze sucrose synthesis, were selected to be silenced using the virus-induced gene silencing technology. Silencing of PsSUS4 or PsSPS2 resulted in decreased sucrose content by 27.6% and 8%, respectively, compared with the control, verifying their important roles in sucrose accumulation. Subsequently, sugar metabolism networks in this high-sugar plum were constructed with 12 key structural genes, 72 putative transcription factors, and 4 major sugar components. These results might facilitate a better understanding of the molecular mechanisms of sugar accumulation in 'Fengtang' plum and provide a framework for future fruit quality improvement.

Transcriptome and Metabolome Reveal Sugar and Organic Acid Accumulation in Rosa roxburghii Fruit

Sugars and organic acids significantly impact fruit sensory quality, but their accumulation patterns and regulatory mechanisms during the development of Rosa roxburghii fruit are still unclear. We utilized transcriptomics and metabolomics to investigate genes related to sugar and organic acid metabolism in Rosa roxburghii. Metabolomics data revealed that sucrose, glucose and fructose were the primary sugars, whereas citric acid and malic acid were the primary organic acids in Rosa roxburghii fruit. We constructed the metabolic pathways of major sugars and organic acids in Rosa roxburghii and identified five key genes involved in sugar and organic acid synthesis. In addition, we identified a module containing 132 transcription factors that was significantly associated with sucrose, citric acid and malic acid. Based on quantitative polymerase chain reaction (qPCR), we identified 13 transcription factors involved in sugar and organic acid metabolism, including the transcription factor RrANL2 and the sucrose synthase gene RrSUS3. Further yeast one-hybrid and dual luciferase assays showed that RrANL2 could bind to the promoter of RrSUS3 to increase its expression. These results provide new insights into the metabolism of sugars and organic acids in Rosa roxburghii fruit.

Formation of aroma characteristics driven by volatile components during long-term storage of An tea

The aim of this study was to reveal the molecular basis of aroma changes during storage of An tea (AT). The key volatile compounds in AT were screened using SPME-GC-MS and SPE-GC-MS analytical techniques in combination with odor activity value (OAV) and flavor dilution factor (FD). The results showed that with the increase of storage time the stale and woody aromas were revealed. Esters, acids and hydrocarbons are the main types of volatile compounds in AT, and their content accounts for 52.69 %-61.29 % of the total volatile compounds. The key volatile compounds with stale and woody aromas during AT storage were obtained by OAV value and FD value, namely ketoisophorone (flavor dilution factor, FD = 64), linalool oxide C (FD = 64), 1-octen-3-ol (OAV > 1, FD = 32), 1,2-dimethoxybenzene (FD = 16), naphthalene (OAV > 1, FD = 32), 3,4-dimethoxytoluene (FD = 16), and 1,2,3-trimethoxybenzene (FD = 8). Our research provides a scientific basis and insights for the improvement of quality during the storage of dark tea.

Transcriptome Analysis and VIGS Identification of Key Genes Regulating Citric Acid Metabolism in Citrus

Citrus (Citrus reticulata) is one of the world's most widely planted and highest-yielding fruit trees. Citrus fruits are rich in a variety of nutrients. The content of citric acid plays a decisive role in the flavor quality of the fruit. There is a high organic acid content in early-maturing and extra-precocious citrus varieties. Reducing the amount of organic acid after fruit ripening is significant to the citrus industry. In this study, we selected a low-acid variety, "DF4", and a high-acid variety, "WZ", as research materials. Through WGCNA analysis, two differentially expressed genes, citrate synthase (CS) and ATP citrate-pro-S-lyase (ACL), were screened out, which related to the changing citric acid. The two differentially expressed genes were preliminarily verified by constructing a virus-induced gene-silencing (VIGS) vector. The VIGS results showed that the citric acid content was negatively correlated with CS expression and positively correlated with ACL expression, while CS and ACL oppositely control citric acid and inversely regulate each other. These results provide a theoretical basis for promoting the breeding of early-maturing and low-acid citrus varieties.

OsTST1, a key tonoplast sugar transporter from source to sink, plays essential roles in affecting yields and height of rice (Oryza sativa L.)

MAIN CONCLUSION

OsTST1 affects yield and development and mediates sugar transportation of plants from source to sink in rice, which influences the accumulation of intermediate metabolites from tricarboxylic acid cycle indirectly. Tonoplast sugar transporters (TSTs) are essential for vacuolar sugar accumulation in plants. Carbohydrate transport across tonoplasts maintains the metabolic balance in plant cells, and carbohydrate distribution is crucial to plant growth and productivity. Large plant vacuoles store high concentrations of sugars to meet plant requirements for energy and other biological processes. The abundance of sugar transporter affects crop biomass and reproductive growth. However, it remains unclear whether the rice (Oryza sativa L.) sugar transport protein OsTST1 affects yield and development. In this study, we found that OsTST1 knockout mutants generated via CRISPR/Cas9 exhibited slower development, smaller seeds, and lower yield than wild type (WT) rice plants. Notably, plants overexpressing OsTST1 showed the opposite effects. Changes in rice leaves at 14 days after germination (DAG) and at 10 days after flowering (DAF) suggested that OsTST1 affected the accumulation of intermediate metabolites from the glycolytic pathway and the tricarboxylic acid (TCA) cycle. The modification of the sugar transport between cytosol and vacuole mediated by OsTST1 induces deregulation of several genes including transcription factors (TFs). In summary, no matter the location of sucrose and sink is, these preliminary results revealed that OsTST1 was important for sugar transport from source to sink tissues, thus affecting plant growth and development.

Genetic analysis of mixed models of fruit sugar-acid fractions in a cross between jujube (Ziziphus jujuba Mill.) and wild jujube (Z. acido jujuba)

Chinese jujube (Ziziphus jujuba Mill.), an economically significant species in the Rhamnaceae family, is a popular fruit tree in Asia. The sugar and acid concentrations in jujube are considerably higher than those in other plants. Due to the low kernel rate, it is extremely difficult to establish hybrid populations. Little is known about jujube evolution and domestication, particularly with regard to the role of the sugar and acid components of jujube. Therefore, we used cover net control as a hybridization technique for the cross-breeding of Ziziphus jujuba Mill and 'JMS2' and (Z. acido jujuba) 'Xing16' to obtain an F₁ population (179 hybrid progeny). The sugar and acid levels in the F₁ and parent fruit were determined by HPLC. The coefficient of variation ranged from 28.4 to 93.9%. The sucrose and quinic acid levels in the progeny were higher than those in the parents. The population showed continuous distributions with transgressive segregation on both sides. Analysis by the mixed major gene and polygene inheritance model was performed. It was found that glucose is controlled by one additive-dominant major gene and polygenes, malic acid is controlled by two additive-dominant major genes and polygenes, and oxalic acid and quinic acid are controlled by two additive-dominant-epistatic major genes and polygenes. The results of this study provide insights into the genetic predisposition and molecular mechanisms underlying the role of sugar acids in jujube fruit.

Targeted multi-platform metabolome analysis and enzyme activity analysis of kiwifruit during postharvest ripening

Kiwifruit is a climacteric fruit, in which the accumulation of flavor substances mainly occurs at the postharvest ripening stage. However, the dynamic changes in metabolite composition remain poorly understood. Here, targeted multi-platform metabolome analysis based on GC-MS and UPLC-MS/MS and enzyme activity analysis were performed at different postharvest ripening stages of kiwifruit. A total of 12 soluble sugars and 31 organic acids were identified. The main soluble sugars are sucrose, glucose and fructose, which exhibited similar variation tendencies along with the extension of ripening. The main organic acids are citric acid, quinic acid and malic acid, which showed different variation patterns. A total of 48 energy metabolites were identified, which were classified into two groups based on the content variation. The content of substances related to the respiratory metabolic pathway decreased gradually along with postharvest ripening, and there was obvious accumulation of downstream products such as amino acids at the late ripening stage. A total of 35 endogenous hormones were identified, among which seven cytokinins were highly accumulated at the later stage of softening. We further investigated the dynamic changes in the activities of 28 ripening-related enzymes. As a result, the activities of 13 enzymes were highly correlated with changes in starch, total pectin, and soluble sugars, and those of seven enzymes were closely associated with the change in firmness. In conclusion, this study comprehensively describes the dynamic changes in soluble sugars, organic acids, hormones, energy substances, and ripening-related enzyme activities during kiwifruit postharvest ripening, and provides a theoretical basis for the postharvest quality improvement of kiwifruit.

Combined Metabolome and Transcriptome Analysis Elucidates Sugar Accumulation in Wucai (Brassica campestris L.)

Wucai (Brassica campestris L.) is a leafy vegetable that originated in China, its soluble sugars accumulate significantly to improve taste quality during maturation, and it is widely accepted by consumers. In this study, we investigated the soluble sugar content at different developmental stages. Two periods including 34 days after planting (DAP) and 46 DAP, which represent the period prior to and after sugar accumulation, respectively, were selected for metabolomic and transcriptomic profiling. Differentially accumulated metabolites (DAMs) were mainly enriched in the pentose phosphate pathway, galactose metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, and fructose and mannose metabolism. By orthogonal projection to latent structures-discriminant s-plot (OPLS-DA S-plot) and MetaboAnalyst analyses, D-galactose and β-D-glucose were identified as the major components of sugar accumulation in wucai. Combined with the transcriptome, the pathway of sugar accumulation and the interact network between 26 DEGs and the two sugars were mapped. CWINV4, CEL1, BGLU16, and BraA03g023380.3C had positive correlations with the accumulation of sugar accumulation in wucai. The lower expression of BraA06g003260.3C, BraA08g002960.3C, BraA05g019040.3C, and BraA05g027230.3C promoted sugar accumulation during the ripening of wucai. These findings provide insights into the mechanisms underlying sugar accumulation during commodity maturity, providing a basis for the breeding of sugar-rich wucai cultivars.

Integrated untargeted metabolome, full-length sequencing, and transcriptome analyses reveal insights into the fruit quality at different harvest times of Chaenomeles speciosa

Chaenomeles speciosa fruit is a homologous medicine and food plant with a long history of multiple uses. It could be harvested near maturity and last for a long time. However, the optimal harvest strategy of Chaenomeles speciosa for various uses is currently unavailable. Here, untargeted metabolome at different harvest times during maturation was investigated for the first time, and 896 metabolites, including sugars, organic acids, amino acids, and phenylpropanoids, were identified. Optimal harvesting methods were proposed for different purposes. During the early maturation stages (before 105 days after full bloom), Ch. speciosa fruit could be harvested as Chinesemedicine. Whereas as snacks and food, Ch. speciosa fruit might be harvested at late maturity (after 120 days after full bloom). In addition, the overall network was revealed by integrating full-length Iso-seq and transcriptomics (RNA-seq) to investigate the association between quality-associated metabolites and Chaenomeles speciosa fruit gene expression during maturation. A few putative genes were captured via screening, dissecting and correlation analysis with the quality-associated metabolites (including d-glucose, catechin, gallocatechin, and succinic acid). Overall, in addition to providing a harvesting strategy for food and medicine, we also investigated the metabolism and gene expression pattern of Chaenomeles speciosa fruit during maturation. This comprehensive data and analyses laid the foundation for further investigating potential regulatory mechanisms during harvest and provided a new possibility for its development and utilization.

Vegetable biology and breeding in the genomics era

Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize, thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.

Exploring the Substrate Specificity of a Sugar Transporter with Biosensors and Cheminformatics

Sugars will eventually be exported transporters (SWEETs) are conserved sugar transporters that play crucial roles in plant physiology and biotechnology. The genomes of flowering plants typically encode about 20 SWEET paralogs that can be classified into four clades. Clades I, II, and IV have been reported to favor hexoses, while clade III SWEETs prefer sucrose. However, the molecular features of substrates required for recognition by members of this family have not been investigated in detail. Here, we show that SweetTrac1, a previously reported biosensor constructed from the Clade I Arabidopsis thaliana SWEET1, can provide insight into the structural requirements for substrate recognition. The biosensor translates substrate binding to the transporter into a change in fluorescence, and its application in a small-molecule screen combined with cheminformatics uncovered 12 new sugars and their derivatives capable of eliciting a response. Furthermore, we confirmed that the wild-type transporter mediates cellular uptake of three of these species, including the diabetes drugs 1-deoxynojirimycin and voglibose. Our results show that SWEETs can recognize different furanoses, pyranoses, and acyclic sugars, illustrating the potential of combining biosensors and computational techniques to uncover the basis of substrate specificity.

Identification of Key Genes Induced by Different Potassium Levels Provides Insight into the Formation of Fruit Quality in Grapes

Inadequate potassium (K) availability is a common abiotic stress that limits the growth and quality of fruit trees. Few studies have investigated the physiological and molecular responses of grapes at different potassium levels. In this study, an integrated approach was developed for grapevines grown at four different potassium fertilization levels [0 (K0-CK), 150 (K150), 300 (K300), and 450 (K450) g/plant] in combination with metabolite measurements and transcript analysis. The results showed that different K levels affected the accumulation of sugars and anthocyanins in the fruit. At 78 days after bloom (DAB), the K150, K300, and K450 treatments increased soluble sugar content by 37.39%, 31.10% and 32.59%, respectively, and anthocyanin content by 49.78%, 24.10%, and 13.06%, respectively, compared to K0. Weighted gene co-expression network analysis (WGCNA) of DEGs identified a network of 11 grapevines involved. During fruit development, potassium application promoted the accumulation of anthocyanins and sugars in fruit by regulating the up-regulation of GST, AT, UFGT and SPS, HT, PK gene expressions. These results suggest that potassium deficiency inhibits anthocyanin and sugar metabolism. In addition, it promotes the up-regulation of KUP expression, which is the main cause of K accumulation in fruits. Together, our data revealed the molecular mechanism in response to different K levels during fruit quality formation and provides the scientific foundation for the improvement of fruit quality by adding K fertilizer.

FaGAPC2/FaPKc2.2 and FaPEPCK reveal differential citric acid metabolism regulation in late development of strawberry fruit

Citric acid is the primary organic acid that affects the taste of strawberry fruit. Glycolysis supplies key substrates for the tricarboxylic acid cycle (TCA cycle). However, little is known about the regulatory mechanisms of glycolytic genes on citric acid metabolism in strawberry fruits. In this study, the citric acid content of strawberry fruit displayed a trend of rising and decreasing from the initial red stage to the full red stage and then dark red stage. Thus, a difference in citric acid metabolic regulation was suspected during strawberry fruit development. In addition, overexpression of either cytoplasm glyceraldehyde-3-phosphate dehydrogenase (FxaC_14g13400, namely FaGAPC2) or pyruvate kinase (FxaC_15g00080, namely FaPKc2.2) inhibited strawberry fruit ripening and the accumulation of citric acid, leading to a range of maturity stages from partial red to full red stage. The combined transcriptome and metabolome analysis revealed that overexpression of FaGAPC2 and FaPKc2.2 significantly suppressed the expression of phosphoenolpyruvate carboxykinase (FxaC_1g21491, namely FaPEPCK) but enhanced the content of glutamine and aspartic acid. Meanwhile, the activities of PEPCK and glutamate decarboxylase (GAD) were inhibited, but the activities of glutamine synthase (GS) were increased in FaGAPC2/FaPKc2.2-overexpressed fruit. Further, functional verification demonstrated that overexpression of FaPEPCK can promote strawberry fruit ripening, resulting in a range of maturity stage from full red to dark red stage, while the citric acid synthase (CS) activities and citric acid content were significantly decreased. Overall, this study revealed that FaGAPC2/FaPKc2.2 and FaPEPCK perform an important role in reducing citric acid content in strawberry fruit, and FaGAPC2/FaPKc2.2 mainly by promoting the GS degradation pathway and FaPEPCK mainly by inhibiting the CS synthesis pathway.

Association mapping for protein, total soluble sugars, starch, amylose and chlorophyll content in rice

BACKGROUND

Protein, starch, amylose and total soluble sugars are basic metabolites of seed that influence the eating, cooking and nutritional qualities of rice. Chlorophyll is responsible for the absorption and utilization of the light energy influencing photosynthetic efficiency in rice plant. Mapping of these traits are very important for detection of more number of robust markers for improvement of these traits through molecular breeding approaches.

RESULTS

A representative panel population was developed by including 120 germplasm lines from the initial shortlisted 274 lines for mapping of the six biochemical traits using 136 microsatellite markers through association mapping. A wide genetic variation was detected for the traits, total protein, starch, amylose, total soluble sugars, chlorophyll a, and chlorophyll b content in the population. Specific allele frequency, gene diversity, informative markers and other diversity parameters obtained from the population indicated the effectiveness of utilization of the population and markers for mapping of these traits. The fixation indices values estimated from the population indicated the existence of linkage disequilibrium for the six traits. The population genetic structure at K = 3 showed correspondence with majority of the members in each group for the six traits. The reported QTL, qProt1, qPC6.2, and qPC8.2 for protein content; qTSS8.1 for total soluble sugar; qAC1.2 for amylose content; qCH2 and qSLCHH for chlorophyll a (Chl. a) while qChl5D for chlorophyll b (Chl. b) were validated in this population. The QTL controlling total protein content qPC1.2; qTSS7.1, qTSS8.2 and qTSS12.1 for total soluble sugars; qSC2.1, qSC2.2, qSC6.1 and qSC11.1 for starch content; qAC11.1, qAC11.2 and qAC11.3 for amylose content; qChla8.1 for Chl. a content and qChlb7.1 and qChlb8.1 for Chl. b identified by both Generalized Linear Model and Mixed Linear Model were detected as novel QTL. The chromosomal regions on chromosome 8 at 234 cM for grain protein content and total soluble sugars and at 363 cM for Chl. a and Chl. b along with the position at 48 cM on chromosome 11 for starch and amylose content are genetic hot spots for these traits.

CONCLUSION

The validated, co-localized and the novel QTL detected in this study will be useful for improvement of protein, starch, amylose, total soluble sugars and chlorophyll content in rice.

Transcriptome profiling provides insights into leaf color changes in two Acer palmatum genotypes

BACKGROUND

Ornamental trees with seasonally-dependent leaf color, such as Acer palmatum, have gained worldwide popularity. Leaf color is a main determinant of the ornamental and economic value of A. palmatum. However, the molecular mechanisms responsible for leaf color changes remain unclear.

RESULTS

We chose A. palmatum cultivars with yellow ('Jinling Huangfeng') and red ('Jinling Danfeng') leaves as the ideal material for studying the complex metabolic networks responsible for variations in leaf coloration. The 24 libraries obtained from four different time points in the growth of 'Jinling Huangfeng' and 'Jinling Danfeng' was subjected to Illumina high-throughput sequencing. We observed that the difference in cyanidin and delphinidin content is the primary reason behind the varying coloration of the leaves. Transcriptomic analyses revealed 225,684 unigenes, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes (DEGs) confirmed that they were involved in 'anthocyanin biosynthesis.' Eighteen structural genes involved in anthocyanin biosynthesis were thought to be related to anthocyanin accumulation, whereas 46 MYBs, 33 basic helix-loop-helixs (bHLHs), and 29 WD40s were presumed to be involved in regulating anthocyanin biosynthesis. Based on weighted gene co-expression network analysis (WGCNA), three candidate genes (ApRHOMBOID, ApMAPK, and ApUNE10) were screened in the significant association module with a correlation coefficient (r²) of 0.86.

CONCLUSION

In this study, the leaf color changes of two A. palmatum genotypes were analyzed. These findings provide novel insights into variations in leaf coloration and suggest pathways for targeted genetic improvements in A. palmatum.

Genome-wide association study provides genetic insights into natural variation in watermelon rind thickness and single fruit weight

Rind thickness and fruit weight are agronomic traits closely related to quality and yield, which have attracted much attention from consumers and breeders. However, the genetic mechanism of these two traits is still not well understood in natural populations. In this study, rind thickness and single fruit weight in 151 watermelon accessions were determined in 2019 and 2020, and genome-wide association analysis was performed by integrating phenotypic and genotype data. Abundant phenotypic variation was found in the test population, and the watermelon with thinner rind thickness tended to have smaller fruit weights. Five significant SNPs were closely associated with rind thickness on chromosome 2 by Genome-wide association study (GWAS), i.e., 32344170, 32321308, 32304738, 32328501, and 32311192. And there were 21 genes were annotated in the candidate interval, most notably, Cla97C02G044160 belonged to the MADS family, and part of the genes in this family played an important role in regulating organ size, further analysis of gene structure, gene expression level, and phylogenetic tree showed that Cla97C02G044160 was a candidate gene for regulating target traits. In conclusion, our study provides molecular insights into the natural variation of watermelon rind thickness and single fruit weight, meanwhile, providing data support for molecular marker-assisted breeding.

Seed Myco-priming improves crop yield and herbivory induced defenses in maize by coordinating antioxidants and Jasmonic acid pathway

BACKGROUND

Seed Myco-priming based on consortium of entomopathogenic fungi is very effective seed treatment against Ostrinia furnacalis herbivory. Maize regulates defense responses against herbivory by the production of defense-related enzymatic and non-enzymatic antioxidants, phytohormones, and their corresponding genes. Jasmonic acid (JA) plays a key role in plant-entomopathogenic fungi-herbivore interaction.

RESULTS

To understand how a consortium of the entomopathogenic fungi Beauveria bassiana and Trichoderma asperellum induce changes in the response of maize to herbivory and increase the crop yield, 2-year field experiment, antioxidant enzymes, leaf transcriptome, and phytohormone were performed. Fungal inoculation enhanced the production of antioxidant enzymes and JA signaling pathway more than the normal herbivory. The comparison between single inoculated, consortium inoculated, and non-inoculated plants resulted in distinct transcriptome profiles representing a considerable difference in expression of antioxidant- and JA- responsive genes identified through Weighted gene co-expression network analysis (WGCNA) and expression analysis, respectively. Seed priming with a consortium of B. bassiana and T. asperellum significantly enhanced the expression of genes involved in antioxidants production and JA biosynthesis cascade, with the highest expression recorded at 24-h post O. furnacalis larval infestation. They reduced the larval nutritional indices and survival up to 87% and enhancing crop yield and gross return up to 82-96% over the year 2018 and 2019.

CONCLUSION

From our results we suggest that a consortium of B. bassiana and T. asperellum can be used synergistically against O. furnacalis in maize under field condition and can mediate antioxidants- and JA- associated maize defense response by boosting up the expression of their responsive genes, thereby enhancing crop yield.

Active compound analysis of Ziziphus jujuba cv. Jinsixiaozao in different developmental stages using metabolomic and transcriptomic approaches

Jujube (Ziziphus jujuba Mill.) is a popular fruit with health benefits ascribed to its various metabolites. These metabolites determine the flavors and bioactivities of the fruit, as well as their desirability. However, the dynamics of the metabolite composition and the underlying gene expression that modulate the overall flavor and accumulation of active ingredients during fruit development remain largely unknown. Therefore, we conducted an integrated metabolomic and transcriptomic investigation covering various developmental stages in the jujube cultivar Z. jujuba cv. Jinsixiaozao, which is famous for its nutritional and bioactive properties. A total of 407 metabolites were detected by non-targeted metabolomics. Metabolite accumulation during different jujube developmental stages was examined. Most nucleotides and amino acids and their derivatives accumulated during development, with cAMP increasing notably during ripening. Triterpenes gradually accumulated and were maintained at high concentrations during ripening. Many flavonoids were maintained at relatively high levels in early development, but then rapidly decreased later. Transcriptomic and metabolomic analyses revealed that chalcone synthase (CHS), chalcone isomerase (CHI), flavonol synthase (FLS), and dihydroflavonol 4-reductase (DFR) were mainly responsible for regulating the accumulation of flavonoids. Therefore, the extensive downregulation of these genes was probably responsible for the decreases in flavonoid content during fruit ripening. This study provide an overview of changes of active components in 'Jinsixiaozao' during development and ripening. These findings enhance our understanding of flavor formation and will facilitate jujube breeding for improving both nutrition and function.

WGCNA analysis revealing molecular mechanism that bio-organic fertilizer improves pear fruit quality by increasing sucrose accumulation and reducing citric acid metabolism

It's been long known that the application of organic fertilizer (OF) and bio-organic fertilizer (BF) which containing beneficial microorganisms to pear trees can both significantly improve fruit quality and yield. In order to reveal the mechanism of BF and OF regulating fruit growth and quality in pear, the effects of BF and OF on the photosynthetic characteristics and the accumulation of major sugars and organic acids of the pear fruit were quantified compared with chemical fertilizer (CF). Additionally, the molecular mechanisms regulating pear fruit development and quality were studied through transcriptome analysis. The three treatments were conducted based on the same amounts of nitrogen supply. The results showed that compared with CF, BF and OF treatments increased the fruit yield, and also significantly improved the photosynthesis efficiency in pear. BF and OF both significantly increased the sucrose content but significantly decreased the fructose and glucose content within the pear fruit. The amount of malic acid was significantly higher in OF treatment. Compared with CF and OF, BF significantly increased the sugar-acid ratio and thus improved the fruit quality. Transcriptome analysis and weighted correlation network analysis (WGCNA) revealed that the sugar metabolism of fruits applied with the BF was enhanced compared with those applied with CF or OF. More specifically, the expression of SDH (Sorbitol dehydrogenase) was higher in BF, which converts sorbitol into fructose. For both of the OF and BF, the transcript abundance of sugar transporter genes was significantly increased, such as SOT (Sorbitol transporter), SUT14 (Sugar transport 14), UDP-GLUT4 (UDP-glucose transporter 4), UDP-SUT (UDP-sugar transporter), SUC4 (Sucrose transport 4), SUT7 (Sugar transporter 7), SWEET10 and SWEET15 (Bidirectional sugar transporter), which ensures sugar transportation. The genes involved in organic acid metabolism showed decreased transcripts abundance in both BF and OF treatments, such as VAP (Vesicle-associated protein) and cyACO (Cytosolic aconitase), which reduce the conversion from succinate to citric acid, and decrease the conversion from citric acid to malic acid in the TCA cycle (Tricarboxylic Acid cycle) through Pept6 (Oligopeptide transporter). In conclusion, the application of BF and OF improved fruit quality by regulating the expression of sugar and organic acid metabolism-related genes and thus altering the sugar acid metabolism. Both BF and OF promote sucrose accumulation and citric acid degradation in fruits, which may be an important reason for improving pear fruit quality. The possible mechanism of bio-organic fertilizer to improve fruit quality was discussed.

Transcriptome analysis of Harumi tangor fruits: Insights into interstock-mediated fruit quality

Harumi tangor fruit with Ponkan as an interstock contains significantly higher levels of total soluble solids compared to Harumi tangor fruit cv.with no interstock. Transcriptome analysis of two graft combinations (Harumi/Hongjv (HP) and cv. cv.Harumi/Ponkan/Hongjv (HPP)) was conducted to identify the genes related to use of the Ponkan interstock. Soluble sugars and organic acids were also measured in the two graft combinations. The results showed that the contents of sucrose, glucose, and fructose were higher in the fruits of HPP than in those of HP; additionally, the titratable acid levels were lower in grafts with interstocks than in grafts without interstocks. Transcriptome analysis of HPP and HP citrus revealed that the interstock regulated auxin and ethylene signals, sugar and energy metabolism, and cell wall metabolism. Trend and Venn analyses suggested that genes related to carbohydrate-, energy-, and hormone-metabolic activities were more abundant in HPP plants than in HP plants during different periods. Moreover, weighted gene co-expression network analysis demonstrated that carbohydrates, hormones, cell wall, and transcription factors may be critical for interstock-mediated citrus fruit development and ripening. The contents of ethylene, auxin, cytokinin, transcription factors, starch, sucrose, glucose, fructose, and total sugar in HPP plants differed considerably than those in HP fruits. Interstocks may help to regulate the early ripening and quality of citrus fruit through the above-mentioned pathways. These findings provide information on the effects of interstock on plant growth and development.

A time-course transcriptome analysis of wax gourd fruit development reveals predominant genes regulating taste and nutrition

Wax gourd, which belongs to Cucurbitaceae, is an excellent plant resource with the concomitant function of both medicine and foodstuff. Its unique taste and rich nutrition are deeply accepted by consumers. However, the main flavor and nutrients are still unclear, which restricts the quality breeding process of wax gourd. Here, we discovered that monosaccharides, malic acid and citrulline affect the flavor and nutrition of wax gourd and clarified the dynamic accumulation process of these metabolites. To gain insights into the underlying predominant genes regulating accumulation of these metabolites, we performed a time-course transcriptome analysis using RNA-sequencing analysis and compared the expression of screened genes among twenty-four germplasms with different metabolites levels. In addition, the expression abundance among the homologous genes were also analyzed. Finally, a total of 8 genes related to sugar [AGA2 (Bhi03G001926), SUS (Bhi12G001032)], malic acid [MDH (Bhi12G001426, Bhi01G000427), PEPC (Bhi12G000721, Bhi09G002867), ME (Bhi01G002616)] and citrulline [ASS (Bhi02G000401)], respectively were determined. In summary, understanding the core genes influencing taste or nutrition will provide a theoretical basis for fruit quality improvement in wax gourd.

Metabolomic and transcriptomic analyses reveal the mechanism of sweet-acidic taste formation during pineapple fruit development

Pineapple (Ananas comosus L.) is one of the most valuable subtropical fruit crop in the world. The sweet-acidic taste of the pineapple fruits is a major contributor to the characteristic of fruit quality, but its formation mechanism remains elusive. Here, targeted metabolomic and transcriptomic analyses were performed during the fruit developmental stages in two pineapple cultivars ("Comte de Paris" and "MD-2") to gain a global view of the metabolism and transport pathways involved in sugar and organic acid accumulation. Assessment of the levels of different sugar and acid components during fruit development revealed that the predominant sugar and organic acid in mature fruits of both cultivars was sucrose and citric acid, respectively. Weighted gene coexpression network analysis of metabolic phenotypes and gene expression profiling enabled the identification of 21 genes associated with sucrose accumulation and 19 genes associated with citric acid accumulation. The coordinated interaction of the 21 genes correlated with sucrose irreversible hydrolysis, resynthesis, and transport could be responsible for sucrose accumulation in pineapple fruit. In addition, citric acid accumulation might be controlled by the coordinated interaction of the pyruvate-to-acetyl-CoA-to-citrate pathway, gamma-aminobutyric acid pathway, and tonoplast proton pumps in pineapple. These results provide deep insights into the metabolic regulation of sweetness and acidity in pineapple.

Identification of key genes controlling L-ascorbic acid during Jujube (Ziziphus jujuba Mill.) fruit development by integrating transcriptome and metabolome analysis

Chinese jujube (Ziziphus jujuba) is a vital economic tree native to China. Jujube fruit with abundant L-Ascorbic Acid (AsA) is an ideal material for studying the mechanism of AsA biosynthesis and metabolism. However, the key transcription factors regulating AsA anabolism in jujube have not been reported. Here, we used jujube variety "Mazao" as the experimental material, conducted an integrative analysis of transcriptome and metabolome to investigate changes in differential genes and metabolites, and find the key genes regulating AsA during jujube fruit growth. The results showed that AsA was mostly synthesized in the young stage and enlargement stage, ZjMDHAR gene takes an important part in the AsA recycling. Three gene networks/modules were highly correlated with AsA, among them, three genes were identified as candidates controlling AsA, including ZjERF17 (LOC107404975), ZjbZIP9 (LOC107406320), and ZjGBF4 (LOC107421670). These results provide new directions and insights for further study on the regulation mechanism of AsA in jujube.

Transcriptomic and Metabolomic Analysis of Quality Changes during Sweet Cherry Fruit Development and Mining of Related Genes

Sweet cherries are economically important fruit trees, and their quality changes during development need to be determined. The mechanism of fruit quality changes in sweet cherries were determined by analyzing sweet cherry fruits at 12 developmental stages. The results showed that the soluble sugar, anthocyanin content, and hormones of sweet cherries all changed drastically during the color transition. Therefore, the fruits at the beginning of color conversion, at the end of color conversion, and at the ripening state were selected for the comprehensive analysis of their metabolome and transcriptome. Different sugars, such as D-glucose, sucrose, and trehalose, were identified in the metabolome. Dihydroquercetin, delphinidin-3-glucoside, cyanidin-3-rutincoside, and other flavonoid species were also identified. D-glucose and cyanidin-3-rutinoside were among the most important components of sweet cherry soluble sugars and anthocyanins, respectively. The transcriptional analysis identified key structural genes and nine transcription factors involved in the ABA, sugar, organic acid, and anthocyanin synthesis pathways, with the following specific regulatory patterns. NAC71, WRKY57, and WRKY3 regulate fruit sugar accumulation mainly by acting on INV, SPS, and SUS. MYC2 is involved in the synthesis of anthocyanin precursors by activating PAL and C4H, whereas TCP7 mainly regulates CHI and F3H. WRKY3, NAC71, and WRKY57 have important positive regulatory significance on anthocyanin accumulation, mainly by activating the expression of DFR, ANS, and 3GT.

Fine Mapping and Functional Analysis of Major Regulatory Genes of Soluble Solids Content in Wax Gourd (Benincasa hispida)

Soluble solids content (SSC) is an important quality trait of wax gourd, but reports about its regulatory genes are scarce. In this study, the SSC regulatory gene BhSSC2.1 in wax gourd was mined via quantitative trait locus (QTL) mapping based on high-density genetic mapping containing 12 linkage groups (LG) and bulked segregant analysis (BSA)-seq. QTL mapping and BSA-seq revealed for the first time that the SSC QTL (107.658–108.176 cM) of wax gourd was on Chr2 (LG2). The interpretable phenotypic variation rate and maximum LOD were 16.033% and 6.454, respectively. The QTL interval contained 13 genes. Real-time fluorescence quantitative expression analysis, functional annotation, and sequence analysis suggested that Bch02G016960, named BhSSC2.1, was a candidate regulatory gene of the SSC in wax gourd. Functional annotation of this gene showed that it codes for a NADP-dependent malic enzyme. According to BhSSC2.1 sequence variation, an InDel marker was developed for molecular marker-assisted breeding of wax gourd. This study will lay the foundation for future studies regarding breeding and understanding genetic mechanisms of wax gourd.

Chemotaxonomic Identification of Key Taste and Nutritional Components in 'Shushanggan Apricot' Fruits by Widely Targeted Metabolomics

The chemotypic and the content variation in taste substances and nutrients in ‘Shushanggan apricot’ fruits were detected by UPLC-MS/MS. A total of 592 compounds were identified, of which sucrose contributed mainly to the sweet taste and malic acid and citric acid were important organic acids affecting sweet–sour taste. γ-linolenic acid, α-linolenic acid and linoleic acid were the dominant free fatty acids, and neochlorogenic acid and chlorogenic acid were the predominant phenolic acids. Fruit taste was positively correlated with sucrose and negatively correlated with malic acid and citric acid. The differential metabolites were significantly enriched in the biosynthesis of amino acids and 2-oxocarboxylic acid metabolism pathways, regulating the sugar and organic acid biosynthesis. Taste and nutrient differences could be revealed by variations in composition and abundance of carbohydrates, organic acids and amino acids. The purpose of this study was to provide a comprehensive chemical characterization of taste and nutrient compounds in ‘Shushanggan apricot’ fruits.

Metabolome and Transcriptome Analysis Reveals the Transcriptional Regulatory Mechanism of Triterpenoid Saponin Biosynthesis in Soapberry (Sapindus mukorossi Gaertn.)

Soapberry (Sapindus mukorossi Gaertn.) pericarps are rich in valuable bioactive triterpenoid saponins. However, the saponin content dynamics and the molecular regulatory network of saponin biosynthesis in soapberry pericarps remain largely unclear. Here, we performed combined metabolite profiling and transcriptome analysis to identify saponin accumulation kinetic patterns, investigate gene networks, and characterize key candidate genes and transcription factors (TFs) involved in saponin biosynthesis in soapberry pericarps. A total of 54 saponins were tentatively identified, including 25 that were differentially accumulated. Furthermore, 49 genes putatively involved in sapogenin backbone biosynthesis and some candidate genes assumed to be responsible for the backbone modification, including 41 cytochrome P450s and 45 glycosyltransferases, were identified. Saponin-specific clusters/modules were identified by Mfuzz clustering and weighted gene coexpression network analysis, and one TF-gene regulatory network underlying saponin biosynthesis was proposed. The results of yeast one-hybrid assay and electrophoretic mobility shift assay suggested that SmbHLH2, SmTCP4, and SmWRKY27 may play important roles in the triterpenoid saponin biosynthesis by directly regulating the transcription of SmCYP71D-3 in the soapberry pericarp. Overall, these findings provide valuable information for understanding the molecular regulatory mechanism of saponin biosynthesis, enriching the gene resources, and guiding further research on triterpenoid saponin accumulation in soapberry pericarps.

Metabolomics Combined with Transcriptomics Analysis Revealed the Amino Acids, Phenolic Acids, and Flavonol Derivatives Biosynthesis Network in Developing Rosa roxburghii Fruit

Rosa roxburghii Tratt. is a specific fruit with high nutritional value and antioxidative activities. However, the key metabolites and their biosynthesis are still unknown. Herein, a main cultivated variety, ‘Guinong 5’ (Rr5), was chosen to analyze the metabolomics of the three developmental stages of R. roxburghii fruit by liquid chromatography–tandem mass spectrometry (LC-MS/MS). A total of 533 metabolites were identified, of which 339 were significantly altered. Total phenols, flavonoids, and amino acids were significantly correlated to at least one in vitro antioxidant activity. The conjoint Kyoto Encyclopedia of Genes and Genomes (KEGG) co-enrichment analysis of metabolome and transcriptome was focused on amino acid, phenylpropanoid, and flavonoid biosynthesis pathways. The amino acid, phenolic acid, and flavonol biosynthesis networks were constructed with 32 structural genes, 48 RrMYBs, and 23 metabolites. Of these, six RrMYBs correlated to 9–15 metabolites in the network were selected to detect the gene expression in six different R. roxburghii genotypes fruits. Subsequently, 21 key metabolites were identified in the in vitro antioxidant activities in the fruits at various developmental stages or in fruits of different R. roxburghii genotypes. We found that four key RrMYBs were related to the significantly varied amino acids, phenolic acids, and flavonol derivatives in the network during fruit development and the key metabolites in the in vitro antioxidative activities in the fruits of six R. roxburghii genotypes. This finding provided novel insights into the flavonoid, polyphenol, and amino acid synthesis in R. roxburghii.

Identification of Key Gene Networks Controlling Soluble Sugar and Organic Acid Metabolism During Oriental Melon Fruit Development by Integrated Analysis of Metabolic and Transcriptomic Analyses

Oriental melon (Cucumis melo var. acidulus) is one of the most economically important fruit crops worldwide. To elucidate the molecular basis related to soluble sugar and organic acid metabolism in the fruits of two oriental melon cultivars with different sweetness, we performed integrated metabolomic and transcriptomic analyses of the fruits of 'Tianbao' (A) with high sweetness and 'Xiaocuigua' (B) with low sweetness at different ripening stages. The high accumulation of sucrose, D-glucose, D-(+)-raffinose, and the relatively lower citric acid and malic acid might contribute to the sweet taste of A. By screening the differentially expressed genes (DEGs) and correlation analysis of the DEGs and differentially accumulated metabolites, we deduced that the B cultivar might promote the conversion of glucose and fructose into intermediate compounds for downstream processes such as glycolysis. The tricarboxylic acid (TCA) cycle might also be enhanced compared to A, thus resulting in the differential accumulation of soluble sugars and organic acids, ultimately causing the taste difference between the two oriental melon cultivars. Our finding provides important information for further exploring the metabolic mechanisms of soluble sugars and organic acids in oriental melon.

PpybZIP43 contributes to sucrose synthesis in pear fruits by activating PpySPS3 expression and interacts with PpySTOP1

Sucrose is an important factor affecting sweetness and flavor in pear fruits, but the molecular mechanism of sucrose synthesis regulation is relatively unknown. Here, we characterized a transcription factor gene from pear (Pyrus pyrifolia Nakai cv. "Hosui") fruits, PpybZIP43, and found that the transient overexpression of PpybZIP43 in pear fruits significantly increased the sucrose content and the relative expression level of sucrose phosphate synthase genes (PpySPS3 and PpySPS8). Subcellular localization analysis in tobacco leaves showed that PpybZIP43 was localized in the nucleus. Yeast one-hybrid, electrophoretic mobility shift assay (EMSA), and dual-luciferase reporter assays indicated that PpybZIP43 was able to activate the expression of PpySPS3 by binding specifically to the G-box (CACGTG) element in the promoter. The protein-protein interaction assays using yeast two-hybrid, bimolecular fluorescence complementation (BiFC), firefly luciferase complementation imaging (LCI), and glutathione S-transferase (GST) pull-down demonstrated that PpybZIP43 could directly interact with PpySTOP1 to form a transcription complex. This study is helpful for understanding the molecular basis of sucrose synthesis and accumulation in pear fruits and provides candidate genes for breeding.

Quantitative Transcriptomic and Proteomic Analysis of Fruit Development and Ripening in Watermelon (Citrullus lanatus)

Fruit ripening is a highly complicated process, which is modulated by phytohormones, signal regulators and environmental factors playing in an intricate network that regulates ripening-related genes expression. Although transcriptomics is an effective tool to predict protein levels, protein abundances are also extensively affected by post-transcriptional and post-translational regulations. Here, we used RNA sequencing (RNA-seq) and tandem mass tag (TMT)-based quantitative proteomics to study the comprehensive mRNA and protein expression changes during fruit development and ripening in watermelon, a non-climacteric fruit. A total of 6,226 proteins were quantified, and the large number of quantitative proteins is comparable to proteomic studies in model organisms such as Oryza sativa L. and Arabidopsis. Base on our proteome methodology, integrative analysis of the transcriptome and proteome showed that the mRNA and protein levels were poorly correlated, and the correlation coefficients decreased during fruit ripening. Proteomic results showed that proteins involved in alternative splicing and the ubiquitin proteasome pathway were dynamically expressed during ripening. Furthermore, the spliceosome and proteasome were significantly enriched by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, suggesting that post-transcriptional and post-translational mechanisms might play important roles in regulation of fruit ripening-associated genes expression, which might account for the poor correlation between mRNAs and proteins during fruit ripening. Our comprehensive transcriptomic and proteomic data offer a valuable resource for watermelon research, and provide new insights into the molecular mechanisms underlying the complex regulatory networks of fruit ripening.

Genetic Analysis of Fruit Quality Traits in Sweet Watermelon (Citrullus lanatus var. lanatus): A Review

Fruit quality traits of sweet watermelon (Citrullus lanatus var. lanatus) are crucial for new product development and commercialization. Sweet watermelon fruit quality traits are affected by the compositions of phytochemical compounds, phytohormones, and fruit flesh firmness which are affected by genes, the growing environment and their interaction. These compositions determine fruit ripening, eating quality, and postharvest shelf-life. Knowledge of the genetic profile and analyses of quality traits in watermelon is vital to develop improved cultivars with enhanced nutritional compositions, consumer-preferred traits, and extended storage life. This review aims to present the opportunities and progress made on the genetic analysis of fruit quality traits in watermelon as a guide for quality breeding based on economic and end-user attributes. The first section of the review highlights the genetic mechanisms involved in the biosynthesis of phytochemical compounds (i.e., sugars, carotenoids, amino acids, organic acids, and volatile compounds), phytohormones (i.e., ethylene and abscisic acid) and fruit flesh structural components (i.e., cellulose, hemicellulose, and pectin) elicited during watermelon fruit development and ripening. The second section pinpoints the progress on the development of molecular markers and quantitative trait loci (QTL) analysis for phytochemical compounds, phytohormones and fruit quality attributes. The review presents gene-editing technology and innovations associated with fruit quality traits for selection and accelerated cultivar development. Finally, the paper discussed gene actions conditioning fruit ripening in citron watermelon (C. lanatus var. citroides [L. H. Bailey] Mansf. ex Greb.) as reference genetic resources to guide current and future breeding. Information presented in this review is useful for watermelon variety design, product profiling and development to serve the diverse value chains of the crop.

Integrative analysis of transcriptomic and metabolomic profiles reveals new insights into the molecular foundation of fruit quality formation in Citrullus lanatus (Thunb.) Matsum. & Nakai

In this study, an integrated transcriptome and metabolome analysis was used to explore the molecular foundation of fruit quality in two parent lines of Citrullus lanatus with distinct flesh characteristics, including ‘14-1’ (sweet, red, and soft) and ‘W600’ (bitter, light yellow, and firm), as well as the corresponding F1 population (bitter, light yellow, and firm). Numerous differentially expressed genes (DEGs) were identified in the fruit samples: 3,766 DEGs for ‘14-1’ vs. ‘W600’, 2,767 for ‘14-1’ vs. F1, and 1,178 for F1 vs. ‘W600’ at the transition stage; and 4,221 for ‘14-1’ vs. ‘W600’, 2,447 for ‘14-1’ vs. F1, and 446 for F1 vs. ‘W600’ at the maturity stage. Weighted gene co-expression network analysis (WGCNA) revealed that a gene module including 1,111 DEGs was closely associated with flesh taste and color, and another gene module including 1,575 DEGs contributed significantly to flesh texture. The metabolomic results showed that there were 447 differential metabolites (DMs) for ‘14-1’ vs. ‘W600’ fruits, 394 for ‘14-1’ vs. F1, and 298 for F1 vs. ‘W600’ at the maturity stage. Combining WGNCA and metabolomic results, several DEGs and DMs were further identified as hub players in fruit quality formation: six DEGs with four DMs for flesh sweetness; six DEGs with 13 DMs for bitterness; nine DEGs with 10 DMs for flesh color; and nine DEGs with four DMs for flesh texture. Altogether, these observations not only expand our knowledge of the molecular basis of fruit quality in watermelon, but also provide potential targets for future watermelon improvement.

Metabolic Profiling of Sugars and Organic Acids, and Expression Analyses of Metabolism-Associated Genes in Two Yellow-Peel Pitaya Species

Sugar and organic acids are important factors determining pitaya fruit quality. However, changes in sugars and acids, and expressions of metabolism-associated genes during fruit maturation of yellow-peel pitayas are not well-documented. In this study, metabolic and expression analyses in pulps of different fruit developmental stages of ‘Wucihuanglong’ (‘WCHL’, Hylocereus undatus) and ‘Youcihuanglong’ pitaya (‘YCHL’, Hylocereus megalanthus) were used to explore the sugar and organic acid metabolic process. Total phenols and flavonoids were mainly accumulated at S1 in pitaya pulps. Ascorbic acid contents of ‘WCHL’ pitaya were higher than that of ‘YCHL’ pitaya during fruit maturation. Starch was mainly accumulated at early fruit development stages while soluble sugars were rich in late stages. Sucrose, fructose, and glucose were the main sugar components of ‘YCHL’ pitaya while glucose was dominant in ‘WCHL’ pitaya. Malic and citric acids were the main organic acids in ‘WCHL’ and ‘YCHL’ pitayas, respectively. Based on the transcriptome analyses, 118 genes involved in pitaya sugar and organic acid metabolism were obtained. Results from the correlation analyses between the expression profiling of candidate genes and the contents of sugar and organic acid showed that 51 genes had a significant correlation relationship and probably perform key role in pitaya sugar and organic acid metabolism processes. The finding of the present study provides new information for quality regulation of pitayas.

Identification of key gene networks controlling anthocyanin biosynthesis in peach flower

Flavonoids, particularly anthocyanin is the main pigment that determined the red color of peach flowers, and help the plant to attract pollinators, protect the reproductive organs of flower from photo-oxidative effects of light and various non-communicable diseases. Through weightage gene coexpression network analysis (WGCNA) we identified a network of 15 hub genes that co-expressed throughout peach flower development including 5 genes coded for the key enzymes (CHI, F3'H, DFR, LAR and UFGT) of flavonoid biosynthetic pathway and 1 gene Prupe.1G111700 identified as R2R3 family transcription factor MYB108. Over expression of PpMYB108 significantly increased anthocyanin biosynthesis in Tobacco flowers. Moreover, the expression correlation between PpMYB108 and PpDFR, suggests that PpMYB108 play the role of transcriptional activator for PpDFR. This was further supported by a 6 bp insertion of MYB biding site in the core promoter region of PpDFR in red flower. The positive interaction of PpMYB108 with PpDFR promoter from red flower was confirmed in yeast one hybrid assay. These findings may be helpful in peach breeding programs as well as in identifying anthocyanin related genes in other species.

Myco-Synergism Boosts Herbivory-Induced Maize Defense by Triggering Antioxidants and Phytohormone Signaling

BACKGROUND

Biocontrol strategies are the best possible and eco-friendly solution to develop resistance against O furnacalis and improve the maize yield. However, the knowledge about underlying molecular mechanisms, metabolic shifts, and hormonal signaling is limited.

METHODS

Here, we used an axenic and a consortium of entomopathogenic Beauveria bassiana OFDH1-5 and a pathogen-antagonistic Trichoderma asperellum GDFS1009 in maize and observed that consortium applications resulted in higher chlorophyll contents and antioxidants activities [superoxide dismutase (SOD), peroxidase (POD), proline, protease, and polyphenol oxidase (PPO)] with a decrease in O. furnacalis survival. We performed a comprehensive transcriptome and an untargeted metabolome profiling for the first time at a vegetative stage in fungal inoculated maize leaves at 0-, 12-, 24-, 48-, and 72-h post insect infestation.

RESULTS

The consortium of B. bassiana and T. asperellum leads to 80-95% of O. furnacalis mortality. A total of 13,156 differentially expressed genes were used for weighted gene coexpression network analysis. We identified the six significant modules containing thirteen candidate genes [protein kinase (GRMZM2G025459), acyl-CoA dehydrogenase (GRMZM5G864319), thioredoxin gene (GRMZM2G091481), glutathione S-transferase (GRMZM2G116273), patatin-like phospholipase gene (GRMZM2G154523), cytochrome P450 (GRMZM2G139874), protease inhibitor (GRMZM2G004466), (AC233926.1_FG002), chitinase (GRMZM2G453805), defensin (GRMZM2G392863), peroxidase (GRMZM2G144153), GDSL- like lipase (AC212068.4_FG005), and Beta-glucosidase (GRMZM2G031660)], which are not previously reported that are highly correlated with Jasmonic acid - Ethylene (JA-ET) signaling pathway and antioxidants. We detected a total of 130 negative and 491 positive metabolomic features using a ultrahigh-performance liquid chromatography ion trap time-of-flight mass spectrometry (UHPLC-QTOF-MS). Intramodular significance and real time-quantitative polymerase chain reaction (RT-qPCR) expressions showed that these genes are the true candidate genes. Consortium treated maize had higher jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) levels.

CONCLUSION

Our results provide insights into the genetics, biochemicals, and metabolic diversity and are useful for future biocontrol strategies against ACB attacks.

Hormonal interactions underlying parthenocarpic fruit formation in horticultural crops

In some horticultural crops, such as Cucurbitaceae, Solanaceae, and Rosaceae species, fruit set and development can occur without the fertilization of ovules, a process known as parthenocarpy. Parthenocarpy is an important agricultural trait that can not only mitigate fruit yield losses caused by environmental stresses but can also induce the development of seedless fruit, which is a desirable trait for consumers. In the present review, the induction of parthenocarpic fruit by the application of hormones such as auxins (2,4 dichlorophenoxyacetic acid; naphthaleneacetic acid), cytokinins (forchlorfenuron; 6-benzylaminopurine), gibberellic acids, and brassinosteroids is first presented. Then, the molecular mechanisms of parthenocarpic fruit formation, mainly related to plant hormones, are presented. Auxins, gibberellic acids, and cytokinins are categorized as primary players in initiating fruit set. Other hormones, such as ethylene, brassinosteroids, and melatonin, also participate in parthenocarpic fruit formation. Additionally, synergistic and antagonistic crosstalk between these hormones is crucial for deciding the fate of fruit set. Finally, we highlight knowledge gaps and suggest future directions of research on parthenocarpic fruit formation in horticultural crops.

Spatial and Temporal Transcriptomic Heredity and Asymmetry in an Artificially Constructed Allotetraploid Wheat (AADD)

Polyploidy, or whole-genome duplication (WGD), often induces dramatic changes in gene expression due to "transcriptome shock. " However, questions remain about how allopolyploidy (the merging of multiple nuclear genomes in the same nucleus) affects gene expression within and across multiple tissues and developmental stages during the initial foundation of allopolyploid plants. Here, we systematically investigated the immediate effect of allopolyploidy on gene expression variation in an artificial allopolyploidy system consisting of a constructed allotetraploid wheat (AADD genome, accession AT2) and its diploid progenitors Triticum urartu and Aegilops tauschii. We performed comprehensive RNA sequencing of 81 samples from different genotypes, tissues, and developmental stages. First, we found that intrinsic interspecific differences between the diploid parents played a major role in establishing the expression architecture of the allopolyploid. Nonetheless, allopolyploidy per se also induced dramatic and asymmetric patterns of differential gene expression between the subgenomes, and genes from the D subgenome exhibited a more drastic response. Second, analysis of homoeolog expression bias (HEB) revealed that the D subgenome exhibited significant expression bias and that de novo-generated HEB was attributed mainly to asymmetrical differential gene expression. Homoeolog-specific expression (HSE) analyses showed that the cis-only regulatory pattern was predominant in AT2, reflecting significant divergence between the parents. Co-expression network analysis revealed that homoeolog expression connectivity (HEC) was significantly correlated with sequence divergence in cis elements between subgenomes. Interestingly, allopolyploidy-induced reconstruction of network modules was also associated with different HSE patterns. Finally, a transcriptome atlas of spike development demonstrated that the phenotypic similarity of AT2 to T. urartu may be attributed to the combination of relatively stable expression of A-subgenome genes and drastic downregulation of their D-subgenome homoeologs. These findings provide a broad, multidimensional characterization of allopolyploidy-induced transcriptomic responses and suggest that allopolyploidy can have immediate and complex regulatory effects on the expression of nuclear genes.

Integrative analyses of metabolome and transcriptome reveals metabolomic variations and candidate genes involved in sweet cherry (Prunus avium L.) fruit quality during development and ripening

Sweet cherry (Prunus avium L.), one of the most appreciated and most important commercial temperate fruits, has high sensory quality and nutritional value. Investigating its metabolic variations provides valuable information on the formation of fruit quality. In this study, widely targeted LC-MS/MS based metabolomics was used to identify and quantify metabolic changes during 'Black Pearl' sweet cherry development and ripening. A total of 263 significant differentially expressed metabolites (DEMs) were detected during the four fruit-development stages. Significant differences were observed in the composition and content of compounds in the four stages of cherry development, especially sugars, organic acids, and flavonoids. Moreover, transcriptome analysis provided a molecular basis for metabolic variations during fruit development. A total of 6724 significant differentially expressed genes (DEGs) were identified. Further correlation analysis of major DEMs and DEGs showed that 19 key DEGs were involved in sugar metabolism, 23 key DEGs in organic acid metabolism, and 13 key DEGs in flavonoid metabolism. The upregulated genes involved in the flavonoid pathway probably play an important role in regulating the rapid increase of anthocyanin content during fruit development. These comprehensive analysis data provide a better understanding to improve fruit quality traits based on molecular and metabolic levels.

Identification of the Carbohydrate and Organic Acid Metabolism Genes Responsible for Brix in Tomato Fruit by Transcriptome and Metabolome Analysis

Background

Sugar and organic acids not only contribute to the formation of soluble solids (Brix) but also are an essential factor affecting the overall flavor intensity. However, the possible metabolic targets and molecular synthesis mechanisms remain to be further clarified.

Methods

UHPLC-HRMS (ultrahigh-performance liquid chromatography and high-resolution mass spectrometry) combined with comparative transcriptome analysis were performed in fruits at green ripe (S1), turning-color (S2), and red ripe (S3) stages of two tomato genotypes TM-1 (Solanum galapagense L., LA0436) and TM-38 (S. lycopersicum L. cultivar M82, LA3475) that vary in fruit Brix.

Results

The fruit Brix of TM-1 was nearly twice that of TM-38 at S3. Nevertheless, TM-1 accumulated 1.84- and 2.77-fold the L-malic acid and citric acid in red ripe fruit (S3) compared with TM-38, respectively. D-glucose and D-fructose in TM-1 and TM-38 fruits tended to be similar at S3. Concomitantly, the sugar/organic acid ratio of TM-38 fruits were 23. 08-, 4. 38-, and 2.59-fold higher than that of TM-1 fruits at S1, S2, and S3, respectively. Among starch and sucrose (carbohydrate, CHO) metabolism (ko00500) genes, SUS (Solyc07g042550.3) and BAM (Solyc08g077530.3) were positively (r = 0.885–0.931) correlated with the sugar/organic acid ratio. Besides, INV (Solyc09g010080.3 and Solyc09g010090.5.1), AAM (Solyc04g082090.3), 4-α-GTase (Solyc02g020980.2.1), BGL2 (Solyc06g073750.4, Solyc06g073760.3, and Solyc01g081170.3), TPS (Solyc01g005210.2 and Solyc07g006500.3), and TPP (Solyc08g079060.4) were negatively (r = −0.823 to −0.918) correlated with the sugar/organic acid ratio. The organic acid (TCA cycle) metabolism (ko00020) gene ALMT (Solyc01g096140.3) was also negatively (r = −0.905) correlated with the sugar/organic acid ratio.

Conclusion

Citric acid may play a more dominant role in the sugar/organic acid ratio of the tomato fruit, and the contribution of both L-malic acid and citric acid to the fruit Brix was much greater than that of D-glucose and D-fructose. Genes involved in CHO and TCA metabolism, which have a significant correlation with the sugar/organic acid ratio were considered to be the contributing factors of fruit Brix.