Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin C content in tomato fruit

Wheat derived glucuronokinase as a potential target for regulating ascorbic acid and phytic acid content with increased root length under drought and ABA stresses in Arabidopsis thaliana

Glucuronokinase (GlcAK) converts glucuronic acid into glucuronic acid-1-phosphate, which is then converted into UDP-glucuronic acid (UDP-GlcA) via myo-inositol oxygenase (MIOX) pathway. UDP-GlcA acts as a precursor in the synthesis of nucleotide-sugar moieties forming cell wall biomass. GlcAK being present at the bifurcation point between UDP-GlcA and ascorbic acid (AsA) biosyntheses, makes it necessary to study its role in plants. In this study, the three homoeologs of GlcAK gene from hexaploid wheat were overexpressed in Arabidopsis thaliana. The GlcAK overexpressing transgenic lines showed decreased contents of AsA and phytic acid (PA) as compared to control plants. Root length and seed germination analyses under abiotic stress (drought and abscisic acid) conditions revealed enhanced root length in transgenic lines as compared to control plants. These results indicate that the MIOX pathway might be contributing towards AsA biosynthesis as evident by the decreased AsA content in the GlcAK overexpressing transgenic Arabidopsis thaliana plants. Findings of the present study will enhance the understanding of the involvement of GlcAK gene in MIOX pathway and subsequent physiological effects in plants.

Genome-Wide Analysis of Ascorbic Acid Metabolism Related Genes in Fragaria × ananassa and Its Expression Pattern Analysis in Strawberry Fruits

Ascorbic acid (AsA) is an important antioxidant for scavenging reactive oxygen species and it is essential for human health. Strawberry (Fragaria × ananassa) fruits are rich in AsA. In recent years, strawberry has been regarded as a model for non-climacteric fruit ripening. However, in contrast to climacteric fruits, such as tomato, the regulatory mechanism of AsA accumulation in strawberry fruits remains largely unknown. In this study, we first identified 125 AsA metabolism-related genes from the cultivated strawberry "Camarosa" genome. The expression pattern analysis using an available RNA-seq data showed that the AsA biosynthetic-related genes in the D-mannose/L-galactose pathway were downregulated remarkably during fruit ripening which was opposite to the increasing AsA content in fruits. The D-galacturonate reductase gene (GalUR) in the D-Galacturonic acid pathway was extremely upregulated in strawberry receptacles during fruit ripening. The FaGalUR gene above belongs to the aldo-keto reductases (AKR) superfamily and has been proposed to participate in AsA biosynthesis in strawberry fruits. To explore whether there are other genes in the AKR superfamily involved in regulating AsA accumulation during strawberry fruit ripening, we further implemented a genome-wide analysis of the AKR superfamily using the octoploid strawberry genome. A total of 80 FaAKR genes were identified from the genome and divided into 20 subgroups based on phylogenetic analysis. These FaAKR genes were unevenly distributed on 23 chromosomes. Among them, nine genes showed increased expression in receptacles as the fruit ripened, and notably, FaAKR23 was the most dramatically upregulated FaAKR gene in receptacles. Compared with fruits at green stage, its expression level increased by 142-fold at red stage. The qRT-PCR results supported that the expression of FaAKR23 was increased significantly during fruit ripening. In particular, the FaAKR23 was the only FaAKR gene that was significantly upregulated by abscisic acid (ABA) and suppressed by nordihydroguaiaretic acid (NDGA, an ABA biosynthesis blocker), indicating FaAKR23 might play important roles in ABA-mediated strawberry fruit ripening. In a word, our study provides useful information on the AsA metabolism during strawberry fruit ripening and will help understand the mechanism of AsA accumulation in strawberry fruits.

Development of a Genome-Edited Tomato With High Ascorbate Content During Later Stage of Fruit Ripening Through Mutation of SlAPX4

Ascorbate is an essential antioxidant substance for humans. Due to the lack of ascorbate biosynthetic enzyme, a human must intake ascorbate from the food source. Tomato is one of the most widely consumed fruits, thus elevation of ascorbate content in tomato fruits will improve their nutritional value. Here we characterized Solanum lycopersicum ASCORBATE PEROXIDASE 4 (SlAPX4) as a gene specifically induced during fruit ripening. In tomatoes, ascorbate accumulates in the yellow stage of fruits, then decreases during later stages of fruit ripening. To investigate whether SlAPX is involved in the decrease of ascorbate, the expression of SlAPXs was analyzed during fruit maturation. Among nine SlAPXs, SlAPX4 is the only gene whose expression was induced during fruit ripening. Mutation of SlAPX4 by the CRISPR/Cas9 system increased ascorbate content in ripened tomato fruits, while ascorbate content in leaves was not significantly changed by mutation of SlAPX4. Phenotype analysis revealed that mutation of SlAPX4 did not induce an adverse effect on the growth of tomato plants. Collectively, we suggest that SlAPX4 mediates a decrease of ascorbate content during the later stage of fruit ripening, and mutation of SlAPX4 can be used for the development of genome-edited tomatoes with elevated ascorbate content in fruits.

Regulation of Vitamin C Accumulation for Improved Tomato Fruit Quality and Alleviation of Abiotic Stress

Ascorbic acid (AsA) is an essential multifaceted phytonutrient for both the human diet and plant growth. Optimum levels of AsA accumulation combined with balanced redox homeostasis are required for normal plant development and defense response to adverse environmental stimuli. Notwithstanding its moderate AsA levels, tomatoes constitute a good source of vitamin C in the human diet. Therefore, the enhancement of AsA levels in tomato fruit attracts considerable attention, not only to improve its nutritional value but also to stimulate stress tolerance. Genetic regulation of AsA concentrations in plants can be achieved through the fine-tuning of biosynthetic, recycling, and transport mechanisms; it is also linked to changes in the whole fruit metabolism. Emerging evidence suggests that tomato synthesizes AsA mainly through the l-galactose pathway, but alternative pathways through d-galacturonate or myo-inositol, or seemingly unrelated transcription and regulatory factors, can be also relevant in certain developmental stages or in response to abiotic factors. Considering the recent advances in our understanding of AsA regulation in model and other non-model species, this review attempts to link the current consensus with novel technologies to provide a comprehensive strategy for AsA enhancement in tomatoes, without any detrimental effect on plant growth or fruit development.

The Multiple Roles of Ascorbate in the Abiotic Stress Response of Plants: Antioxidant, Cofactor, and Regulator

Ascorbate (ASC) plays a critical role in plant stress response. The antioxidant role of ASC has been well-studied, but there are still several confusing questions about the function of ASC in plant abiotic stress response. ASC can scavenge reactive oxygen species (ROS) and should be helpful for plant stress tolerance. But in some cases, increasing ASC content impairs plant abiotic stress tolerance, whereas, inhibiting ASC synthesis or regeneration enhances plant stress tolerance. This confusing phenomenon indicates that ASC may have multiple roles in plant abiotic stress response not just as an antioxidant, though many studies more or less ignored other roles of ASC in plant. In fact, ACS also can act as the cofactor of some enzymes, which are involved in the synthesis, metabolism, and modification of a variety of substances, which has important effects on plant stress response. In addition, ASC can monitor and effectively regulate cell redox status. Therefore, we believe that ASC has atleast triple roles in plant abiotic stress response: as the antioxidant to scavenge accumulated ROS, as the cofactor to involve in plant metabolism, or as the regulator to coordinate the actions of various signal pathways under abiotic stress. The role of ASC in plant abiotic stress response is important and complex. The detail role of ASC in plant abiotic stress response should be analyzed according to specific physiological process in specific organ. In this review, we discuss the versatile roles of ASC in the response of plants to abiotic stresses.

Plant growth-regulating molecules as thermoprotectants: functional relevance and prospects for improving heat tolerance in food crops

Among various abiotic stresses, heat stress is one of the most damaging, threatening plant productivity and survival all over the world. Warmer temperatures due to climatic anomalies above optimum growing temperatures have detrimental impacts on crop yield potential as well as plant distribution patterns. Heat stress affects overall plant metabolism in terms of physiology, biochemistry, and gene expression. Membrane damage, protein degradation, enzyme inactivation, and the accumulation of reactive oxygen species are some of the harmful effects of heat stress that cause injury to various cellular compartments. Although plants are equipped with various defense strategies to counteract these adversities, their defensive means are not sufficient to defend against the ever-rising temperatures. Hence, substantial yield losses have been observed in all crop species under heat stress. Here, we describe the involvement of various plant growth-regulators (PGRs) (hormones, polyamines, osmoprotectants, antioxidants, and other signaling molecules) in thermotolerance, through diverse cellular mechanisms that protect cells under heat stress. Several studies involving the exogenous application of PGRs to heat-stressed plants have demonstrated their role in imparting tolerance, suggesting the strong potential of these molecules in improving the performance of food crops grown under high temperature.

Production, Signaling, and Scavenging Mechanisms of Reactive Oxygen Species in Fruit-Pathogen Interactions

Reactive oxygen species (ROS) play a dual role in fruit–pathogen interaction, which largely depends on their different levels in cells. Fruit recognition of a pathogen immediately triggers an oxidative burst that is considered an integral part of the fruit defense response. ROS are also necessary for the virulence of pathogenic fungi. However, the accumulation of ROS in cells causes molecular damage and finally leads to cell death. In this review, on the basis of data regarding ROS production and the scavenging systems determining ROS homeostasis, we focus on the role of ROS in fruit defense reactions against pathogens and in fungi pathogenicity during fruit–pathogen interaction.

Genome-wide association analysis identifies a natural variation in basic helix-loop-helix transcription factor regulating ascorbate biosynthesis via D-mannose/L-galactose pathway in tomato

Tomato (Solanum lycopersicum) is one of the highest-value vegetable crops worldwide. Understanding the genetic regulation of primary metabolite levels can inform efforts aimed toward improving the nutrition of commercial tomato cultivars, while maintaining key traits such as yield and stress tolerance. We identified 388 suggestive association loci (including 126 significant loci) for 92 metabolic traits including nutrition and flavor-related loci by genome-wide association study from 302 accessions in two different environments. Among them, an ascorbate quantitative trait locus TFA9 (TOMATOFRUITASCORBATEON CHROMOSOME9) co-localized with SlbHLH59, which promotes high ascorbate accumulation by directly binding to the promoter of structural genes involved in the D-mannose/L-galactose pathway. The causal mutation of TFA9 is an 8-bp InDel, named InDel_8, located in the promoter region of SlbHLH59 and spanned a 5’UTR Py-rich stretch motif affecting its expression. Phylogenetic analysis revealed that differentially expressed SlbHLH59 alleles were selected during tomato domestication. Our results provide a dramatic illustration of how ascorbate biosynthesis can be regulated and was selected during the domestication of tomato. Furthermore, the findings provide novel genetic insights into natural variation of metabolites in tomato fruit, and will promote efficient utilization of metabolite traits in tomato improvement.

Deciphering the diverse, interconnected plant metabolome can facilitate crop improvement. In this study, the use of a combination of multiple technologies has allowed us to obtain novel functional and genetic insights into our GWAS investigating variation in ascorbate accumulation in tomato. The InDel_8 in the promoter of SlbHLH59 was selected during tomato domestication and determines fruit ascorbate content by directly regulating the expression of structural genes involved in ascorbate biosynthesis in tomato fruit. The genes and polymorphisms responsible for the variations identified in this study lay the foundation for further comparative genomic studies and for improving nutrition quality in tomato and other fruit crops.

Vitamin C Content in Fruits: Biosynthesis and Regulation

Throughout evolution, a number of animals including humans have lost the ability to synthesize ascorbic acid (ascorbate, vitamin C), an essential molecule in the physiology of animals and plants. In addition to its main role as an antioxidant and cofactor in redox reactions, recent reports have shown an important role of ascorbate in the activation of epigenetic mechanisms controlling cell differentiation, dysregulation of which can lead to the development of certain types of cancer. Although fruits and vegetables constitute the main source of ascorbate in the human diet, rising its content has not been a major breeding goal, despite the large inter- and intraspecific variation in ascorbate content in fruit crops. Nowadays, there is an increasing interest to boost ascorbate content, not only to improve fruit quality but also to generate crops with elevated stress tolerance. Several attempts to increase ascorbate in fruits have achieved fairly good results but, in some cases, detrimental effects in fruit development also occur, likely due to the interaction between the biosynthesis of ascorbate and components of the cell wall. Plants synthesize ascorbate de novo mainly through the Smirnoff-Wheeler pathway, the dominant pathway in photosynthetic tissues. Two intermediates of the Smirnoff-Wheeler pathway, GDP-D-mannose and GDP-L-galactose, are also precursors of the non-cellulosic components of the plant cell wall. Therefore, a better understanding of ascorbate biosynthesis and regulation is essential for generation of improved fruits without developmental side effects. This is likely to involve a yet unknown tight regulation enabling plant growth and development, without impairing the cell redox state modulated by ascorbate pool. In certain fruits and developmental conditions, an alternative pathway from D-galacturonate might be also relevant. We here review the regulation of ascorbate synthesis, its close connection with the cell wall, as well as different strategies to increase its content in plants, with a special focus on fruits.

Genetic Control of Ascorbic Acid Biosynthesis and Recycling in Horticultural Crops

Ascorbic acid (AsA) is an essential compound present in almost all living organisms that has important functions in several aspects of plant growth and development, hormone signaling, as well as stress defense networks. In recent years, the genetic regulation of AsA metabolic pathways has received much attention due to its beneficial role in human diet. Despite the great variability within species, genotypes, tissues and developmental stages, AsA accumulation is considered to be controlled by the fine orchestration of net biosynthesis, recycling, degradation/oxidation, and/or intercellular and intracellular transport. To date, several structural genes from the AsA metabolic pathways and transcription factors are considered to significantly affect AsA in plant tissues, either at the level of activity, transcription or translation via feedback inhibition. Yet, all the emerging studies support the notion that the steps proceeding through GDP-_L-galactose phosphorylase and to a lesser extent through GDP-_D-mannose-3,5-epimerase are control points in governing AsA pool size in several species. In this mini review, we discuss the current consensus of the genetic regulation of AsA biosynthesis and recycling, with a focus on horticultural crops. The aspects of AsA degradation and transport are not discussed herein. Novel insights of how this multifaceted trait is regulated are critical to prioritize candidate genes for follow-up studies toward improving the nutritional value of fruits and vegetables.

Ascorbic Acid-A Potential Oxidant Scavenger and Its Role in Plant Development and Abiotic Stress Tolerance

Over-production of reactive oxygen species (ROS) in plants under stress conditions is a common phenomenon. Plants tend to counter this problem through their ability to synthesize ROS neutralizing substances including non-enzymatic and enzymatic antioxidants. In this context, ascorbic acid (AsA) is one of the universal non-enzymatic antioxidants having substantial potential of not only scavenging ROS, but also modulating a number of fundamental functions in plants both under stress and non-stress conditions. In the present review, the role of AsA, its biosynthesis, and cross-talk with different hormones have been discussed comprehensively. Furthermore, the possible involvement of AsA-hormone crosstalk in the regulation of several key physiological and biochemical processes like seed germination, photosynthesis, floral induction, fruit expansion, ROS regulation and senescence has also been described. A simplified and schematic AsA biosynthetic pathway has been drawn, which reflects key intermediates involved therein. This could pave the way for future research to elucidate the modulation of plant AsA biosynthesis and subsequent responses to environmental stresses. Apart from discussing the role of different ascorbate peroxidase isoforms, the comparative role of two key enzymes, ascorbate peroxidase (APX) and ascorbate oxidase (AO) involved in AsA metabolism in plant cell apoplast is also discussed particularly focusing on oxidative stress perception and amplification. Limited progress has been made so far in terms of developing transgenics which could over-produce AsA. The prospects of generation of transgenics overexpressing AsA related genes and exogenous application of AsA have been discussed at length in the review.

Plant Resistance Inducers against Pathogens in Solanaceae Species-From Molecular Mechanisms to Field Application

This review provides a current summary of plant resistance inducers (PRIs) that have been successfully used in the Solanaceae plant family to protect against pathogens by activating the plant's own defence. Solanaceous species include many important crops such as potato and tomato. We also present findings regarding the molecular processes after application of PRIs, even if the number of such studies still remains limited in this plant family. In general, there is a lack of patterns regarding the efficiency of induced resistance (IR) both between and within solanaceous species. In many cases, a hypersensitivity-like reaction needs to form in order for the PRI to be efficient. "-Omics" studies have already given insight in the complexity of responses, and can explain some of the differences seen in efficacy of PRIs between and within species as well as towards different pathogens. Finally, examples of field applications of PRIs for solanaceous crops are presented and discussed. We predict that PRIs will play a role in future plant protection strategies in Solanaceae crops if they are combined with other means of disease control in different spatial and temporal combinations.

Exploring New Alleles Involved in Tomato Fruit Quality in an Introgression Line Library of Solanum pimpinellifolium

We have studied a genomic library of introgression lines from the Solanum pimpinellifolium accession TO-937 into the genetic background of the "Moneymaker" cultivar in order to evaluate the accession's breeding potential. Overall, no deleterious phenotypes were observed, and the plants and fruits were phenotypically very similar to those of "Moneymaker," which confirms the feasibility of translating the current results into elite breeding programs. We identified chromosomal regions associated with traits that were both vegetative (plant vigor, trichome density) and fruit-related (morphology, organoleptic quality, color). A trichome-density locus was mapped on chromosome 10 that had not previously been associated with insect resistance, which indicates that the increment of trichomes by itself does not confer resistance. A large number of quantitative trait loci (QTLs) have been identified for fruit weight. Interestingly, fruit weight QTLs on chromosomes 1 and 10 showed a magnitude effect similar to that of QTLs previously defined as important in domestication and diversification. Low variability was observed for fruit-shape-related traits. We were, however, able to identify a QTL for shoulder height, although the effects were quite low, thus demonstrating the suitability of the current population for QTL detection. Regarding organoleptic traits, consistent QTLs were detected for soluble solid content (SSC). Interestingly, QTLs on chromosomes 2 and 9 increased SSC but did not affect fruit weight, making them quite promising for introduction in modern cultivars. Three ILs with introgressions on chromosomes 1, 2, and 10 increased the internal fruit color, making them candidates for increasing the color of modern cultivars. Comparing the QTL detection between this IL population and a recombinant inbred line population from the same cross, we found that QTL stability across generations depended on the trait, as it was very high for fruit weight but low for organoleptic traits. This difference in QTL stability may be due to a predominant additive gene action for QTLs involved in fruit weight, whereas epistatic and genetic background interactions are most likely important for the other traits.

Hypobaric Treatment Effects on Chilling Injury, Mitochondrial Dysfunction, and the Ascorbate-Glutathione (AsA-GSH) Cycle in Postharvest Peach Fruit

In this study, hypobaric treatment effects were investigated on chilling injury, mitochondrial dysfunction, and the ascorbate-glutathione (AsA-GSH) cycle in peach fruit stored at 0 °C. Internal browning of peaches was dramatically reduced by applying 10-20 kPa pressure. Hypobaric treatment markedly inhibited membrane fluidity increase, whereas it kept mitochondrial permeability transition pore (MPTP) concentration and cytochrome C oxidase (CCO) and succinic dehydrogenase (SDH) activity relatively high in mitochondria. Similarly, 10-20 kPa pressure treatment reduced the level of decrease observed in AsA and GSH concentrations, while it enhanced ascorbate peroxidase (APX), glutathione reductase (GR), and monodehydroascorbate reductase (MDHAR) activities related to the AsA-GSH cycle. Furthermore, comparative transcriptomic analysis showed that differentially expressed genes (DEGs) associated with the metabolism of glutathione, ascorbate, and aldarate were up-regulated in peaches treated with 10-20 kPa for 30 days at 0 °C. Genes encoding GR, MDHAR, and APX were identified and exhibited higher expression in fruits treated with low pressure than in fruits treated with normal atmospheric pressure. Our findings indicate that the alleviation of chilling injury by hypobaric treatment was associated with preventing mitochondrial dysfunction and triggering the AsA-GSH cycle by the transcriptional up-regulation of related enzymes.

Transcriptome Profiling of Tomato Fruit Development Reveals Transcription Factors Associated with Ascorbic Acid, Carotenoid and Flavonoid Biosynthesis

Tomato (Solanum lycopersicum) serves as a research model for fruit development; however, while it is an important dietary source of antioxidant nutrients, the transcriptional regulation of genes that determine nutrient levels remains poorly understood. Here, the transcriptomes of fruit at seven developmental stages (7, 14, 21, 28, 35, 42 and 49 days after flowering) from two tomato cultivars (Ailsa Craig and HG6-61) were evaluated using the Illumina sequencing platform. A total of 26,397 genes, which were expressed in at least one developmental stage, were detected in the two cultivars, and the expression patterns of those genes could be divided into 20 groups using a K-mean cluster analysis. Gene Ontology term enrichment analysis indicated that genes involved in RNA regulation, secondary metabolism, hormone metabolism and cell wall metabolism were the most highly differentially expressed genes during fruit development and ripening. A co-expression analysis revealed several transcription factors whose expression patterns correlated with those of genes associated with ascorbic acid, carotenoid and flavonoid biosynthesis. This transcriptional correlation was confirmed by agroinfiltration mediated transient expression, which showed that most of the enzymatic genes in the ascorbic acid biosynthesis were regulated by the overexpression of each of the three transcription factors that were tested. The metabolic dynamics of ascorbic acid, carotenoid and flavonoid were investigated during fruit development and ripening, and some selected transcription factors showed transcriptional correlation with the accumulation of ascorbic acid, carotenoid and flavonoid. This transcriptome study provides insight into the regulatory mechanism of fruit development and presents candidate transcription factors involved in secondary metabolism.

Increased antioxidant capacity in tomato by ectopic expression of the strawberry D-galacturonate reductase gene

Increasing L-ascorbic acid (AsA, vitamin C) content in fruits is a common goal in current breeding programs due to its beneficial effect on human health. Attempts to increase AsA content by genetic engineering have resulted in variable success likely due to AsA's complex regulation. Here, we report the effect of ectopically expressing in tomato the D-galacturonate reductase (FaGalUR) gene from strawberry, involved in AsA biosynthesis, either under the control of the constitutive 35S or the tomato fruit-specific polygalucturonase (PG) promoters. Although transgenic lines showed a moderate increase on AsA content, complex changes in metabolites were found in transgenic fruits. Metabolomic analyses of ripe fruits identified a decrease in citrate, glutamate, asparagine, glucose, and fructose, accompanied by an increase of sucrose, galactinol, and chlorogenic acid. Significant metabolic changes also occurred in leaves of 35S-FaGalUR lines, which showed higher non-photochemical fluorescence quenching (NPQ), indicative of a higher constitutive photo-protective capacity. Overall, overexpression of FaGalUR increased total antioxidant capacity in fruits and the results suggest a tight control of AsA content, probably linked to a complex regulation of cellular redox state and metabolic adjustment.

Annotation of gene function in citrus using gene expression information and co-expression networks

BACKGROUND

The genus Citrus encompasses major cultivated plants such as sweet orange, mandarin, lemon and grapefruit, among the world's most economically important fruit crops. With increasing volumes of transcriptomics data available for these species, Gene Co-expression Network (GCN) analysis is a viable option for predicting gene function at a genome-wide scale. GCN analysis is based on a "guilt-by-association" principle whereby genes encoding proteins involved in similar and/or related biological processes may exhibit similar expression patterns across diverse sets of experimental conditions. While bioinformatics resources such as GCN analysis are widely available for efficient gene function prediction in model plant species including Arabidopsis, soybean and rice, in citrus these tools are not yet developed.

RESULTS

We have constructed a comprehensive GCN for citrus inferred from 297 publicly available Affymetrix Genechip Citrus Genome microarray datasets, providing gene co-expression relationships at a genome-wide scale (33,000 transcripts). The comprehensive citrus GCN consists of a global GCN (condition-independent) and four condition-dependent GCNs that survey the sweet orange species only, all citrus fruit tissues, all citrus leaf tissues, or stress-exposed plants. All of these GCNs are clustered using genome-wide, gene-centric (guide) and graph clustering algorithms for flexibility of gene function prediction. For each putative cluster, gene ontology (GO) enrichment and gene expression specificity analyses were performed to enhance gene function, expression and regulation pattern prediction. The guide-gene approach was used to infer novel roles of genes involved in disease susceptibility and vitamin C metabolism, and graph-clustering approaches were used to investigate isoprenoid/phenylpropanoid metabolism in citrus peel, and citric acid catabolism via the GABA shunt in citrus fruit.

CONCLUSIONS

Integration of citrus gene co-expression networks, functional enrichment analysis and gene expression information provide opportunities to infer gene function in citrus. We present a publicly accessible tool, Network Inference for Citrus Co-Expression (NICCE, http://citrus.adelaide.edu.au/nicce/home.aspx), for the gene co-expression analysis in citrus.

The transcription factor AREB1 regulates primary metabolic pathways in tomato fruits

Tomato fruit development is regulated both by the action of plant hormones and by tight genetic control. Recent studies suggest that abscisic acid (ABA) signalling may affect different aspects of fruit maturation. Previously, it was shown that SlAREB1, an ABA-regulated transcription factor involved in stress-induced responses, is expressed in seeds and in fruit tissues in tomato. Here, the role of SlAREB1 in regulating the expression of genes relevant for primary metabolic pathways and affecting the metabolic profile of the fruit was investigated using transgenic tomato lines. Metabolite profiling using gas chromatography-time of flight mass spectrometry (GC-TOF-MS) and non-targeted liquid chromatography-mass spectrometry (LC-MS) was performed on pericarp tissue from fruits harvested at three stages of fruit development. Principal component analysis of the data could distinguish the metabolite profiles of non-transgenic fruits from those that overexpress and down-regulate SlAREB1. Overexpression of SlAREB1 resulted in increased content of organic acids, hexoses, hexose-phosphates, and amino acids in immature green, mature green, and red ripe fruits, and these modifications correlated with the up-regulation of enzyme-encoding genes involved in primary carbohydrate and amino acid metabolism. A non-targeted LC-MS analysis indicated that the composition of secondary metabolites is also affected in transgenic lines. In addition, gene expression data revealed that some genes associated with fruit ripening are also up-regulated in SlAREB1-overexpressing lines compared with wild-type and antisense lines. Taken together, the results suggest that SlAREB1 participates in the regulation of the metabolic programming that takes place during fruit ripening and that may explain part of the role of ABA in fruit development in tomato.

Differential transcriptional regulation of L-ascorbic acid content in peel and pulp of citrus fruits during development and maturation

Citrus fruits are an important source of ascorbic acid (AsA) for human nutrition, but the main pathways involved in its biosynthesis and their regulation are still not fully characterized. To study the transcriptional regulation of AsA accumulation, expression levels of 13 genes involved in AsA biosynthesis, 5 in recycling and 5 in degradation were analyzed in peel and pulp of fruit of two varieties with different AsA concentration: Navel orange (Citrus sinensis) and Satsuma mandarin (Citrus unshiu). AsA accumulation in peel and pulp correlated with the transcriptional profiling of the L-galactose pathway genes, and the myo-inositol pathway appeared to be also relevant in the peel of immature-green orange. Differences in AsA content between varieties were associated with differential gene expression of GDP-mannose pyrophosphorylase (GMP), GDP-L-galactose phosphorylase (GGP) and L-galactose-1-phosphate phosphatase (GPP), myo-inositol oxygenase in peel, and GGP and GPP in pulp. Relative expressions of monodehydroascorbate reductase 3 (MDHAR3) and dehydroascorbate reductase1 (DHAR1) correlated with AsA accumulation during development and ripening in peel and pulp, respectively, and were more highly expressed in the variety with higher AsA contents. Collectively, results indicated a differential regulation of AsA concentration in peel and pulp of citrus fruits that may change during the different stages of fruit development. The L-galactose pathway appears to be predominant in both tissues, but AsA concentration is regulated by complex mechanisms in which degradation and recycling also play important roles.

Deciphering ascorbic acid regulatory pathways in ripening tomato fruit using a weighted gene correlation network analysis approach

Genotype is generally determined by the co-expression of diverse genes and multiple regulatory pathways in plants. Gene co-expression analysis combining with physiological trait data provides very important information about the gene function and regulatory mechanism. L-Ascorbic acid (AsA), which is an essential nutrient component for human health and plant metabolism, plays key roles in diverse biological processes such as cell cycle, cell expansion, stress resistance, hormone synthesis, and signaling. Here, we applied a weighted gene correlation network analysis approach based on gene expression values and AsA content data in ripening tomato (Solanum lycopersicum L.) fruit with different AsA content levels, which leads to identification of AsA relevant modules and vital genes in AsA regulatory pathways. Twenty-four modules were compartmentalized according to gene expression profiling. Among these modules, one negatively related module containing genes involved in redox processes and one positively related module enriched with genes involved in AsA biosynthetic and recycling pathways were further analyzed. The present work herein indicates that redox pathways as well as hormone-signal pathways are closely correlated with AsA accumulation in ripening tomato fruit, and allowed us to prioritize candidate genes for follow-up studies to dissect this interplay at the biochemical and molecular level.

From manual curation to visualization of gene families and networks across Solanaceae plant species

High-quality manual annotation methods and practices need to be scaled to the increased rate of genomic data production. Curation based on gene families and gene networks is one approach that can significantly increase both curation efficiency and quality. The Sol Genomics Network (SGN; http://solgenomics.net) is a comparative genomics platform, with genetic, genomic and phenotypic information of the Solanaceae family and its closely related species that incorporates a community-based gene and phenotype curation system. In this article, we describe a manual curation system for gene families aimed at facilitating curation, querying and visualization of gene interaction patterns underlying complex biological processes, including an interface for efficiently capturing information from experiments with large data sets reported in the literature. Well-annotated multigene families are useful for further exploration of genome organization and gene evolution across species. As an example, we illustrate the system with the multigene transcription factor families, WRKY and Small Auxin Up-regulated RNA (SAUR), which both play important roles in responding to abiotic stresses in plants.

Database URL:http://solgenomics.net/

Genome-wide gene expression profiles in antioxidant pathways and their potential sex differences and connections to vitamin C in mice

Vitamin C (VC) is well known as an antioxidant in humans, primates and guinea pigs. Studies have suggested gender differences in VC requirements in humans, and gender differences in oxidant injury vulnerability in early life may represent a biological mechanism contributing to gender disparity in later life. Using spontaneous bone fracture (sfx) mice, which lack the gene for L-Gulonolactone oxidase (Gulo), we studied the potential sex difference in expression profiles of oxidative genes at the whole-genome level. Then, we analyzed data of gene expressions in a mouse population of recombinant inbred (RI) strains originally derived by crossing C57BL/6J (B6) and DBA/2J (D2) mice. Our data indicated that there were sex differences in the regulation of pre- and pro-oxidative genes in sfx mice. The associations of expression levels among Gulo, its partner genes and oxidative genes in the BXD (B6 × D2) RI strains showed a sex difference. Transcriptome mapping suggests that Gulo was regulated differently between female and male mice in BXD RI strains. Our study indicates the importance of investigating sex differences in Gulo and its oxidative function by using available mouse models.

Pyrophosphate levels strongly influence ascorbate and starch content in tomato fruit

Ascorbate (vitamin C) deficiency leads to low immunity, scurvy, and other human diseases and is therefore a global health problem. Given that plants are major ascorbate sources for humans, biofortification of this vitamin in our foodstuffs is of considerable importance. Ascorbate is synthetized by a number of alternative pathways: (i) from the glycolytic intermediates D-glucose-6P (the key intermediates are GDP-D-mannose and L-galactose), (ii) from the breakdown of the cell wall polymer pectin which uses the methyl ester of D-galacturonic acid as precursor, and (iii) from myo-inositol as precursor via myo-inositol oxygenase. We report here the engineering of fruit-specific overexpression of a bacterial pyrophosphatase, which hydrolyzes the inorganic pyrophosphate (PPi) to orthophosphate (Pi). This strategy resulted in increased vitamin C levels up to 2.5-fold in ripe fruit as well as increasing in the major sugars, sucrose, and glucose, yet decreasing the level of starch. When considered together, these finding indicate an intimate linkage between ascorbate and sugar biosynthesis in plants. Moreover, the combined data reveal the importance of PPi metabolism in tomato fruit metabolism and development.