Network analysis of the metabolome and transcriptome reveals novel regulation of potato pigmentation

Analysis of Flavonoid Metabolites in Citrus Peels (Citrus reticulata "Dahongpao") Using UPLC-ESI-MS/MS

Flavonoids are a kind of essential substance for the human body because of their antioxidant properties and extremely high medicinal value. Citrus reticulata “Dahongpao” (DHP) is a special citrus variety that is rich in flavonoids, however little is known about its systematic flavonoids profile. In the present study, the presence of flavonoids in five important citrus varieties, including DHP, Citrus grandis Tomentosa (HZY), Citrus ichangensis Swingle (YCC), Citrus sinensis (L.) Osbeck (TC), and Citrus reticulata ‘Buzhihuo’ (BZH), was determined using a UPLC-ESI-MS/MS-based, widely targeted metabolome. Results showed that a total of 254 flavonoid metabolites (including 147 flavone, 39 flavonol, 21 flavanone, 24 anthocyanins, 8 isoflavone, and 15 polyphenol) were identified. The total flavonoid content of peels from DHP was the highest. DHP could be clearly separated from other samples through clustering analysis and principal component analysis (PCA). Further, 169 different flavonoid metabolites were observed between DHP peels and the other four citrus peels, and 26 down-regulated differential metabolites displayed important biological activities in DHP. At the same time, a unique flavonoid component, tricin 4′-O-syringyl alcohol, was only found in DHP, which could be used as a marker to distinguish between other varieties. This work might facilitate a better understanding of flavonoid metabolites between DHP peels and the other four citrus peels and provide a reference for its sufficient utilization in the future.

QTL mapping for maize starch content and candidate gene prediction combined with co-expression network analysis

A major QTL Qsta9.1 was identified on chromosome 9, combined with GWAS, and co-expression network analysis showed that GRMZM2G110929 and GRMZM5G852704 are the potential candidates for association with maize kernel starch content. Increasing maize kernel starch content may not only lead to higher maize kernel yields and qualities, but also help meet industry demands. By using the intermated B73 × Mo17 population, QTLs were mapped for starch content in this study. A major QTL Qsta9.1 was detected in a 1.7 Mb interval on chromosome 9 and validated by allele frequency analysis in extreme tails of a newly constructed segregating population. According to genome-wide association study (GWAS) based on genotyping of a natural population, we identified a significant SNP for starch content within the ORF region of GRMZM5G852704_T01 colocalized with QTL Qsta9.1. Co-expression network analysis was also conducted, and 28 modules were constructed during six seed developmental stages. Functional enrichment was performed for each module, and one module showed the most possibility for the association with carbohydrate-related processes. In this module, one transcripts GRMZM2G110929_T01 located in the Qsta9.1 assigned 1.7 Mb interval encoding GLABRA2 expression modulator. Its expression level in B73 was lower than that in Mo17 across all seed developmental stages, implying the possibility for the candidate gene of Qsta9.1. Our studies combined GWAS, mRNA profiling, and traditional QTL analyses to identify a major locus for controlling seed starch content in maize.

MicroRNA858-mediated regulation of anthocyanin biosynthesis in kiwifruit (Actinidia arguta) based on small RNA sequencing

As important regulators, miRNAs could play pivotal roles in regulation of fruit coloring. Actinidia arguta is a newly emerged fruit tree with extensively application prospects. However, miRNAs involved in A. arguta fruit coloring are unknown. In this study, A. arguta fruit were investigated at three developmental stages by small RNAs high-throughput sequencing. A total of 482 conserved miRNAs corresponding to 526 pre-miRNAs and 581 novel miRNAs corresponding to 619 pre-miRNAs were grouped into 46 miRNA families. Target gene prediction and analysis revealed that miR858, a strongly candidate miRNA, was involved in anthocyanin biosynthesis in which contributes to fruit coloring. The anthocyanin level was determined in three A. arguta cultivars by UPLC-MS/MS (ultra-performance liquid chromatography coupled with tandem mass spectrometry). In addition, qPCR (quantitative real-time PCR), cluster analysis were conducted as well as correlation analysis. All results were combined to propose a model in which describes an association of miRNA and anthocyanin biosynthesis in A. arguta. The data presented herein is the first report on miRNA profile analysis in A. arguta, which can provide valuable information for further research into the regulation of the miRNAs in anthocyanin biosynthesis and fruit coloring.

An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Differential Regulation of Carbon and Nitrogen Metabolism in Response to Nitrogen Availability

Nitrogen (N) is an extremely important macronutrient for plant growth and development. It is the main limiting factor in most agricultural production. However, it is well known that the nitrogen use efficiency (NUE) of rice gradually decreases with the increase of the nitrogen application rate. In order to clarify the underlying metabolic and molecular mechanisms of this phenomenon, we performed an integrated analysis of the rice transcriptome and metabolome. Both differentially expressed genes (DEGs) and metabolite Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that carbon and nitrogen metabolism is significantly affected by nitrogen availability. Further analysis of carbon and nitrogen metabolism changes in rice under different nitrogen availability showed that high N inhibits nitrogen assimilation and aromatic metabolism pathways by regulating carbon metabolism pathways such as the tricarboxylic acid (TCA) cycle and the pentose phosphate pathway (PPP). Under low nitrogen, the TCA cycle is promoted to produce more energy and α-ketoglutarate, thereby enhancing nitrogen transport and assimilation. PPP is also inhibited by low N, which may be consistent with the lower NADPH demand under low nitrogen. Additionally, we performed a co-expression network analysis of genes and metabolites related to carbon and nitrogen metabolism. In total, 15 genes were identified as hub genes. In summary, this study reveals the influence of nitrogen levels on the regulation mechanisms for carbon and nitrogen metabolism in rice and provides new insights into coordinating carbon and nitrogen metabolism and improving nitrogen use efficiency in rice.

Metabolomics Integrated with Transcriptomics Reveals Redirection of the Phenylpropanoids Metabolic Flux in Ginkgo biloba

Ginkgo biloba is a monotypic species native to China with great economic and ecological values. Leaves extract of this tree contains about 24% flavonoids, which are widely used in the pharmaceutical industry. However, the flavonoids biosynthesis pathway is poorly understood in Ginkgo. In this study, we comprehensively compared the transcriptome and metabolite profiles of Ginkgo high-flavonoids mutant (ZY1) and Anlu1 (control) leaves. A total of 122 significantly changed metabolites and 1683 differentially expressed genes (DEGs), including 45 transcription factors, were identified in ZY1 compared to those in Anlu1. An integrated analysis of metabolic and transcriptomic data revealed that the abundances of some major flavonoids (especially flavone and flavonol) were most significantly increased, while other phenylpropanoid-derived products and lipids showed the most largely reduced abundances in ZY1 compared to those in Anlu1. Quantitative real-time polymerase chain reaction results confirmed the alterations in the expression levels of genes encoding components of pathways involved in phenylpropanoids and lipids. The redirection of metabolic flux may contribute to increased accumulation of flavonoid levels in ZY1 leaves. Our results provide valuable information for metabolic engineering of Ginkgo flavonoids biosynthesis.

Gene Discovery of Characteristic Metabolic Pathways in the Tea Plant (Camellia sinensis) Using 'Omics'-Based Network Approaches: A Future Perspective

Characteristic secondary metabolites, including flavonoids, theanine and caffeine, in the tea plant (Camellia sinensis) are the primary sources of the rich flavors, fresh taste, and health benefits of tea. The decoding of genes involved in these characteristic components is still significantly lagging, which lays an obstacle for applied genetic improvement and metabolic engineering. With the popularity of high-throughout transcriptomics and metabolomics, 'omics'-based network approaches, such as gene co-expression network and gene-to-metabolite network, have emerged as powerful tools for gene discovery of plant-specialized (secondary) metabolism. Thus, it is pivotal to summarize and introduce such system-based strategies in facilitating gene identification of characteristic metabolic pathways in the tea plant (or other plants). In this review, we describe recent advances in transcriptomics and metabolomics for transcript and metabolite profiling, and highlight 'omics'-based network strategies using successful examples in model and non-model plants. Further, we summarize recent progress in 'omics' analysis for gene identification of characteristic metabolites in the tea plant. Limitations of the current strategies are discussed by comparison with 'omics'-based network approaches. Finally, we demonstrate the potential of introducing such network strategies in the tea plant, with a prospects ending for a promising network discovery of characteristic metabolite genes in the tea plant.

Biochemical and functional characterization of AcUFGT3a, a galactosyltransferase involved in anthocyanin biosynthesis in the red-fleshed kiwifruit (Actinidia chinensis)

Much of the diversity of anthocyanin pigmentation in plant tissues is due to the action of glycosyltransferases, which attach sugar moieties to the anthocyanin aglycone. This step can increase both their solubility and stability. We investigated the pigmentation of the outer and inner pericarps of developing fruits of the red-fleshed kiwifruit Actinidia chinensis cv. 'Hongyang'. The results show that the red color of the inner pericarp is due to anthocyanin. Based on expression analyses of structural genes, AcUFGT was shown to be the key gene involved in the anthocyanin biosynthetic pathway. Expression of AcUFGT in developing fruit paralleled changes in anthocyanin concentration. Thirteen putative UFGT genes, including different transcripts, were identified in the genome of 'Hongyang'. Among these, only the expression of AcUFGT3a was found to be highly consistent with anthocyanin accumulation. Fruit infiltrated with virus-induced gene silencing showed delayed red colorations, lower anthocyanin contents and lower expressions of AcUFGT3a. At the same time, transient overexpression of AcUFGT3a in both Actinidia arguta and green apple fruit resulted in higher anthocyanin contents and deeper red coloration. In vitro biochemical assays revealed that recombinant AcUFGT3a recognized only anthocyanidins as substrate but not flavonols. Also, UDP-galactose was used preferentially as the sugar donor. These results indicate AcUFGT3a is the key enzyme regulating anthocyanin accumulation in red-fleshed kiwifruit.

A comparative transcriptome analysis of a wild purple potato and its red mutant provides insight into the mechanism of anthocyanin transformation

In this study, a red mutant was obtained through in vitro regeneration of a wild purple potato. High-performance liquid chromatography and Mass spectrometry analysis revealed that pelargonidin-3-O-glucoside and petunidin-3-O-glucoside were main anthocyanins in the mutant and wild type tubers, respectively. In order to thoroughly understand the mechanism of anthocyanin transformation in two materials, a comparative transcriptome analysis of the mutant and wild type was carried out through high-throughput RNA sequencing, and 295 differentially expressed genes (DEGs) were obtained. Real-time qRT-PCR validation of DEGs was consistent with the transcriptome date. The DEGs mainly influenced biological and metabolic pathways, including phenylpropanoid biosynthesis and translation, and biosynthesis of flavone and flavonol. In anthocyanin biosynthetic pathway, the analysis of structural genes expressions showed that three genes, one encoding phenylalanine ammonia-lyase, one encoding 4-coumarate-CoA ligase and one encoding flavonoid 3′,5′-hydroxylasem were significantly down-regulated in the mutant; one gene encoding phenylalanine ammonia-lyase was significantly up-regulated. Moreover, the transcription factors, such as bZIP family, MYB family, LOB family, MADS family, zf-HD family and C2H2 family, were significantly regulated in anthocyanin transformation. Response proteins of hormone, such as gibberellin, abscisic acid and brassinosteroid, were also significantly regulated in anthocyanin transformation. The information contributes to discovering the candidate genes in anthocyanin transformation, which can serve as a comprehensive resource for molecular mechanism research of anthocyanin transformation in potatoes.

A key structural gene, AaLDOX, is involved in anthocyanin biosynthesis in all red-fleshed kiwifruit (Actinidia arguta) based on transcriptome analysis

Study on kiwifruit (Actinidia chinensis and A. deliciosa) color mainly concentrated in green and yellow-fleshed cultivars, less about molecular mechanism of red-fleshed trait formation, rarely in all red-fleshed fruit. Using 'Tianyuanhong' and 'Yongfengyihao' ('TY', a kind of all red-fleshed cultivar, from Actinidia arguta; 'YF', a kind of all green-fleshed cultivar, also from Actinidia arguta) as experimental material, we performed RNA-seq to obtain 202,742 unigenes with an average length of 603bp and N50 of 873bp via transcriptome data analysis. Of these unigenes, 72,508 (35.76%) were annotated and 997 were assigned to secondary metabolic pathways, of which 104 unigenes were involved in flavonoid and anthocyanin biosynthesis. According to the parameter log2fold-change and p-adjusted, 12 differentially expressed structural genes were selected for performing expression profiles and cluster analysis. Physiological traits including color ration, hue angle, and anthocyanin content were also investigated. From the results, we concluded AaLDOX (genes encoding leucoanthocyanidin dioxygenase) maybe the key gene controlling anthocyanin biosynthesis in flesh of 'TY' kiwifruit, which promoted accumulation of anthocyanin, finally leading to the red flesh coloration.

Potato miR828 Is Associated With Purple Tuber Skin and Flesh Color

Anthocyanins are plant pigments responsible for the colors of many flowers, fruits and storage organs and have roles in abiotic and biotic stress resistance. Anthocyanins and polyphenols are bioactive compounds in plants including potato (Solanum tuberosum L.) which is the most important non-cereal crop in the world, cultivated for its tubers rich in starch and nutrients. The genetic regulation of the flavonoid biosynthetic pathway is relatively well known leading to the formation of anthocyanins. However, our knowledge of post-transcriptional regulation of anthocyanin biosynthesis is limited. There is increasing evidence that micro RNAs (miRNAs) and other small RNAs can regulate the expression level of key factors in anthocyanin production. In this study we have found strong associations between the high levels of miR828, TAS4 D4(-) and purple/red color of tuber skin and flesh. This was confirmed not only in different cultivars but in pigmented and non-pigmented sectors of the same tuber. Phytochemical analyses verified the levels of anthocyanins and polyphenols in different tissues. We showed that miR828 is able to direct cleavage of the RNA originating from Trans-acting siRNA gene 4 (TAS4) and initiate the production of phased small interfering RNAs (siRNAs) whose production depends on RNA-dependent RNA polymerase 6 (RDR6). MYB transcription factors were predicted as potential targets of miR828 and TAS4 D4(-) and their expression was characterized. MYB12 and R2R3-MYB genes showed decreased expression levels in purple skin and flesh in contrast with high levels of small RNAs in the same tissues. Moreover, we confirmed that R2R3-MYB and MYB-36284 are direct targets of the small RNAs. Overall, this study sheds light on the small RNA directed anthocyanin regulation in potato, which is an important member of the Solanaceae family.

A comparative synteny analysis tool for target-gene SNP marker discovery: connecting genomics data to breeding in Solanaceae

It is necessary for molecular breeders to overcome the difficulties in applying abundant genomic information to crop breeding. Candidate orthologs would be discovered more efficiently in less-studied crops if the information gained from studies of related crops were used. We developed a comparative analysis tool and web-based genome viewer to identify orthologous genes based synteny as well as sequence similarity between tomato, pepper and potato. The tool has a step-by-step interface with multiple viewing levels to support the easy and accurate exploration of functional orthologs. Furthermore, it provides access to single nucleotide-polymorphism markers from the massive genetic resource pool in order to accelerate the development of molecular markers for candidate orthologs in the Solanaceae. This tool provides a bridge between genome data and breeding by supporting effective marker development, data utilization and communication.

Database URL: http://tgsol.seeders.co.kr/scomp/

Multi-omics analysis reveals that ornithine decarboxylase contributes to erlotinib resistance in pancreatic cancer cells

Molecular and metabolic alterations in cancer cells are one of the leading causes of acquired resistance to chemotherapeutics. In this study, we explored an experimental strategy to identify which of these alterations can induce erlotinib resistance in human pancreatic cancer. Using genetically matched erlotinib-sensitive (BxPC-3) and erlotinib-resistant (BxPC-3ER) pancreatic cancer cells, we conducted a multi-omics analysis of metabolomes and transcriptomes in these cells. Untargeted and targeted metabolomic analyses revealed significant changes in metabolic pathways involved in the regulation of polyamines, amino acids, and fatty acids. Further transcriptomic analysis identified that ornithine decarboxylase (ODC) and its major metabolite, putrescine, contribute to the acquisition of erlotinib resistance in BxPC-3ER cells. Notably, either pharmacological or genetic blockage of ODC was able to restore erlotinib sensitivity, and this could be rescued by treatment with exogenous putrescine in erlotinib-resistant BxPC-3ER cells. Moreover, using a panel of cancer cells we demonstrated that ODC expression levels in cancer cells are inversely correlated with sensitivity to chemotherapeutics. Taken together, our findings will begin to uncover mechanisms of acquired drug resistance and ultimately help to identify potential therapeutic markers in cancer.

Expression Differences of Pigment Structural Genes and Transcription Factors Explain Flesh Coloration in Three Contrasting Kiwifruit Cultivars

Fruits of kiwifruit cultivars (Actinidia chinensis and A. deliciosa) generally have green or yellow flesh when ripe. A small number of genotypes have red flesh but this coloration is usually restricted to the inner pericarp. Three kiwifruit cultivars having red ('Hongyang'), or yellow ('Jinnong-2'), or green ('Hayward') flesh were investigated for their color characteristics and pigment contents during development and ripening. The results show the yellow of the 'Jinnong-2' fruit is due to the combined effects of chlorophyll degradation and of beta-carotene accumulation. The red inner pericarps of 'Hongyang' fruit are due to anthocyanin accumulation. Expression differences of the pathway genes in the inner pericarps of the three different kiwifruits suggest that stay-green (SGR) controls the degradation of chlorophylls, while lycopene beta-cyclase (LCY-β) controls the biosynthesis of beta-carotene. The abundance of anthocyanin in the inner pericarps of the 'Hongyang' fruit is the results of high expressions of UDP flavonoid glycosyltransferases (UFGT). At the same time, expressions of anthocyanin transcription factors show that AcMYBF110 expression parallels changes in anthocyanin concentration, so seems to be a key R2R3 MYB, regulating anthocyanin biosynthesis. Further, transient color assays reveal that AcMYBF110 can autonomously induce anthocyanin accumulation in Nicotiana tabacum leaves by activating the transcription of dihydroflavonol 4-reductase (NtDFR), anthocyanidin synthase (NtANS) and NtUFGT. For basic helix-loop-helix proteins (bHLHs) and WD-repeat proteins (WD40s), expression differences show these may depend on AcMYBF110 forming a MYB-bHLH-WD40 complex to regulate anthocyanin biosynthesis, instead of it having a direct involvement.

Metabolomics for Plant Improvement: Status and Prospects

Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield related traits. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guides researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeder by allowing him to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.

Integrated Transcriptomic and Metabolomic Analysis of Five Panax ginseng Cultivars Reveals the Dynamics of Ginsenoside Biosynthesis

Panax ginseng C.A. Meyer is a traditional medicinal herb that produces bioactive compounds such as ginsenosides. Here, we investigated the diversity of ginsenosides and related genes among five genetically fixed inbred ginseng cultivars (Chunpoong [CP], Cheongsun [CS], Gopoong [GO], Sunhyang [SH], and Sunun [SU]). To focus on the genetic diversity related to ginsenoside biosynthesis, we utilized in vitro cultured adventitious roots from the five cultivars grown under controlled environmental conditions. PCA loading plots based on secondary metabolite composition classified the five cultivars into three groups. We selected three cultivars (CS, SH, and SU) to represent the three groups and conducted further transcriptome and gas chromatography-mass spectrometry analyses to identify genes and intermediates corresponding to the variation in ginsenosides among cultivars. We quantified ginsenoside contents from the three cultivars. SH had more than 12 times the total ginsenoside content of CS, with especially large differences in the levels of panaxadiol-type ginsenosides. The expression levels of genes encoding squalene epoxidase (SQE) and dammarenediol synthase (DDS) were also significantly lower in CS than SH and SU, which is consistent with the low levels of ginsenoside produced in this cultivar. Methyl jasmonate (MeJA) treatment increased the levels of panaxadiol-type ginsenosides up to 4-, 13-, and 31-fold in SH, SU, and CS, respectively. MeJA treatment also greatly increased the quantity of major intermediates and the expression of the underlying genes in the ginsenoside biosynthesis pathway; these intermediates included squalene, 2,3-oxidosqualene, and dammarenediol II, especially in CS, which had the lowest ginsenoside content under normal culture conditions. We conclude that SQE and DDS are the most important genetic factors for ginsenoside biosynthesis with diversity among ginseng cultivars.