MetaboAnalyst (www.metaboanalyst.ca) is a web server designed to permit comprehensive metabolomic data analysis, visualization and interpretation. It supports a wide range of complex statistical calculations and high quality graphical rendering functions that require significant computational resources. First introduced in 2009, MetaboAnalyst has experienced more than a 50X growth in user traffic (>50 000 jobs processed each month). In order to keep up with the rapidly increasing computational demands and a growing number of requests to support translational and systems biology applications, we performed a substantial rewrite and major feature upgrade of the server. The result is MetaboAnalyst 3.0. By completely re-implementing the MetaboAnalyst suite using the latest web framework technologies, we have been able substantially improve its performance, capacity and user interactivity. Three new modules have also been added including: (i) a module for biomarker analysis based on the calculation of receiver operating characteristic curves; (ii) a module for sample size estimation and power analysis for improved planning of metabolomics studies and (iii) a module to support integrative pathway analysis for both genes and metabolites. In addition, popular features found in existing modules have been significantly enhanced by upgrading the graphical output, expanding the compound libraries and by adding support for more diverse organisms.

/pdf/metaboanalyst-3-0-making-metabolomics-more-meaningful-4bytpf65h5.pdf

MetaboAnalyst 3.0—making metabolomics more meaningful

Genome-wide association studies in maize: praise and stargaze.

Flavonoids are a signature class of secondary metabolites formed from a relatively simple collection of scaffolds. They are extensively decorated by chemical reactions including glycosylation, methylation, and acylation. They are present in a wide variety of fruits and vegetables and as such in Western populations it is estimated that 20-50 mg of flavonoids are consumed daily per person. In planta they have demonstrated to contribute to both flower color and UV protection. Their consumption has been suggested to presenta wide range of health benefits. Recent technical advances allowing affordable whole genome sequencing, as well as a better inventory of species-by-species chemical diversity, have greatly advanced our understanding as to how flavonoid biosynthesis pathways vary across species. In parallel, reverse genetics combined with detailed molecular phenotyping is currently allowing us to elucidate the functional importance of individual genes and metabolites and by this means to provide further mechanistic insight into their biological roles. Here we provide an inventory of current knowledge of pathways of flavonoid biosynthesis in both the model plant Arabidopsis thaliana and a range of crop species, including tomato, maize, rice, and bean.

Current understanding of the pathways of flavonoid biosynthesis in model and crop plants

Metabolomics: A Primer

As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality.

Plant Metabolomics: An Indispensable System Biology Tool for Plant Science

Plants produce a variety of metabolites that have a critical role in growth and development. Here we present a comprehensive study of maize metabolism, combining genetic, metabolite and expression profiling methodologies to dissect the genetic basis of metabolic diversity in maize kernels. We quantify 983 metabolite features in 702 maize genotypes planted at multiple locations. We identify 1,459 significant locus-trait associations (P≤1.8 × 10(-6)) across three environments through metabolite-based genome-wide association mapping. Most (58.5%) of the identified loci are supported by expression QTLs, and some (14.7%) are validated through linkage mapping. Re-sequencing and candidate gene association analysis identifies potential causal variants for five candidate genes involved in metabolic traits. Two of these genes were further validated by mutant and transgenic analysis. Metabolite features associated with kernel weight could be used as biomarkers to facilitate genetic improvement of maize.

/pdf/metabolome-based-genome-wide-association-study-of-maize-qqp4d4dqbw.pdf

Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights

Metabolic quantitative trait locus (QTL) studies have allowed us to better understand the genetic architecture underlying naturally occurring plant metabolic variance. Here, we use two recombinant inbred line (RIL) populations to dissect the genetic architecture of natural variation of 155 metabolites measured in the mature maize (Zea mays) kernel. Overall, linkage mapping identified 882 metabolic QTLs in both RIL populations across two environments, with an average of 2.1 QTLs per metabolite. A large number of metabolic QTLs (more than 65%) were identified with moderate effects (r(2) = 2.1%-10%), while a small portion (less than 35%) showed major effects (r(2) > 10%). Epistatic interactions between these identified loci were detected for more than 30% of metabolites (with the proportion of phenotypic variance ranging from 1.6% to 37.8%), implying that genetic epistasis is not negligible in determining metabolic variation. In total, 57 QTLs were validated by our previous genome-wide association study on the same metabolites that provided clues for exploring the underlying genes. A gene regulatory network associated with the flavonoid metabolic pathway was constructed based on the transcriptional variations of 28,769 genes in kernels (15 d after pollination) of 368 maize inbred lines. A large number of genes (34 of 58) in this network overlapped with previously defined genes controlled by maize PERICARP COLOR1, while three of them were identified here within QTL intervals for multiple flavonoids. The deeply characterized RIL populations, elucidation of metabolic phenotypes, and identification of candidate genes lay the foundation for maize quality improvement.

http://www.plantphysiol.org/content/plantphysiol/170/1/136.full.pdf

Combining Quantitative Genetics Approaches with Regulatory Network Analysis to Dissect the Complex Metabolism of the Maize Kernel

The invention discloses a method for efficiently authenticating a plant secondary metabolite product by utilizing LC-MS/MS (Liquid Chromatograph-Mass Spectrometer/Mass Spectrometer), which comprises the following steps of: firstly, carrying out mass charge ratio step-by-step scanning that Q1 is equal to Q3 on a sample; secondly, carrying out section sampling on an ion pair generated in the step 1by utilizing an MRM (Multiple Reaction Monitoring) mode to find out a peak ion pair and carrying out weight reduction according to peak intensity; thirdly, carrying out broken sampling on the peak ion pair found out in the step 2 by utilizing the MRM combining with IDA (Information Dependent Acquisition) and EPI (Enhanced Product Ion), carrying out further weight reduction and finally confirming the ion pair; and delivering the confirmed ion pair into a warehouse By using the method, the high-flux and high-sensitivity authentication can be carried out on the secondary metabolite products of different tissues of a plant The method has the advantages of simpleness and convenience for operation and high applicability and has significance on the research of the plant secondary metabolite product Meanwhile, a secondary metabolite product database of different plants can be established by utilizing the method so as to promote the development of plant metabonomics

Method for efficiently authenticating plant secondary metabolite product by utilizing LC-MS/MS (Liquid Chromatograph-Mass Spectrometer/Mass Spectrometer)

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Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights

Combining Quantitative Genetics Approaches with Regulatory Network Analysis to Dissect the Complex Metabolism of the Maize Kernel

Method for efficiently authenticating plant secondary metabolite product by utilizing LC-MS/MS (Liquid Chromatograph-Mass Spectrometer/Mass Spectrometer)