45 research outputs found

    Mapping the Arabidopsis Metabolic Landscape by Untargeted Metabolomics at Different Environmental Conditions

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    Metabolic genome-wide association studies (mGWAS), whereupon metabolite levels are regarded as traits, can help unravel the genetic basis of metabolic networks. A total of 309 Arabidopsis accessions were grown under two independent environmental conditions (control and stress) and subjected to untargeted LC-MS-based metabolomic profiling; levels of the obtained hydrophilic metabolites were used in GWAS. Our two-condition-based GWAS for more than 3000 semi-polar metabolites resulted in the detection of 123 highly resolved metabolite quantitative trait loci (p ≤ 1.0E-08), 24.39% of which were environment-specific. Interestingly, differently from natural variation in Arabidopsis primary metabolites, which tends to be controlled by a large number of small-effect loci, we found several major large-effect loci alongside a vast number of small-effect loci controlling variation of secondary metabolites. The two-condition-based GWAS was followed by integration with network-derived metabolite-transcript correlations using a time-course stress experiment. Through this integrative approach, we selected 70 key candidate associations between structural genes and metabolites, and experimentally validated eight novel associations, two of them showing differential genetic regulation in the two environments studied. We demonstrate the power of combining large-scale untargeted metabolomics-based GWAS with time-course-derived networks both performed under different abiotic environments for identifying metabolite-gene associations, providing novel global insights into the metabolic landscape of Arabidopsis. By combining large-scale untargeted metabolomics-based GWAS and network analysis with environmental stress-driven perturbations of metabolic homeostasis, this system-wide study provides new global insights into the metabolic landscape of Arabidopsis, using a strategy that could readily be extended to other plant species.</p

    Epigenetic mapping of the metabolome reveals mediators of the epigenotype-phenotype map

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    Identifying the sources of natural variation underlying metabolic differences between plants will enable a better understanding of plant metabolism and provide insights into the regulatory networks that govern plant growth and morphology. So far, however, the contribution of epigenetic variation to metabolic diversity has been largely ignored. In the present study, we utilized a panel of Arabidopsis thaliana epigenetic recombinant inbred lines (epiRILs) to assess the impact of epigenetic variation on the metabolic composition. Thirty epigenetic QTL (QTLepi) were detected, which partly overlap with QTLepi linked to growth and morphology. In an effort to identify causal candidate genes in the QTLepi regions and their putative trans-targets, we performed in silico small RNA and qPCR analyses. Differentially expressed genes were further studied by phenotypic and metabolic analyses of knockout mutants. Three genes were detected that recapitulated the detected QTLepi effects, providing evidence for epigenetic regulation in cis and in trans These results indicate that epigenetic mechanisms impact metabolic diversity, possibly via small RNAs, and thus aid in further disentangling the complex epigenotype-phenotype map

    Interactions between auxin, microtubules and XTHs mediate green shade- induced petiole elongation in arabidopsis.

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    Plants are highly attuned to translating environmental changes to appropriate modifications in growth. Such phenotypic plasticity is observed in dense vegetations, where shading by neighboring plants, triggers rapid unidirectional shoot growth (shade avoidance), such as petiole elongation, which is partly under the control of auxin. This growth is fuelled by cellular expansion requiring cell-wall modification by proteins such as xyloglucan endotransglucosylase/hydrolases (XTHs). Cortical microtubules (cMTs) are highly dynamic cytoskeletal structures that are also implicated in growth regulation. The objective of this study was to investigate the tripartite interaction between auxin, cMTs and XTHs in shade avoidance. Our results indicate a role for cMTs to control rapid petiole elongation in Arabidopsis during shade avoidance. Genetic and pharmacological perturbation of cMTs obliterated shade-induced growth and led to a reduction in XTH activity as well. Furthermore, the cMT disruption repressed the shade-induced expression of a specific set of XTHs. These XTHs were also regulated by the hormone auxin, an important regulator of plant developmental plasticity and also of several shade avoidance responses. Accordingly, the effect of cMT disruption on the shade enhanced XTH expression could be rescued by auxin application. Based on the results we hypothesize that cMTs can mediate petiole elongation during shade avoidance by regulating the expression of cell wall modifying proteins via control of auxin distribution

    DataFieldandClimatechamber

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    Phenotype data of A. thaliana plants grown in either a field environment or in a climate chamber environment. In the climate chamber environment plants were grown under control conditions or salt stress

    Epigenetic Basis of Morphological Variation and Phenotypic Plasticity in Arabidopsis thaliana

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    Epigenetics is receiving growing attention in the plant science community. Epigenetic modifications are thought to play a particularly important role in fluctuating environments. It is hypothesized that epigenetics contributes to plant phenotypic plasticity because epigenetic modifications, in contrast to DNA sequence variation, are more likely to be reversible. The population of decrease in DNA methylation 1-2 (ddm1-2)-derived epigenetic recombinant inbred lines (epiRILs) in Arabidopsis thaliana is well suited for studying this hypothesis, as DNA methylation differences are maximized and DNA sequence variation is minimized. Here, we report on the extensive heritable epigenetic variation in plant growth and morphology in neutral and saline conditions detected among the epiRILs. Plant performance, in terms of branching and leaf area, was both reduced and enhanced by different quantitative trait loci (QTLs) in the ddm1-2 inherited epigenotypes. The variation in plasticity associated significantly with certain genomic regions in which the ddm1-2 inherited epigenotypes caused an increased sensitivity to environmental changes, probably due to impaired genetic regulation in the epiRILs. Many of the QTLs for morphology and plasticity overlapped, suggesting major pleiotropic effects. These findings indicate that epigenetics contributes substantially to variation in plant growth, morphology, and plasticity, especially under stress conditions

    Perturbation of cortical microtubules affects <i>XTH</i> transcript abundance during shade avoidance.

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    <p>(<b>A–E</b>) Relative transcript abundance of five <i>XTH</i> genes in petioles of Col-0 plants after 24 h of white light (white bars) or green shade (gray bars) treatment with or without oryzalin pre-treatment. Values are expressed on a log2 fold scale and were normalized using <i>AtUBQ10</i> as an internal control. Data points represent means ± SE (n = 5). Different letters above each bar indicate statistically significant differences (P<0.05, Tukey's <i>b</i> test).</p
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