Abstract

We profiled 162 lines of Arabidopsis for variation in transcript, protein and metabolite abundance using mRNA microarrays, two-dimensional polyacrylamide gel electrophoresis, gas chromatography time-of-flight mass spectrometry, liquid chromatography quadrupole time-of-flight mass spectrometry, and proton nuclear magnetic resonance. We added all publicly available phenotypic data from the same lines and mapped quantitative trait loci (QTL) for 40,580 molecular and 139 phenotypic traits. We found six QTL hot spots with major, system-wide effects, suggesting there are six breakpoints in a system otherwise buffered against many of the 500,000 SNPs.

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Acknowledgements

This research was supported by the Netherlands Organization for Scientific Research (NWO), the Netherlands Genomics Initiative (NGI) and the UK Biotechnology and Biological Sciences Research Council (BBSRC).

Author information

Author notes

    • Jingyuan Fu
    •  & Joost J B Keurentjes

    These authors contributed equally to this work.

Affiliations

  1. Groningen Bioinformatics Centre, University of Groningen, 9751NN Haren, The Netherlands.

    • Jingyuan Fu
    • , Martijn Dijkstra
    • , Richard A Scheltema
    • , Frank Johannes
    • , Rainer Breitling
    •  & Ritsert C Jansen
  2. Department of Genetics, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands.

    • Jingyuan Fu
    •  & Ritsert C Jansen
  3. Laboratory of Genetics, Wageningen University, 6703BD Wageningen, The Netherlands.

    • Joost J B Keurentjes
    •  & Maarten Koornneef
  4. Laboratory of Plant Physiology, Wageningen University, 6703BD Wageningen, The Netherlands.

    • Joost J B Keurentjes
    • , Harro Bouwmeester
    • , Francel W A Verstappen
    •  & Dick Vreugdenhil
  5. Centre for Biosystems Genomics, Wageningen, 6708PB Wageningen, The Netherlands.

    • Joost J B Keurentjes
    • , Harro Bouwmeester
    • , Twan America
    • , Francel W A Verstappen
    •  & Ric C H de Vos
  6. Plant Research International, Wageningen, 6708PB Wageningen, The Netherlands.

    • Harro Bouwmeester
    • , Twan America
    • , Francel W A Verstappen
    •  & Ric C H de Vos
  7. Rothamsted Research, National Centre for Plant and Microbial Metabolomics, AL5 2JQ Harpenden, Herts, UK.

    • Jane L Ward
    •  & Michael H Beale
  8. Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.

    • Maarten Koornneef

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Contributions

J.F. analyzed the system-wide data, J.J.B.K. managed the system-wide data production, H.B. and F.W.A.V. produced the GC-MS data, T.A. produced the 2D-PAGE data, J.L.W. and M.H.B. produced the NMR data, R.C.H.d.V. produced the LC-MS data, M.D. and R.A.S. helped analyze the GC- and LC-MS data, F.J. helped analyze the NMR data, M.K. coordinated the QTL-Express project and provided the biological materials, D.V. contributed to the biological interpretation, R.B. contributed to the system-wide interpretation and writing of the manuscript, R.C.J. conceived the project and coordinated the analysis and writing of the manuscript.

Corresponding author

Correspondence to Ritsert C Jansen.

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    Supplementary Text and Figures

    Supplementary Table 1, Supplementary Figures 1–5 and Supplementary Methods

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DOI

https://doi.org/10.1038/ng.308

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