Technical Report | Published:

The genetics of plant metabolism

Nature Genetics volume 38, pages 842849 (2006) | Download Citation

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Abstract

Variation for metabolite composition and content is often observed in plants. However, it is poorly understood to what extent this variation has a genetic basis. Here, we describe the genetic analysis of natural variation in the metabolite composition in Arabidopsis thaliana. Instead of focusing on specific metabolites, we have applied empirical untargeted metabolomics using liquid chromatography–time of flight mass spectrometry (LC-QTOF MS). This uncovered many qualitative and quantitative differences in metabolite accumulation between A. thaliana accessions. Only 13.4% of the mass peaks were detected in all 14 accessions analyzed. Quantitative trait locus (QTL) analysis of more than 2,000 mass peaks, detected in a recombinant inbred line (RIL) population derived from the two most divergent accessions, enabled the identification of QTLs for about 75% of the mass signals. More than one-third of the signals were not detected in either parent, indicating the large potential for modification of metabolic composition through classical breeding.

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Acknowledgements

This work was supported by grants from the Netherlands Organization for Scientific Research, Program Genomics (050-10-029) and the Centre for Biosystems Genomics (CBSG, Netherlands Genomics Initiative).

Author information

Author notes

    • Joost J B Keurentjes
    • , Jingyuan Fu
    •  & C H Ric de Vos

    These authors contributed equally to this work.

Affiliations

  1. Laboratory of Genetics, Wageningen University, Arboretumlaan 4, NL-6703 BD Wageningen, The Netherlands.

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

    • Joost J B Keurentjes
    • , Raoul J Bino
    • , Linus H W van der Plas
    •  & Dick Vreugdenhil
  3. Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, NL-9751 NN Haren, The Netherlands.

    • Jingyuan Fu
    •  & Ritsert C Jansen
  4. Plant Research International, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands.

    • C H Ric de Vos
    • , Arjen Lommen
    • , Robert D Hall
    •  & Raoul J Bino
  5. Centre for Biosystems Genomics, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands.

    • C H Ric de Vos
    • , Arjen Lommen
    • , Robert D Hall
    •  & Raoul J Bino
  6. RIKILT–Institute of Food Safety, Bornsesteeg 45, NL-6700 AE Wageningen, The Netherlands.

    • Arjen Lommen
  7. Max Planck Institute for Plant Breeding Research, Carl von Linné weg 10, 50829 Cologne, Germany.

    • Maarten Koornneef

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Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Maarten Koornneef.

Supplementary information

PDF files

  1. 1.

    Supplementary Fig. 1

    Hierarchical clustering of accessions for metabolite content.

  2. 2.

    Supplementary Fig. 2

    Frequency distribution of the number of QTLs detected for each mass signal.

  3. 3.

    Supplementary Fig. 3

    Frequency distribution of broad sense heritability of each detected mass in the RIL population.

  4. 4.

    Supplementary Fig. 4

    Frequency distribution of the contribution to QTL significance of the binominal part in the two-part parametric model.

  5. 5.

    Supplementary Fig. 5

    Binominal and quantitative variance explained by QTLs.

  6. 6.

    Supplementary Table 1

    Arabidopsis thaliana accessions used in the analysis of natural variation for metabolite content.

  7. 7.

    Supplementary Table 2

    Detected QTL at and epistatic effects between MAM and AOP loci for aliphatic glucosinolates.

  8. 8.

    Supplementary Table 3

    Phenotypic and mapping data of aliphatic glucosinolates.

  9. 9.

    Supplementary Table 4

    Identification of flavonols.

  10. 10.

    Supplementary Methods

  11. 11.

    Supplementary Note

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DOI

https://doi.org/10.1038/ng1815

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