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A genomics and multi-platform metabolomics approach to identify new traits of rice quality in traditional and improved varieties

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Abstract

Using a novel approach combining four complementary metabolomic and mineral platforms with genome-wide genotyping at 1536 single nucleotide polymorphism (SNP) loci, we have investigated the extent of biochemical and genetic diversity in three commercially-relevant waxy rice cultivars important to food production in the Lao People’s Democratic Republic (PDR). Following cultivation with different nitrogen fertiliser regimes, multiple metabolomic data sets, including minerals, were produced and analysed using multivariate statistical methods to reveal the degree of similarity between the genotypes and to identify discriminatory compounds supported by multiple technology platforms. Results revealed little effect of nitrogen supply on metabolites related to quality, despite known yield differences. All platforms revealed unique metabolic signatures for each variety and many discriminatory compounds could be identified as being relevant to consumers in terms of nutritional value and taste or flavour. For each platform, metabolomic diversity was highly associated with genetic distance between the varieties. This study demonstrates that multiple metabolomic platforms have potential as phenotyping tools to assist breeders in their quest to combine key yield and quality characteristics. This better enables rice improvement programs to meet different consumer and farmer needs, and to address food security in rice-consuming countries.

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Acknowledgments

All the authors acknowledge funding from the EU for the project META-PHOR (FOOD-CT-2006-036220) which was part of FP VI. RDH, RCHV and RM acknowledge additional support from the Centre for BioSystems Genomics, an initiative under the auspices of the Netherlands Genomics Initiative. MAF acknowledges additional support from the International Rice Research Institute (IRRI). CB acknowledges support from IRRI, KKU and NAFRI. University of Copenhagen acknowledges additional support from HarvestPlus to the Danish Plant Research Network entitled ‘Supporting the Foundation for Iron and Zinc Biofortification in Beans, Rice and Wheat’. Bordeaux Metabolome Facility acknowledge additional support from IBiSA and INRA CNOC, and Daniel Jacob for developing and maintaining the MeRy-B database.

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Authors and Affiliations

  1. Grain Quality, and Nutrition Centre, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines

    M. N. Calingacion, C. Boualaphanh, V. D. Daygon, R. Anacleto, R. Sackville Hamilton & M. A. Fitzgerald

  2. Khon Kaen University, Khon Kaen, Thailand

    C. Boualaphanh

  3. Rice and Cash Crop Research Institute, Vientiane, Lao PDR

    C. Boualaphanh

  4. INRA—UMR1332 Fruit Biology and Pathology, Centre INRA de Bordeaux, 33140, Villenave d’Ornon, France

    B. Biais, C. Deborde & A. Moing

  5. Metabolome-Fluxome Facility of Bordeaux Functional Genomics Center, IBVM, Centre INRA de Bordeaux, 33140, Villenave d’Ornon, France

    C. Deborde, M. Maucourt & A. Moing

  6. Université de Bordeaux—UMR1332 Fruit Biology and Pathology, 33140, Villenave d’Ornon, France

    M. Maucourt

  7. Plant Research International, P.O. Box 98, 6700AB, Wageningen, The Netherlands

    R. Mumm, R. C. H. de Vos & R. D. Hall

  8. Centre for BioSystems Genomics, P.O. Box 98, 6700AB, Wageningen, The Netherlands

    R. Mumm, R. C. H. de Vos & R. D. Hall

  9. Max-Planck-Institute of Molecular Plant Physiology (MPIMP), Am Mühlenberg 1, 14476, Potsdam-Golm, Germany

    A. Erban & J. Kopka

  10. Plant and Soil Science Section, Department of Agriculture and Ecology, Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Copenhagen, Denmark

    T. H. Hansen, K. H. Laursen & J. K. Schjoerring

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  1. M. N. Calingacion
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  2. C. Boualaphanh
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  3. V. D. Daygon
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  4. R. Anacleto
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  5. R. Sackville Hamilton
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  6. B. Biais
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  7. C. Deborde
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  8. M. Maucourt
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  9. A. Moing
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  10. R. Mumm
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  11. R. C. H. de Vos
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  12. A. Erban
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  13. J. Kopka
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  14. T. H. Hansen
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  15. K. H. Laursen
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  16. J. K. Schjoerring
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  17. R. D. Hall
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  18. M. A. Fitzgerald
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Correspondence to M. A. Fitzgerald.

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Calingacion, M.N., Boualaphanh, C., Daygon, V.D. et al. A genomics and multi-platform metabolomics approach to identify new traits of rice quality in traditional and improved varieties. Metabolomics 8, 771–783 (2012). https://doi.org/10.1007/s11306-011-0374-4

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