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Diversity and linkage disequilibrium features in a composite public/private dent maize panel: consequences for association genetics as evaluated from a case study using flowering time

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Abstract

Recent progress in genotyping and resequencing techniques have opened new opportunities for deciphering quantitative trait variation by looking for associations between traits of interest and polymorphisms in panels of diverse inbred lines. Association mapping raises specific issues related to the choice of appropriate (i) panels and marker-densities and (ii) statistical methods to capture associations. In this study, we used a panel of 314 maize inbred lines from the dent pool, composed of inbred material from public institutes (113 inbred lines) and a private company (201 inbred lines). We showed that local LD was higher and genetic diversity lower in the material of private origin than in the public material. We compared the results obtained by different software for identifying population structure and computing relatedness among lines, and ran association tests for earliness related traits. Our results confirmed the importance of the mite polymorphism of Vgt1 on flowering time, but also showed that its effect can be captured by zmRap2.7 polymorphisms located 70 kb apart. We also highlighted associations with polymorphisms within genes putatively involved in lignin biosynthesis pathway, which deserve further investigations.

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Acknowledgments

We thank Pascal Delage, Philippe Jamin, Denis Coubriche, Sophie Pin, Dominique Denoué and Christoph Mainka for the set up of the trials, traits measurements and harvest as well as Jean-Paul Muller for insightful discussions on maize germplasm and phenotypic analyses. Part of this work was financed by Syngenta Seeds; we thank them as well for the phenotypic and genetic material. We thank the University of Oslo Bioportal for providing CPU time. Part of this work was carried out by using the resources of the Computational Biology Service Unit from Cornell University, which is partially funded by Microsoft Corporation.

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Authors and Affiliations

  1. INRA, UMR de Genetique Vegetale INRA/Université Paris-Sud/CNRS, Gif-sur-Yvette, France

    M. Truntzler, S. Nicolas, D. Madur, A. Charcosset & L. Moreau

  2. Molecular Breeding, Syngenta Seeds, Saint-Sauveur, France

    N. Ranc, M. C. Sawkins, D. Lespinasse & J. Betran

  3. Université d’Orsay, UMR de Genetique Vegetale INRA/Université Paris-Sud/CNRS, Gif-sur-Yvette, France

    D. Manicacci

  4. Markers laboratory, Syngenta Seeds, Saint-Sauveur, France

    V. Ribière & P. Galaup

  5. Bioinformatics, Syngenta Seeds, Saint-Sauveur, France

    F. Servant & C. Muller

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  1. M. Truntzler
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  2. N. Ranc
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  10. C. Muller
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Correspondence to M. Truntzler.

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Truntzler, M., Ranc, N., Sawkins, M.C. et al. Diversity and linkage disequilibrium features in a composite public/private dent maize panel: consequences for association genetics as evaluated from a case study using flowering time. Theor Appl Genet 125, 731–747 (2012). https://doi.org/10.1007/s00122-012-1866-y

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