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Potential causes of linkage disequilibrium in a European maize breeding program investigated with computer simulations

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Abstract

Knowledge about the forces generating and conserving linkage disequilibrium (LD) is important for drawing conclusions about the prospects and limitations of association mapping. The objectives of our research were to examine the importance of (1) selection, (2) mutation, and (3) genetic drift for generating LD in a typical maize breeding program. We conducted computer simulations based on genotypic data of Central European maize open-pollinated varieties which have played an important role as founders of the European flint heterotic group. The breeding scheme and the dimensioning underlying our simulations reflect essentially the maize breeding program of the University of Hohenheim. Results suggested that in a plant breeding program of the examined dimension and breeding scheme, genetic drift and selection are major forces generating LD. The currently used population-based association mapping tests do not explicitly correct for LD caused by these two forces. Therefore, increased type I error rates are expected if these tests are applied to plant breeding populations. As a consequence, we recommend to use family-based association tests for association mapping approaches in plant breeding populations.

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Acknowledgments

This research was conducted within the Breeding and Informatics (BRAIN) project of the Genome Analysis of the Plant Biological System (GABI) initiative (http://www.gabi.de). Financial support for B. Stich was provided by a grant from the German National Academic Foundation. The authors appreciate the editorial work of Dr. J. Muminović, whose suggestions considerably improved the style of the manuscript. The authors thank two anonymous reviewers for their valuable suggestions.

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Author notes

  1. Sonia Hamrit

    Present address: Institute for Molecular Physiology and Biotechnology, University of Rostock, 18051, Rostock, Germany

Authors and Affiliations

  1. Institute for Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593, Stuttgart, Germany

    Benjamin Stich, Albrecht E. Melchinger, Sonia Hamrit, Wolfgang Schipprack, Hans P. Maurer & Jochen C. Reif

  2. Institute for Crop Production and Grassland Research, University of Hohenheim, 70593, Stuttgart, Germany

    Hans-Peter Piepho

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  1. Benjamin Stich
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  2. Albrecht E. Melchinger
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  7. Jochen C. Reif
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Correspondence to Albrecht E. Melchinger.

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Communicated by G. Wenzel.

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Stich, B., Melchinger, A.E., Piepho, HP. et al. Potential causes of linkage disequilibrium in a European maize breeding program investigated with computer simulations. Theor Appl Genet 115, 529–536 (2007). https://doi.org/10.1007/s00122-007-0586-1

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  • DOI: https://doi.org/10.1007/s00122-007-0586-1

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