Association mapping in an elite maize breeding population

Theoretical and Applied Genetics volume 123, Article number: 847 (2011) Cite this article

Abstract

Association mapping (AM) is a powerful approach to dissect the genetic architecture of quantitative traits. The main goal of our study was to empirically compare several statistical methods of AM using data of an elite maize breeding program with respect to QTL detection power and possibility to correct for population stratification. These models were based on the inclusion of cofactors (Model A), cofactors and population effect (Model B), and SNP effects nested within populations (Model C). A total of 930 testcross progenies of an elite maize breeding population were field-evaluated for grain yield and grain moisture in multi-location trials and fingerprinted with 425 SNP markers. For grain yield, population stratification was effectively controlled by Model A. For grain moisture with a high ratio of variance among versus within populations, Model B should be applied in order to avoid potential false positives. Model C revealed large differences among allele substitution effects for trait-associated SNPs across multiple plant breeding populations. This heterogeneous SNP allele substitution effects have a severe impact for genomic selection studies, where SNP effects are often assumed to be independent of the genetic background.

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Acknowledgments

We would like to thank Dr. Raffaele Capitanio from Syngenta Seeds for providing the information on phenotypic data. This research was conducted within the Biometric and Bioinformatic Tools for Genomics based Plant Breeding project supported by the German Federal Ministry of Education and Research (BMBF) within the framework of GABI–FUTURE initiative. We thank two anonymous reviewers for their valuable suggestions, which considerably improved the manuscript.

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Affiliations

  1. State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany

    Wenxin Liu, Manje Gowda, Jana Steinhoff, Hans Peter Maurer, Tobias Würschum, Carl Friedrich Horst Longin & Jochen Christoph Reif

  2. Syngenta Seeds SAS, 12, chemin de l’Hobit, B.P. 27, 31790, Saint-Sauveur, France

    Frédéric Cossic

  3. Crop Genetics and Breeding Department, China Agricultural University, 100193, Beijing, China

    Wenxin Liu

Authors
  1. Wenxin Liu
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  2. Manje Gowda
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  3. Jana Steinhoff
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  4. Hans Peter Maurer
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  5. Tobias Würschum
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  6. Carl Friedrich Horst Longin
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  7. Frédéric Cossic
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  8. Jochen Christoph Reif
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Correspondence to Jochen Christoph Reif.

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Communicated by J. Yan.

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Liu, W., Gowda, M., Steinhoff, J. et al. Association mapping in an elite maize breeding population. Theor Appl Genet 123, 847 (2011). https://doi.org/10.1007/s00122-011-1631-7

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Keywords

  • Linkage Disequilibrium
  • Association Mapping
  • Genomic Selection
  • Population Stratification
  • Heterotic Group