Theoretical and Applied Genetics

, 123:847 | Cite as

Association mapping in an elite maize breeding population

  • Wenxin Liu
  • Manje Gowda
  • Jana Steinhoff
  • Hans Peter Maurer
  • Tobias Würschum
  • Carl Friedrich Horst Longin
  • Frédéric Cossic
  • Jochen Christoph Reif
Original Paper

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.

Notes

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.

Supplementary material

122_2011_1631_MOESM1_ESM.doc (150 kb)
Supplementary material 1 (DOC 150 kb)

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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Wenxin Liu
    • 1
    • 3
  • Manje Gowda
    • 1
  • Jana Steinhoff
    • 1
  • Hans Peter Maurer
    • 1
  • Tobias Würschum
    • 1
  • Carl Friedrich Horst Longin
    • 1
  • Frédéric Cossic
    • 2
  • Jochen Christoph Reif
    • 1
  1. 1.State Plant Breeding InstituteUniversity of HohenheimStuttgartGermany
  2. 2.Syngenta Seeds SASSaint-SauveurFrance
  3. 3.Crop Genetics and Breeding DepartmentChina Agricultural UniversityBeijingChina

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