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High-density genotyping: an overkill for QTL mapping? Lessons learned from a case study in maize and simulations

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Abstract

High-density genotyping is extensively exploited in genome-wide association mapping studies and genomic selection in maize. By contrast, linkage mapping studies were until now mostly based on low-density genetic maps and theoretical results suggested this to be sufficient. This raises the question, if an increase in marker density would be an overkill for linkage mapping in biparental populations, or if important QTL mapping parameters would benefit from it. In this study, we addressed this question using experimental data and a simulation based on linkage maps with marker densities of 1, 2, and 5 cM. QTL mapping was performed for six diverse traits in a biparental population with 204 doubled haploid maize lines and in a simulation study with varying QTL effects and closely linked QTL for different population sizes. Our results showed that high-density maps neither improved the QTL detection power nor the predictive power for the proportion of explained genotypic variance. By contrast, the precision of QTL localization, the precision of effect estimates of detected QTL, especially for small and medium sized QTL, as well as the power to resolve closely linked QTL profited from an increase in marker density from 5 to 1 cM. In conclusion, the higher costs for high-density genotyping are compensated for by more precise estimates of parameters relevant for knowledge-based breeding, thus making an increase in marker density for linkage mapping attractive.

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Acknowledgments

This research was financed by the Deutsche Forschungsgemeinschaft (DFG) research grant ME 2260/6-1 and supported by funds from DFG (Grant No. 1070, International Research Training Group “Sustainable Resource Use in North China”) to M. Stange and Albrecht E. Melchinger. Part of the SNP analysis of this research was supported by the project “Cornfed” by the French National Agency for Research (ANR), the German Federal Ministry of Education and Research (BMBF), and the Spanish Ministry of Science and Innovation (MICINN). Part of this research was conducted in collaboration between the University of Hohenheim and CYMMIT under the Federal Ministry for Economic Cooperation and Development (BMZ) founded project “Abiotic stress tolerant maize for increasing income and food security among the poor in South and Southeast Asia”.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standard

The experiments performed within this study comply with the current laws of Germany.

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Authors and Affiliations

  1. Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany

    Michael Stange, H. Friedrich Utz, Tobias A. Schrag & Albrecht E. Melchinger

  2. State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany

    Tobias Würschum

Authors
  1. Michael Stange
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  2. H. Friedrich Utz
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  3. Tobias A. Schrag
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  4. Albrecht E. Melchinger
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  5. Tobias Würschum
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Corresponding author

Correspondence to Tobias Würschum.

Additional information

Communicated by J. Yan.

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Stange, M., Utz, H.F., Schrag, T.A. et al. High-density genotyping: an overkill for QTL mapping? Lessons learned from a case study in maize and simulations. Theor Appl Genet 126, 2563–2574 (2013). https://doi.org/10.1007/s00122-013-2155-0

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  • DOI: https://doi.org/10.1007/s00122-013-2155-0

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