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Population structure, genetic diversity and linkage disequilibrium in elite winter wheat assessed with SNP and SSR markers

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Abstract

Modern genomics approaches rely on the availability of high-throughput and high-density genotyping platforms. A major breakthrough in wheat genotyping was the development of an SNP array. In this study, we used a diverse panel of 172 elite European winter wheat lines to evaluate the utility of the SNP array for genomic analyses in wheat germplasm derived from breeding programs. We investigated population structure and genetic relatedness and found that the results obtained with SNP and SSR markers differ. This suggests that additional research is required to determine the optimum approach for the investigation of population structure and kinship. Our analysis of linkage disequilibrium (LD) showed that LD decays within approximately 5–10 cM. Moreover, we found that LD is variable along chromosomes. Our results suggest that the number of SNPs needs to be increased further to obtain a higher coverage of the chromosomes. Taken together, SNPs can be a valuable tool for genomics approaches and for a knowledge-based improvement of wheat.

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Acknowledgments

This research was conducted within the BMBF-funded HYWHEAT project (Grant ID: FKZ0315945D). S.M. Langer was supported by the Deutsche Forschungsgemeinschaft under Grant number WU 658/1-1.

Author information

Author notes

  1. Jochen C. Reif

    Present address: Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Gatersleben, Germany

Authors and Affiliations

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

    Tobias Würschum, Simon M. Langer, C. Friedrich H. Longin & Jochen C. Reif

  2. KWS LOCHOW GMBH, 29303, Bergen, Germany

    Viktor Korzun & Erhard Ebmeyer

  3. Department of Plant Pathology, 4024 Throckmorton Plant, Sciences Center, Kansas State University, Manhattan, KS, 66506, USA

    Eduard Akhunov

  4. Nordsaat Saatzuchtgesellschaft mbH, 38895, Langenstein, Germany

    Ralf Schachschneider

  5. Limagrain GmbH, 31226, Peine-Rosenthal, Germany

    Johannes Schacht

  6. Lantmännen SW Seed Hadmersleben GmbH, 39398, Hadmersleben, Germany

    Ebrahim Kazman

Authors
  1. Tobias Würschum
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  2. Simon M. Langer
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  3. C. Friedrich H. Longin
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  10. Jochen C. Reif
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Corresponding author

Correspondence to Tobias Würschum.

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Communicated by X. Xia.

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Würschum, T., Langer, S.M., Longin, C.F.H. et al. Population structure, genetic diversity and linkage disequilibrium in elite winter wheat assessed with SNP and SSR markers. Theor Appl Genet 126, 1477–1486 (2013). https://doi.org/10.1007/s00122-013-2065-1

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