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Genetic structure and diversity of European flint maize populations determined with SSR analyses of individuals and bulks

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Abstract

Landraces of maize represent a valuable genetic resource for breeding and genetic studies. Using simple sequence repeat (SSR) markers, we analysed five flint maize populations from Central Europe that had played an important role in the pre-hybrid era in Germany. Our objectives were to (1) investigate the molecular genetic diversity within and among the populations based on the SSR analysis of individuals, (2) compare these results of the SSR analysis based on individuals with those based on bulks, (3) examine genotype frequencies for deviations from Hardy–Weinberg equilibrium (HWE) at individual loci, and (4) test for linkage disequilibrium (LD) between pairs of loci within populations. Thirty individuals and their bulked DNA per population were fingerprinted with 55 SSR markers. Across all populations, 46.7% of the SSR markers deviated significantly from HWE, with an excess of homozygosity in 97% of the cases. This excess of homozygosity can largely be explained by experimental errors during the amplification of SSRs apart from genuine genetic causes. Allele frequencies of the SSR analyses of individuals and bulks were significantly correlated (r=0.85, P< 0.01), suggesting that SSR analysis of bulks is very cost-effective for large-scale molecular characterisation of germplasm collections. No evidence for genome-wide LD among pairs of loci was observed, indicating that the populations are well suited for high resolution association mapping studies.

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Acknowledgments

This research was part of project ‘Genetic Diversity in Agriculture: Temporal Flux, Sustainable Productivity and Food Security’, which was supported by a research grant from the European Union in Framework 5 Quality of life and management of living resources program (QLRT-2000-00934). We gratefully acknowledge the technical assistance of Ms. E. Kokai-Kota in generating part of the SSR data. The authors thank two anonymous reviewers for their valuable suggestions.

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Authors and Affiliations

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

    Jochen C. Reif, Sonia Hamrit, Martin Heckenberger, Wolfgang Schipprack, Hans Peter Maurer & Albrecht E. Melchinger

  2. Crop Science Department, University of Illinois, S-110 Turner Hall MC 046 1102 S Goodwin Ave, Urbana Champaign, IL, 61801, USA

    Martin Bohn

Authors
  1. Jochen C. Reif
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  2. Sonia Hamrit
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  3. Martin Heckenberger
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  4. Wolfgang Schipprack
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  5. Hans Peter Maurer
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  6. Martin Bohn
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  7. Albrecht E. Melchinger
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Correspondence to Albrecht E. Melchinger.

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Communicated by D. A. Hoisington

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Reif, J.C., Hamrit, S., Heckenberger, M. et al. Genetic structure and diversity of European flint maize populations determined with SSR analyses of individuals and bulks. Theor Appl Genet 111, 906–913 (2005). https://doi.org/10.1007/s00122-005-0016-1

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  • DOI: https://doi.org/10.1007/s00122-005-0016-1

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