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Linked vs. unlinked markers: multilocus microsatellite haplotype-sharing as a tool to estimate gene flow and introgression

Authors

  • WIM J. M. KOOPMAN,

    1. Plant Research International, Wageningen UR, PO Box 16, 6700 AA Wageningen, The Netherlands,
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    • §

      These authors contributed equally to this study.

  • YINGHUI LI,

    1. The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Germplasm & Biotechnology (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, China,
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    • §

      These authors contributed equally to this study.

  • ELS COART,

    1. Unit Plant, Institute for Agricultural and Fisheries Research (ILVO), Caritasstraat 21, 9090 Melle, Belgium
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    • §

      These authors contributed equally to this study.

  • W. ERIC VAN DE WEG,

    1. Plant Research International, Wageningen UR, PO Box 16, 6700 AA Wageningen, The Netherlands,
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  • BEN VOSMAN,

    1. Plant Research International, Wageningen UR, PO Box 16, 6700 AA Wageningen, The Netherlands,
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  • ISABEL ROLDÁN-RUIZ,

    1. Unit Plant, Institute for Agricultural and Fisheries Research (ILVO), Caritasstraat 21, 9090 Melle, Belgium
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  • MARINUS J. M. SMULDERS

    1. Plant Research International, Wageningen UR, PO Box 16, 6700 AA Wageningen, The Netherlands,
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M.J.M. Smulders, Fax: +31317418094; E-mail: rene.smulders@wur.nl

Abstract

We have explored the use of multilocus microsatellite haplotypes to study introgression from cultivated (Malus domestica) into wild apple (Malus sylvestris), and to study gene flow among remnant populations of M. sylvestris. A haplotype consisted of alleles at microsatellite loci along one chromosome. As destruction of haplotypes through recombination occurs much faster than loss of alleles due to genetic drift, the lifespan of a multilocus haplotype is much shorter than that of the underlying alleles. When different populations share the same haplotype, this may indicate recent gene flow between populations. Similarly, haplotypes shared between two species would be a strong signal for introgression. As the expected lifespan of a haplotype depends on the strength of the linkage, the length [in centiMorgans (cM)] of the haplotype shared contains information on the number of generations passed. This application of shared haplotypes is distinct from using haplotype-sharing to detect association between markers and a certain trait. We inferred haplotypes for four to eight microsatellite loci on Linkage Group 10 of apple from genotype data using the program phase, and then identified those haplotypes shared between populations and species. Compared with a Bayesian analysis of unlinked microsatellite loci using the program structure, haplotype-sharing detected a partially different set of putative hybrids. Cultivated haplotypes present in M. sylvestris were short (< 1.5 cM), indicating that introgression had taken place many generations ago, except for two Belgian plants that contained a haplotype of 47.1 cM, indicating recent introgression. In the estimation of gene flow, FST based on unlinked loci indicated small (0.032–0.058) but statistically significant differentiation between some populations only. However, various M. sylvestris haplotypes were shared in nearly all pairwise comparisons of populations, and their length indicated recent gene flow. Hence, all Dutch populations should be considered as one conservation unit. The added value of using sharing of multilocus microsatellite haplotypes as a source of population genetic information is discussed.

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