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Lep-MAP: fast and accurate linkage map construction for large SNP datasets.

Pasi Rastas1, Lars Paulin, Ilkka Hanski

  • 1Department of Biosciences, Metapopulation Research Group, University of Helsinki, P.O. Box 65, FI-00014, Finland and Institute of Biotechnology, University of Helsinki, P.O. Box 56, FI-00014, Finland.

Bioinformatics (Oxford, England)
|October 1, 2013
PubMed
Summary

A new tool, Lepidoptera-MAP (Lep-MAP), efficiently constructs accurate linkage maps from large single nucleotide polymorphism (SNP) datasets. This method improves genome assembly and genetic studies by accounting for unique meiotic processes in certain species.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • High-throughput sequencing enables cost-efficient genotyping of millions of single nucleotide polymorphisms (SNPs).
  • Existing tools for constructing linkage maps are not optimized for large datasets, hindering genomic analyses.
  • Accurate linkage maps are crucial for de novo genome assembly, validation, refinement, and various genetic studies.

Purpose of the Study:

  • To develop a novel, efficient, and automated tool for constructing accurate linkage maps from ultradense genome-wide SNP data.
  • To address the limitations of current tools in handling large-scale genomic datasets.
  • To improve the accuracy of linkage maps by incorporating species-specific meiotic features.

Main Methods:

  • Development of Lepidoptera-MAP (Lep-MAP), a Java-based tool for linkage map construction.

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  • Utilizing data from multiple outbred families simultaneously.
  • Incorporating achiasmatic meiosis (no recombination in one sex) into the mapping process.
  • Application of a novel in-house SOLiD restriction site-associated DNA tag sequencing protocol.

    • Main Results:

    • Lep-MAP demonstrates superior performance compared to existing methods on both real and simulated data.
    • A genome-wide linkage map for the Glanville fritillary butterfly (Melitaea cinxia) was constructed using over 40,000 SNPs.
    • The tool is fast, memory-efficient, and largely automated, requiring minimal user intervention.
    • Lep-MAP successfully accounts for achiasmatic meiosis, enhancing map accuracy in relevant taxa.

    Conclusions:

    • Lep-MAP is a powerful and efficient tool for constructing accurate linkage maps from large SNP datasets.
    • The developed linkage map provides a valuable resource for the Glanville fritillary butterfly genome.
    • The method has broad applicability in genomics, particularly for species with unique meiotic characteristics.