, Volume 136, Issue 1, pp 97–107 | Cite as

Gene mapping in the wild with SNPs: guidelines and future directions

  • Jon Slate
  • Jake Gratten
  • Dario Beraldi
  • Jessica Stapley
  • Matt Hale
  • Josephine M. Pemberton


One of the biggest challenges facing evolutionary biologists is to identify and understand loci that explain fitness variation in natural populations. This review describes how genetic (linkage) mapping with single nucleotide polymorphism (SNP) markers can lead to great progress in this area. Strategies for SNP discovery and SNP genotyping are described and an overview of how to model SNP genotype information in mapping studies is presented. Finally, the opportunity afforded by new generation sequencing and typing technologies to map fitness genes by genome-wide association studies is discussed.


Gene discovery QTL Linkage Mapping SNP Wild population 



This article was prepared for a workshop on Ecological Genomics that was organised by Jacob Höglund and Gernot Segelbacher, and funded by the European Science Foundation (ESF). The authors have benefitted from insightful discussion on this and related topics with Terry Burke, Peter Visscher, Gavin Hinten and Allan McRae. Peter Visscher made the suggestion to study the variance in halfsib IBD coefficients as an indicator of marker informativeness.


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Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Jon Slate
    • 1
  • Jake Gratten
    • 1
  • Dario Beraldi
    • 2
  • Jessica Stapley
    • 1
  • Matt Hale
    • 1
    • 3
  • Josephine M. Pemberton
    • 2
  1. 1.Department of Animal & Plant SciencesUniversity of SheffieldSheffieldUK
  2. 2.Institute of Evolutionary BiologyUniversity of EdinburghEdinburghScotland, UK
  3. 3.Department of Forestry and Natural ResourcesPurdue UniversityIndianaUSA

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