Review

Nature Reviews Genetics 12, 499-510 (July 2011) | doi:10.1038/nrg3012

Article series: Study designs

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

John W. Davey1, Paul A. Hohenlohe2, Paul D. Etter3, Jason Q. Boone4, Julian M. Catchen2 & Mark L. Blaxter1,5  About the authors

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The advent of next-generation sequencing (NGS) has revolutionized genomic and transcriptomic approaches to biology. These new sequencing tools are also valuable for the discovery, validation and assessment of genetic markers in populations. Here we review and discuss best practices for several NGS methods for genome-wide genetic marker development and genotyping that use restriction enzyme digestion of target genomes to reduce the complexity of the target. These new methods — which include reduced-representation sequencing using reduced-representation libraries (RRLs) or complexity reduction of polymorphic sequences (CRoPS), restriction-site-associated DNA sequencing (RAD-seq) and low coverage genotyping — are applicable to both model organisms with high-quality reference genome sequences and, excitingly, to non-model species with no existing genomic data.

Author affiliations

  1. Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King's Buildings, West Mains Road, Edinburgh, EH9 3JT, UK.
  2. Institute of Ecology and Evolution, University of Oregon, Pacific Hall, Eugene, Oregon 97403-5289, USA.
  3. Institute of Molecular Biology, University of Oregon, Klamath Hall, Eugene, Oregon 97403-1229, USA.
  4. Floragenex, Inc., 1,900 Millrace Drive, Eugene, Oregon 97403, USA.
  5. The GenePool Genomics Facility, University of Edinburgh, Ashworth Laboratories, King's Buildings, West Mains Road, Edinburgh, EH9 3JT, UK.

Correspondence to: John W. Davey1 Email: john.davey@ed.ac.uk

Published online 17 June 2011