Genome-wide Genetic Marker Discovery and Genotyping Using Next-Generation Sequencing

Nat Rev Genet. 2011 Jun 17;12(7):499-510. doi: 10.1038/nrg3012.

Abstract

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Algorithms
  • Animals
  • Chromosome Mapping / methods*
  • Genetic Association Studies / methods*
  • Genetic Association Studies / trends
  • Genetic Markers* / genetics
  • Genetic Markers* / physiology
  • Genome / genetics*
  • Genomics / methods*
  • Genomics / trends
  • Genotype
  • High-Throughput Nucleotide Sequencing / methods*
  • High-Throughput Nucleotide Sequencing / trends
  • Humans
  • Models, Biological

Substances

  • Genetic Markers