title: Genome-wide genetic marker discovery and genotyping using next-generation sequencing.
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.
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King's Buildings, West Mains Road, Edinburgh, EH9 3JT, UK. john.davey@ed.ac.uk
authors.forename: John W
authors.initials: JW
authors.lastname: Davey
authors.forename: Paul A
authors.initials: PA
authors.lastname: Hohenlohe
authors.forename: Paul D
authors.initials: PD
authors.lastname: Etter
authors.forename: Jason Q
authors.initials: JQ
authors.lastname: Boone
authors.forename: Julian M
authors.initials: JM
authors.lastname: Catchen
authors.forename: Mark L
authors.initials: ML
authors.lastname: Blaxter
mesh_terms: D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D056726:Genetic Association Studies / Q000379:methods* / Q000639:trends; D005819:Genetic Markers / Q000235:genetics / Q000502:physiology; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods* / Q000639:trends; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000639:trends; D006801:Humans; D008954:Models, Biological
chemical_list: D005819:Genetic Markers