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

Overview

Journal Nat Rev Genet

Specialty Genetics

Date 2011 Jun 18

PMID 21681211

Citations 908

Authors

John W Davey

Paul A Hohenlohe

Paul D Etter

Jason Q Boone

Julian M Catchen

Mark L Blaxter

Affiliations

Soon will be listed here.

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.

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