Document Detail

SNP discovery and genotyping for evolutionary genetics using RAD sequencing.
MedLine Citation:
PMID:  22065437     Owner:  NLM     Status:  MEDLINE    
Next-generation sequencing technologies are revolutionizing the field of evolutionary biology, opening the possibility for genetic analysis at scales not previously possible. Research in population genetics, quantitative trait mapping, comparative genomics, and phylogeography that was unthinkable even a few years ago is now possible. More importantly, these next-generation sequencing studies can be performed in organisms for which few genomic resources presently exist. To speed this revolution in evolutionary genetics, we have developed Restriction site Associated DNA (RAD) genotyping, a method that uses Illumina next-generation sequencing to simultaneously discover and score tens to hundreds of thousands of single-nucleotide polymorphism (SNP) markers in hundreds of individuals for minimal investment of resources. In this chapter, we describe the core RAD-seq protocol, which can be modified to suit a diversity of evolutionary genetic questions. In addition, we discuss bioinformatic considerations that arise from unique aspects of next-generation sequencing data as compared to traditional marker-based approaches, and we outline some general analytical approaches for RAD-seq and similar data. Despite considerable progress, the development of analytical tools remains in its infancy, and further work is needed to fully quantify sampling variance and biases in these data types.
Paul D Etter; Susan Bassham; Paul A Hohenlohe; Eric A Johnson; William A Cresko
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.    
Journal Detail:
Title:  Methods in molecular biology (Clifton, N.J.)     Volume:  772     ISSN:  1940-6029     ISO Abbreviation:  Methods Mol. Biol.     Publication Date:  2011  
Date Detail:
Created Date:  2011-11-08     Completed Date:  2012-02-22     Revised Date:  2013-06-27    
Medline Journal Info:
Nlm Unique ID:  9214969     Medline TA:  Methods Mol Biol     Country:  United States    
Other Details:
Languages:  eng     Pagination:  157-78     Citation Subset:  IM    
Institute of Molecular Biology, University of Oregon, Eugene, OR, USA.
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MeSH Terms
Base Sequence
DNA / isolation & purification
DNA Restriction Enzymes / metabolism
Electrophoresis, Agar Gel
Evolution, Molecular*
Gene Library
Genetics, Population
Genome / genetics
Genotyping Techniques / methods*
Molecular Sequence Data
Polymerase Chain Reaction
Polymorphism, Single Nucleotide / genetics*
Restriction Mapping / methods*
Ribonucleases / metabolism
Sequence Alignment
Sequence Analysis, DNA / methods*
Grant Support
1R24GM079486-01A1/GM/NIGMS NIH HHS; F32 GM078949/GM/NIGMS NIH HHS; R24 GM079486/GM/NIGMS NIH HHS; R24 OD011199/OD/NIH HHS; R24 RR032670/RR/NCRR NIH HHS
Reg. No./Substance:
9007-49-2/DNA; EC 3.1.-/Ribonucleases; EC 3.1.21.-/DNA Restriction Enzymes

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