@article{0734b6fc2aa047e3a4b42cc10dbf6143,
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.",
author = "Davey, {John W.} and Hohenlohe, {Paul A.} and Etter, {Paul D.} and Boone, {Jason Q.} and Catchen, {Julian M.} and Blaxter, {Mark L.}",
note = "Funding Information: We are grateful to P. Andolfatto, E. Buckler, W. Cresko, R. Elshire, E. Johnson, S. Mitchell, D. Stern and four anonymous referees for reviewing and discussing drafts of this manuscript. We thank S. Bassham, S. Baxter, C. Eland, K. Gharbi, M. Liu, J. Taggart, and P. Fuentes Utrilla for discussions that have improved our understanding of these methods. J.W.D. and M.L.B. are funded by the UK Natural Environment Research Council, grant NE/H019804/1.P.A.H. and J.M.C. received funding support from the US National Institutes of Health (NIH) grant 1R24GM079486-01A1, the US National Science Foundation grant IOS-0843392 and a Keck Foundation grant to W. Cresko. J.M.C. was also funded by the NIH National Research Service Award Ruth L. Kirschstein postdoctoral fellowship 1F32GM095213-01. P.D.E. was supported by grants R21HG003834 and R21HG006036 from the US National Human Genome Research Institute awarded to E. Johnson.",
year = "2011",
month = jun,
doi = "10.1038/nrg3012",
language = "English (US)",
volume = "12",
pages = "499--510",
journal = "Nature Reviews Genetics",
issn = "1471-0056",
publisher = "Nature Research",
number = "7",
}