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RAD-SeqEdit

Restriction site-associatied DNA Sequencing (RAD-seq) is a de novo sequencing tool that allows the use of a reduced representation of an organism's genome (i.e. enzymatic restricted sites), leading to deep sequence coverage of fragments near a specific type of restriction site. It is a up-and-coming genomics tool to identify high-throughput markers, mostly SNPs, in non-model organisms.

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Rad-seq method for SNP discovery. http://www.nature.com/nrg/journal/v12/n7/fig_tab/nrg3012_F1.html#figure-title

The method was pioneered using Illumina Sequencing, and it is based on the incorporation of next generation tools and RAD-tags previously used in microsatelites for SNP profiling.  

Novel papers using Rad-tags and Rad-seq for populagion-wide studies are Lewis, et al. (2007) study using EcoRI-RAD markers across Neurospora chromosomes to differenciate polymorphics loci between wild and bred crassa strains; and Baird et al. (2008) study on Stickleback fish to identify polymorphic loci, and alleles that are overly represented in a specific population. 

REFERENCESEdit

Baird, N.A., et al. 2008. Rapid SNP Discovery and Gentic Mapping Using Sequence RAD Markers. PloS One 3(10): doi:10/1271/journal.pone.0003376

Lewis, Z. et al. 2007. High-density detection of restriction-site-associated DNA markers for rapid mapping of mutated loci in Neurospora. Genetics 177, 1163-1171. 

 

 

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