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.
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.
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.