Restriction site associated DNA sequencing (RAD Sequencing) is a method that involves cutting a genome with at least one restriction enzyme and sequencing the ends of the resulting fragments on a next-generation sequencer (preferably on an Illumina platform). The fragments from one individual are ligated to a modified Illumina adapter containing a unique identifying sequence (Barcodes). The fragments from many samples can be pooled together and sequenced on a single flow cell lane.
The resulting reads can be identified and separated by means of the unique barcodes at the start of each sequencing read. By sequencing a lot of samples of interest in just one lane this way, and comparing the tags to the individuals, many biologically relevant SNPs and genetic loci can be identified in a single experiment. It is a very economical way of identifying SNPs even when the reference genome is not defined. AgriGenome has optimized dd (Double digest) RAD in-house and can offer this service to clients at an affordable cost, using Illumina HiSeq and MiSeq platforms.