RAD-SEQ
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WHAT IS RAD-SEQ?
Restriction site-associated DNA sequencing (RAD-Seq) is a genomic sequencing technique that sequences the same subset of a genome across a large number of samples at one time. RAD-Seq uses a single restriction enzyme to selectively fragment the DNA, followed by high-throughput sequencing of a specific portion of the fragments. Because it selectively sequences the same smaller portion of the genome, many individuals can be multiplexed into a single lane while achieving deep coverage. RAD-Seq’s strengths include its versatility, cost-effectiveness, and ability to generate large amounts of data from the same regions of a genome across a large population of samples quickly and without the need for a reference genome.
APPLICATIONS
Because RAD-Seq does not require a reference genome it can be used for a variety of applications in fields such as ecology, evolution, conservation biology, and population genetics where most organisms have limited or no genomics resources. RAD-Seq data can be used to identify genetic markers and create a genetic map, study population structure, and perform phylogenetic analysis. RAD-Seq is unique from SBG in its ability to be used in a paired-end context to build contigs (ave. 400-800 bp) and remove PCR duplicates, which can improve the accuracy of downstream analyses. This makes RAD-Seq highly desirable for applications such as:
Linkage Mapping
Phylogenetics
Population Genetics
Genome-Wide Association Studies
Haplotyping
EXAMPLE RAD-SEQ PROJECT
Genetic Mapping, Phylogenetics, Molecular Breeding
Surveyed >95 agronomically important non-food crop
Used PstI enzyme to fragment genome at 60,000+ locations
Generated 4M 2x150 bp Illumina Reads per sample
Assembled 5.7K contigs with N50 of 426 bp. Detected 7.4K SNPs that were filtered down to a core set of 1.3K for phylogenetic analysis