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 simultaneously. RAD-Seq uses a single restriction enzyme to selectively fragment the DNA, followed by high-throughput sequencing of a specific portion of the fragments. This approach allows for the multiplexing of many individuals into a single sequencing lane while achieving deep coverage. RAD-Seq's strengths include its versatility, cost-effectiveness, and ability to generate large amounts of data from consistent genomic regions across extensive sample populations, all without the need for a reference genome.

APPLICATIONS

Due to its independence from a reference genome, RAD-Seq is applicable in various fields such as ecology, evolution, conservation biology, and population genetics, especially for organisms with limited genomic resources. RAD-Seq data can be utilized to identify genetic markers, construct genetic maps, analyze population structure, and perform phylogenetic studies. Unlike Sequence-Based Genotyping (SBG), RAD-Seq supports paired-end sequencing to build contigs (average 400-800 bp) and eliminate PCR duplicates, enhancing the accuracy of downstream analyses. This makes RAD-Seq particularly suitable for applications such as:

  • Linkage Mapping

  • Phylogenetics

  • Population Genetics

  • Genome-Wide Association Studies (GWAS)

  • Haplotyping

EXAMPLE RAD-SEQ PROJECT

Genetic Mapping, Phylogenetics, Molecular Breeding

Surveyed >95 agronomically important non-food crop

Employed the PstI enzyme to fragment genomes at over 60,000 locations

Generated 4 million 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

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SBG/ddRAD-Seq