Discovery and Genotyping using next gen DNA sequencing
Restriction site Associated DNA Sequencing (RAD-Seq) is a fractional genome sequencing strategy, designed to interrogate anywhere from 0.1 to 10% of a selected genome. By digesting the genome with a restriction nuclease and attaching a series of adapters to the resulting DNA fragments, large numbers of genetic variations such as SNPs can be readily identified from analysis of next generation DNA sequence data.
Discovery & Genotyping Applications
Linkage and QTL Mapping
RAD-Seq is widely used for a variety of molecular genetic studies:
- Identification of genetic variants (SNPs)
- Germplasm assessment
- Population structure
- Linkage and quantitative trait locus mapping
- Genome wide association studies
- Surveyed >95 Antarctic Krill samples with 50 Gb genome size
- Used SbfI enzyme to fragment genome at 100,000+ locations
- Generated 6.8M 1x100bp Illumina Reads per sample
- 12K sequence variants detected, filtered down to core set of 2.1K SNPs for PopGen analysis
How RAD-Seq Works
RAD-Seq works by first fragmenting the target genome using a restriction enzyme. After digestion, a series of molecular processing steps transform the DNA into a fragment library suitable for sequencing on a NGS platform.
Depending on the end goal, either single end or paired end sequencing can be used to generate the appropriate amount of information.
Sequence data is then analyzed to identify and score genetic variations in the samples or population of interest.