Rapid SNP Discovery Using Sequenced RAD Markers
Building on our RAD marker technology, we have published a major advance that combines Restriction site Associated DNA (RAD) with next-generation sequencing for unprecedented power in genetic analysis.
The Innovation
This paper describes “RAD-seq” - the combination of RAD markers with Illumina sequencing technology. This enables simultaneous discovery and genotyping of thousands of single nucleotide polymorphisms (SNPs) in any organism.
Key Advances
The method provides:
- Thousands of genetic markers without prior sequence information
- Simultaneous SNP discovery and genotyping
- Cost-effective analysis of many individuals
- Applicable to any organism
- Enables genetic mapping and population genomics
Applications Demonstrated
We demonstrated the power of this approach for:
- Genetic mapping in model and non-model organisms
- QTL identification for complex traits
- Population genetic studies
- Rapid analysis of crosses and populations
Technical Details
The approach uses:
- Restriction enzyme digestion to sample consistent genomic locations
- Illumina sequencing of RAD tags
- Bioinformatic pipelines for SNP identification
- Statistical methods for genotype calling
Research Team
- Nathan A. Baird
- Paul D. Etter
- Tressa S. Atwood
- Mark C. Currey
- Anthony L. Shiver
- Zachary A. Lewis
- Eric U. Selker
- William A. Cresko
- Eric A. Johnson
Impact
This paper helped launch the “RAD-seq revolution” in population genomics. The method has been adopted by thousands of laboratories worldwide and has enabled genetic studies in organisms from bacteria to vertebrates.
The combination of RAD with next-generation sequencing democratized population genomics, making it accessible to researchers studying any organism, regardless of available genomic resources.
Publication: Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008). Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3(10):e3376.