2b-RAD
2b-RAD
2b-RAD is similar to ddRadseq, but uses type IIB restriction enzymes (BsaXI or AlfI) that will cleave upstream and downstream of a recognition site. This shears the target genome into a large number of DNA fragments with a constant length of 33 bp (BsaXI) or 36 bp (Alfl). These short DNA fragments can be sequenced to determine the genetic variants.
In this method, genomic DNA is first digested with a restriction enzyme (BsaXI) and adaptors with partial (NNN) overhangs are ligated to the fragments. The adaptor-ligated fragments from different samples are combined and the fragments amplified.
Pros:
- The highly reduced 2b-RAD libraries require much less sequencing for accurate genotyping
- High density of markers
- No interim purification steps reduce losses and processing time
Cons:
- Requires a reference genome
- The short tags may not be long enough for efficient locus discrimination in complex genomes
- Pecoraro C., Babbucci M., Villamor A., Franch R., Papetti C., et al. (2016) Methodological assessment of 2b-RAD genotyping technique for population structure inferences in yellowfin tuna (Thunnus albacares). Mar Genomics 25: 43-48
- Fu B., Liu H., Yu X. and Tong J. (2016) A high-density genetic map and growth related QTL mapping in bighead carp (Hypophthalmichthys nobilis). Sci Rep 6: 28679