GBS and RADseq

Question

[shynilasanthi]

Can someone please tell me the difference between GBS and RADseq? and which one is better for SNP discovery?

[h.mon]

Why don't you do some searching and reading? There are lots of forum posts (e.g. here and here), papers (e.g. here), technical brochures (e.g. here) and presentations (e.g. here)

[shynilasanthi]

Thank you very much. I will refer them. I got some confusing answers when I was searching. That's why I thought to post my question here.

Answer 1

[William]

As umbrella terms GBS and RadSeq mean the same thing. A sequencing protocol where restriction enzymes and DNA restriction sites are involved.

See also this RadSeq/GBS Nature Genetics Review from beginning of 2016. It has some nice tables of all different GBS/RadSeq methods: http://www.nature.com/nrg/journal/v17/n2/full/nrg.2015.28.html

My preference here is to use RadSeq as the umbrella term, it actually specifies that restriction enzymes are involved, which distinguishes RadSeq/GBS from other sequencing technologies. RadSeq: restriction site-associated DNA sequencing

The term GBS, Genotyping By Sequencing, only makes sense from the perspective of outdated non-sequencing gel based genotyping methods like Restriction Fragment Length Polymorphism (RFLP). The term GBS implicitly assumes you are talking about restriction site based genotyping, as if that is the only way to genotype. Some people also use GBS as an umbrella term for RNA-seq, but that is just plain wrong and very confusing in my view.

From the perspective of the sequencing world the term GBS, Genotyping By Sequencing, does not mean anything. Every sequencing technology does Genotyping By Sequencing:

• whole genome Genotyping By Sequencing,
• exome Genotyping By Sequencing,
• amplicon Genotyping By Sequencing

• capture based Genotyping By Sequencing

  etc. In the sequencing world it is impossible to Genotype Without Sequencing, GWS ;).

Next to being umbrella terms GBS and RadSeq are also trademark names and used in product names and product description. So it depends on which company you talk to which name they will use.

But in the ends, all these RadSeq and GBS products are a variation to the idea/technology of doing sequencing associated to restriction sites in the genome. Look at the above mentioned nature genetics review so see pro's and con's of the different RadSeq/GBS variations.

[shynilasanthi]

Thank you so much William. That was descriptive and helpful.