What is Genotyping-by-Sequencing?

Genotyping-by-Sequencing (GBS) is a method for molecular marker discovery and genotyping which has enjoyed broad use in many areas of genomics research. GBS allows the simultaneous discovery and genotyping of thousands to millions of single nucleotide polymorphisms depending on the genetic diversity sampled. It was first developed to provide a low cost, high throughput genetic marker platform for plant breeding in corn.

That was just the beginning. In addition to agricultural applications, genotyping-by-sequencing has enabled the use of modern genomics tools for researchers in fields such as ecology and conservation biology. This system can be used without a reference genome and is ideal for non-model organisms. To see how you can work with the original developer to apply GBS to your research question, go to our services page.

How does it work?

GBS combines the data generation power of Illumina DNA sequencing with long used and well known molecular biology techniques in a streamlined method to generate many molecular markers. To take advantage of the huge amount of sequence data generated by Illumina sequencing and reduce the cost per sample, GBS uses an efficient DNA bar coding system which allows us to combine up to 384 samples for sequencing.

5 Main Steps

  1. Cut up the DNA into fragments in a predictable way using methylation sensitive restriction enzymes. One can think of these as very specialised molecular scissors.
  2. Attach specially designed DNA molecules (incorporating bar codes and Illumina sequencing regions) to the cut DNA using DNA ligase. Ligase can be thought of as glue or sellotape.
  3. Make many, many copies of the DNA molecules using a DNA polymerase to make a library — much like a copy machine.
  4. Sequence the library using Illumina technology, thereby generating a large data set.
  5. Perform an analysis of the data comparing the sequences and looking for differences. These differences are genetic markers.

Pictorial Overview of Laboratory Method