Genotyping by Sequencing (GBS)


Genotyping-by-sequencing (GBS) is a unique, cost-effective sequencing-based method for the large scale discovery and genotyping of genetic polymorphisms. 

GBS can reproducibly generate a large number of single nucleotide polymorphisms (SNPs) in complex genomes that lack reference sequences.

The approach is simpler to generate a dataset and will provide a higher level of resolution over microsatellite based genotyping.  In this way it is becoming increasingly important for genetic analysis in novel species.


Genotyping-by-sequencing (GBS) data can be used in following studies:

  • - Non-model organisms that lack reference genomes or genotyping array options
  • - Model organisms that have limited resolution genotyping array options
  • - Genetic, QTL and association mapping
  • - Population genomics and phylogeny

    The AGRF advantage

    The method developed by AGRF is a variant of the double digest RAD (ddRAD) protocol, which means it is optimised to improve efficiency and reproducibility of genotype calls while providing cost efficiencies.

    This method provides increased data quality and sequencing output, longer reads and suitability for single or paired-end sequencing.


    GBS workflow at AGRF

    To enable efficient library prep at AGRF we offer two levels of establishment services for any new project prior to batch processing.


    Standard establishment service

    All new genomes processed by AGRF for GBS will first undergo an establishment phase to determine the most suitable enzyme combination for genome digestion.


    Premium establishment service

    This option estimates tag number and polymorphism rates in two size selection windows to tune the optimal coverage of the genome to suit the scientific question.


    Batch processing

    Following the establishment of the optimal enzyme combination, GBS projects are ready for batch processing allowing up to 192x sample multiplexing which enables very high sequencing economies.


    Data delivery and options

    Once sequencing is complete de-multiplexed FastQ outputs are provided with individual SNP calling in Stacks software.

    Analysis options include;

    • - Tab-delimited maps of all the alleles in the population for the set of loci sampled
    • - Genetic linkage mapping including JoinMap, OneMap, R/QTL
    • - Population genetic analysis including Structure and GenePoP
    • - Phasing included PHASE, fastPHASE, Beagle and Plink


    Our customised approach

    We know every project is unique and that’s why we offer customised and tailor-made solutions for analysing every individual’s research topic.

    Get in touch with us to find out more on how we can help develop the right solution for your project and customise data analysis for your project.

    Want to find out more?

    Contact a local account manager.