Best practices for implementing targeted genotyping by sequencing

Updated : Fri, November 20, 2020 @ 5:16 PM

In breeding programmes, selections based on a single or small number of markers to target traits in marker assisted selection (MAS) often miss the contributions of a large proportion of the genetic variants or small effects from small loci, which require additional breeding cycles and selections to identify the best lines to take forward. Traditional genotyping data from PCR and microsatellites or single sequence repeats (SSRs) doesn’t provide the details of variation at the sequence level while the fixed nature of arrays prevents them from being adapted to varying accessions, populations and breeding strategies.

Targeted genotyping by sequencing (GBS) combines whole genome assessment with specificity. It takes advantage of the increasing abundance of molecular markers made available through resequencing efforts in all species, which includes SNP markers, while providing the option to incorporate traits of specific markers for additional screening power. 

As more breeders are seeking better ways to improve the accuracy of their selections, many are turning towards targeted next generation sequencing (NGS) methods like targeted GBS to select and screen for their desired traits in less time. As a more forgiving technology due to its flexibility, targeted GBS assays can be modified to change its marker density according to the evolving needs of breeders on a year-to-year basis. This enables a variety of key AgBio applications such as:

  • Genomic selection/genomic prediction
  • Marker assisted selection/breeding (MAS/MAB)
  • Marker assisted backcrossing (MABC)

If you’re looking to implement targeted GBS to your plant, livestock or aquaculture breeding programmes, we've consulted with our Senior Scientist, Dusty Vyas, for her expertise in best practices. Download the article to learn about the prerequisites for a targeted GBS approach and why they’re important to reduce any hiccups you might encounter within your agrigenomic workflow.


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