KASP Platform to Accelerate Sub-Saharan Breeding
The KASP genotyping platform complements the IGSS platform and will take up the breeding journey from the discovery science carried out under the IGSS platform to push it to the level of improved variety/product development.
-Dr Nasser Yao, Plant Molecular Breeder, BecA-ILRI Hub
Kompetitive Allele Specific PCR (KASP) is a fluorescent-based assay used to identify differences in DNA sequences. In the last four months at the BecA-ILRI Hub, a KASP genotyping platform has been established that offers the potential to dramatically empower African breeding and enable Sub-Saharan researchers to conduct globally competitive genetic research.
In a collaboration between the BecA-ILRI Hub and the John Innes Centre, Ben Kiawa and Lucy Muthui have been working with Oluwaseyi Shorinola to offer further cutting-edge breeding technologies to the BecA-ILRI Hub’s growing infrastructure. KASP itself is fast becoming a gold standard in single nucleotide polymorphism (SNP) genotyping and is certain to be an important tool in the Next-Generation breeding toolkit.
Not only is this technology comparatively easy to use, it offers high accuracy at a low cost and flexible throughput, swiftly making it the go-to platform for modern breeding approaches. Its establishment alongside the BecA-ILRI Hub’s molecular breeding platform puts this tool in the hands of the wider African research community and has already seen the platform implemented in four different crop improvement projects.
KASP works by assessing (genotyping) DNA sequence differences (polymorphisms) between individuals of the same species. These polymorphisms could be in the form of single nucleotide polymorphisms or small insertions or deletions (Indels) between individual DNA sequences.
In the past, SNPs have traditionally been genotyped using long laborious gel-based methods. More modern SNP genotyping using Next Generation Sequencing technologies (e.g Genotyping-by-Sequencing) have also been developed but these are usually expensive and only economical for genotyping enormous number of SNPs (hundreds to millions), of which only few are informative. KASP genotyping occupies a perfect middle ground between these two extremes as it offers a quick and easy-to-use method for genotyping selected number of important and informative SNPs in a fast and affordable way.
An Integrated Platform
These developments at the Hub comes at a time when the DartSeq high-throughput GBS platform, implemented by the Integrated Genotyping Service and Support (IGSS) platform, is also operating at the BecA-ILRI Hub. This IGSS-KASP combination enables the BecA-ILRI Hub to translate the big data generated by the high-throughput sequencer to breeder-friendly marker resources for developing improved sub-Saharan crop and livestock breeds. This platform is currently used for R&D and is actively building the capacity of scientists to apply the technology.
This project has been made possible by the productive partnership between the John Innes Centre (JIC) and the BecA-ILRI hub. The BecA-ILRU Hub funded the procurement of the FLUOstar Omega fluorescent plate reader used for reading the fluorescent output produced from the KASP assay.
The John Innes Centre supported the capacity building efforts on KASP genotyping at BecA-ILRI Hub by sponsoring a post-doctoral scientist- Oluwaseyi Shorinola – to training BecA staff Ben Kiawa and Lucy Muthui as well as ABCF fellows on the use of the platform. This work was overseen by BecA-ILRI Hub members, Nasser Yao, Josephine Birungi and Julius Osaso.