Universiteit Leiden

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Research project

Versatile SNP genotyping

The SNP genotyping line offers flexible genotyping for small and large projects at affordable price and high quality. The use as SNPs as molecular markers is very versatile and can be used for a wide variety of scientific questions ranging from paternity analysis, conservatuion genetis towards QTL mapping and marker assisted breeding.

Klaas Vrieling


NCB Naturalis

Scientific relevance

Next generation sequencing brought the capacity to develop, at affordable prices, large numbers of molecular markers for non-model species. To apply next generation sequence derived markers in ecological, evolutionary and medical research, flexible high throughput genome variant genotyping, such as SNPs, is needed to advance these. The flexibility in use is the key factor in this equipment which is lacking in other high throughput genotyping techniques such as arrays. Fields of research for which a genome variant analyzer will prove indispensable for the applicants include: studying natural selection in the wild, detecting the origin and evolutionary change of invasive species, the risk assessment of GMOs, (meta-)population genetics at molecular level, plant breeding, forensics and individualized medicine.

Material & Methods

The SNP line use the patented KASP technique. In single wells an allelespecific PCR lables the different SNP alleles that can be autamtically by a plate reader. The SNP line is able to handel 1536 wells plates to assure high throughput.

Results & Conclusions

The SNP line is well established and produces high quality SNP calling for widely different organisms.


Findings of the different projects are published in peer reviewed journals and serve a starting point for new projects.

Why Leiden University?

Leiden University in cooperation with LUMC and Naturalis have strong reputation for Evolutionary, molecular and medical research. The SNP genotyping line is embedded in the existing molecular facilities (DNAmarkerpoint and the Leiden Genome and Technology Centre) that serve the needs of the participants

Social relevance

Results of the SNP genotyping line are used for markerassisted breeding in several project for improving crop resistance . The results are also used for the protection of endangered species by providing data on conservation genetics.

  • Rong J, Lammers Y, Strasburg  JL, Schidlo NS, Ariyurek Y, de Jong TJ, Klinkhamer PGL, Smulders MJM, Vrieling K. 2014. New insights into domestication of carrot from root transcriptome analyses. BMC Genomics 15:895 doi:10.1186/1471-2164-15-895.

The SNP genotyping line is used for educational purposes in research projects of student internships and is a part of the course Molecular Techniques.

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