Project properties

Title Development of a SNP marker set for parental tests in quinoa
Group Plant Breeding, Laboratory of
Project type thesis
Credits 36 or 39
Supervisor(s) Robert van Loo en Mathijs Peters
Examiner(s) Robert van Loo
Contact info robert.vanloo@wur.nl ; Luisa.trindade@wur.nl
Begin date 2021/02/01
End date 2022/01/01
Description Quinoa is a relatively new crop that has gained popularity in the last decades. The WUR quinoa breeding programme aims to lead the transition of quinoa into a staple crop. A key element in this transition, is to develop a molecular marker set that can be used for large-scale parental tests. In other words: to identify crosses in an early stage of development. This is key, because quinoa is a self-pollinating crop with only ~2.5 - 10% outcrossing. Early identification of crosses results in saving space and time.

The project
By comparing the C. quinoa reference genome and the genomes of varieties �Red-Carina� and �Pasto� we were able to find thousands of polymorphic loci. By using Nugen technology (https://www.nugen.com/products/allegro-targeted-genotyping-v2) these polymorphic loci were used to identify ~5000 SNP positions, of which 1200 SNPs were mapped. The set of SNP positions can be used to make parental tests that would allow us to identify F1s in a very early stage of development and thereby save a lot work, space and time.

The same Nugen test was performed for 18 entries, including varieties, advanced lines and some exotic accessions. A possible thesis would be to develop a SNP marker set that can be used for parental testing for these 18 varieties. It would also involve identifying SNPs for every chromosome arm. In addition, we want to develop the SNP marker set in such a way that it allows for large-scale parental testing. A possible method would be a Competitive Allele Specific PCR (CASP or KASP).
Used skills - Developing SNP Markers
- Molecular marker mapping
- Bioinformatics
Requirements GEN30306 Genetic Analysis, Tools and Concepts (GATC), ABG30306 Genomics