Potato Cultivar Identification in South Africa Using a Custom SNP Panel

Abstract

DNA fingerprinting is a molecular technique applied to identify genetic differences between plant cultivars or lines and is used for genetic purity testing. The suitability of single nucleotide polymorphism (SNP) panels for the fingerprinting of tetraploid potato were investigated as a new high throughput, objective, and cost-effective method instead of simple sequence repeats (SSRs) and polyacrylamide gel electrophoresis (PAGE). One-hundred and ninety (190) potato cultivars, including various cultivars currently important in South Africa, were genotyped at 500 SNP positions utilising SeqSNP by LGC Biosearch Technologies. An optimal panel of 25 SNP markers was identified that could discriminate between South African potato cultivars on genetic allele dosage. The genotypes of these SNPs were validated on selected potato genotypes using KASP (Kompetitive Allele Specific PCR) SNP assays. A database of SNP genotype profiles was compiled for all the entries of the germplasm database. The panel of 21 successful SNPs accurately identified the unique potato cultivars in the database. The KASP SNP assays of the successful SNP panel are therefore available for potato DNA fingerprinting as new germplasm, or purity test requests are submitted to ARC-VIMP. This panel provides an objective method for assigning putative cultivar identity to unknown samples submitted for fingerprinting.