Development and application of high-resolution melting DNA markers for the polygenic control of tuber skin colour in autotetraploid potato

Abstract

There is a growing niche market for coloured-skin potatoes, and breeders are developing new cultivars that not only exhibit coloured tuber skin but are also improved for agronomic and nutritional traits. Molecular markers provide a mechanism to increase the efficiency of such breeding programmes through marker-assisted selection (MAS) of both parents and elite seedlings in breeding populations. In our study, we used next-generation sequencing and high-resolution DNA melting (HRM) to develop single nucleotide polymorphism (SNP)-based markers from candidate genes associated with tuber skin colour in tetraploid potato, including small amplicon assays and dosage-sensitive unlabelled probes. We present SNP-based HRM markers for Stan2 and Stan3 (D locus), dfr (R locus) and f3′5′h (P locus) as predictors of tuber skin colour in potato, employing a genetic resource of 19 parental accessions for marker development and then demonstrating their application in three segregating populations. To our knowledge, this is not only the first report of HRM unlabelled probe and short amplicon assays at the D locus, but also the first report of the implementation of MAS for tuber skin colour, using a combination of markers at the D, R and P loci. Our estimation of allele dosage for these genes highlights the usefulness of this methodology for parental selection targeting oligogenic traits.