Allelic diversity of three anthocyanin synthesis genes in accessions of native Solanum tuberosum L. ssp. tuberosum at the Potato Genebank of the Universidad Austral de Chile

The potato (Solanum tuberosum L.) is the fourth most important crop for global food security. Its tubers contain high concentrations of antioxidants, especially in genotypes with red or purple pigmentation. The Potato Genebank of the Universidad Austral of Chile includes accessions that show pigmentation in their flesh and/or skin as well as high levels of anthocyanins, but little is known about the genetic basis of these characteristics. We determined the allelic diversity at the D, P and R loci which control anthocyanin biosynthesis and consequently potato tuber pigmentation in the 96 accessions with high and low levels of anthocyanins. Next-generation sequencing analysis revealed that the different allelic variants did not cluster for anthocyanin content. However, SNP584(G) in the D locus was a base mutation present in all high-anthocyanin accessions and also in 12 accessions with low levels of these metabolites. Greater allelic diversity was observed at the P locus, where alleles correlated positively with purple pigmentation in most of the accessions. The R locus showed lower allelic diversity, probably due to the lower number of red-pigmented accessions. This study provides insight into the diversity of Chilean native potatoes, enabling the molecular selection of high-pigmented accessions to assess new breeding material that can be used in applications for healthy nutrition.