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.

马铃薯（Solanum tuberosum L.）是全球粮食安全第四重要的作物。它的块茎含有高浓度的抗氧化剂，特别是在具有红色或紫色色素沉着的基因型中。智利南方大学的马铃薯种质库包括在其肉和/或皮中显示色素沉着以及高水平花青素的种质，但对这些特征的遗传基础知之甚少。我们确定了D、P和R的等位基因多样性控制花青素生物合成的位点，从而控制花青素水平高和低的 96 个种质中的马铃薯块茎色素沉着。下一代测序分析表明，不同的等位基因变异体没有花青素含量的聚类。然而，D基因座中的 SNP584(G)是存在于所有高花青素种质以及 12 种具有低水平这些代谢物的种质中的碱基突变。在P基因座观察到更大的等位基因多样性，其中在大多数种质中等位基因与紫色色素沉着呈正相关。在[R位点显示较低的等位基因多样性，可能是由于红色色素种质数量较少。这项研究提供了对智利本地马铃薯多样性的深入了解，使高色素种质的分子选择能够评估可用于健康营养应用的新育种材料。