Harnessing the Genetic Diversity of the Colombian Central Collection of Potatoes to Dissect Pigmentation Genomics in Andigenum Landraces

Abstract The Colombian Central Collection of potatoes (CCC) is one of the most diverse germplasm resources in the country and a primary source of genetic variability for breeding. Approximately 67% of its accessions belong to the Andigenum group, which exhibits remarkable color diversity and associated nutraceutical potential. However, the genetic architecture of the color traits in this group remains poorly understood. In this study, we analyzed historical phenotypic data to explore the genetic basis of pigmentation in Andigenum accessions from the CCC. Color traits across tuber skin, tuber flesh, flowers, stems, and sprouts were assessed using the Royal Horticultural Society Color Chart, and Genome-Wide Association Studies (GWAS) and genomic prediction were performed using high-density SNP markers. We identified 21 significant SNP–trait associations, 12 of which overlapped or were located near loci previously reported for pigmentation or tuber-related traits, whereas the remaining nine represented novel associations. Several color traits showed moderate to high heritability ( $$h^2$$ > 0.55), and genomic prediction achieved predictive abilities of up to 0.84 for primary flower color and 0.71 for stem color. We conclude that these findings provide new insights into the genetic control of color traits in Andigenum potatoes, identify valuable molecular markers for selection, and underscore the importance of conserving and utilizing traditional landraces for the development of nutritionally enhanced cultivars and advancement of food security.