Integrated Analysis of Transcriptome and Metabolome Reveals Metabolite Biosynthesis in Pigmented Potatoes

Potato (<i>Solanum tuberosum</i> L.), the fourth most important food crop worldwide, serves as a multi-purpose resource for food, feed and industrial raw materials, and plays a pivotal role in safeguarding food security, diversifying dietary structure and boosting the development of agricultural economy. With increasing consumer demand for nutritional quality, elucidating the regulatory mechanisms of potato quality traits has become a research priority. In this study, three potato cultivars with distinct coloration were employed as materials. Metabolomic profiling identified a total of 1128 metabolites, and revealed that pigmented potato cultivars accumulated higher levels of flavonoids and linoleic acid derivatives compared with the white-fleshed cultivar. Transcriptomic analysis uncovered numerous differentially expressed genes (DEGs) among the three cultivars; notably, DEGs in pigmented cultivars were significantly enriched in pathways related to terpenoid backbone biosynthesis, flavonoid biosynthesis, linoleic acid metabolism, and starch and sucrose metabolism. Integrated multi-omics analysis revealed that the high expression of structural genes in the flavonoid biosynthesis pathway is strongly associated with flavonoid accumulation in pigmented potatoes, suggesting that transcriptional upregulation of these genes may be a key driver of flavonoid biosynthesis. Furthermore, several MYB and WD40 family transcription factors were identified as potential regulators of flavonoid and anthocyanin biosynthesis in potato. Collectively, our study provides insight into the regulatory mechanisms underlying the biosynthesis of secondary metabolites in potato by combining transcriptomic and metabolomic approaches, and the findings provide a valuable theoretical basis for the genetic improvement of potato nutritional quality in future breeding programs.