Multi-omics analyses unveil dynamic metabolic and transcriptomic changes of swelling potato tubers

• Demonstrating metabolic and transcriptional dynamics in potato tubers • Sorting out stage and genotype-specific metabolic patterns from two genotypes • Identifying novel genes related to SGA and phenylpropanoid biosynthesis • MYB113 positively regulated phenolic acids biosynthesis in tuber flesh Potato is a vital global food source, yet the metabolic and transcriptional regulation governing tuber development and quality remains poorly understood. Here, we performed integrated metabolomic and transcriptomic analyses on wild and cultivated potato tubers, revealing dynamic and distinct metabolic accumulation patterns. The 849 metabolites exhibited 10 distinct temporal accumulation patterns, including six shared patterns between accessions and four genotype-specific patterns. The wild genotype exhibited an early decrease in lipids, followed by an increase in phenolic acids, whereas the cultivated genotype displayed an early increase in phenolic acids, accompanied by a decrease in some phenolic acids, amino acids, and flavonoids. A comparative analysis highlighted a key metabolic trade-off: the cultivated genotype exhibited significantly lower levels of bitter steroidal glycoalkaloids (SGAs) but higher levels of beneficial flavonoids compared to its wild counterpart. Co-expression network analysis revealed 35 SGA- and 57 phenylpropanoid-related genes that underlie metabolite dynamics. Notably, we functionally validated that the transcription factor StMYB113 plays a previously unknown role in positively regulating phenolic acid biosynthesis in tuber flesh. Our work provides a comprehensive map of tuber metabolism and a valuable resource of high-confidence targets for accelerating the genetic improvement of key potato quality traits.