Although the role of WRKY transcription factors (TFs) in colour formation has been reported in several species, their function in potato (Solanum tuberosum L.) anthocyanin biosynthesis remains unclear. In this study, the potato WRKY gene StWRKY13 was isolated and characterised. Expression analysis revealed a significantly higher StWRKY13 expression in chromatic tubers than in yellow ones. Transient activation assays showed that StWRKY13 could enhance the role of StAN2 in promoting anthocyanin biosynthesis in tobacco (Nicotiana tabacum L.). Over-expressing the StWRKY13 gene promoted anthocyanin biosynthesis in potato tubers. Further investigations indicated that StWRKY13 could interact with the StCHS, StF3H, StDFR, and StANS gene promoters and significantly enhance their activities. Our findings showed that StWRKY13 could promote anthocyanin biosynthesis by activating StCHS, StF3H, StDFR, and StANS transcription in potato tubers, thereby supporting the theoretical basis for anthocyanins formation in coloured potato tubers.

Potato, the fourth largest food crop in the world, stores nutrients in underground tubers. However, light exposure induces tuber accumulation of chlorophyll and toxic steroidal glycoalkaloids (SGAs); this unwanted trait called tuber greening causes a decline in potato quality and renders parts of tuber inedible. Despite progress in enzymatic cascades governing SGAs biosynthesis, the regulatory scheme of SGAs and chlorophyll metabolism in light-exposed tubers persists as a critical knowledge gap. Here, we identify that the blue light receptor StCRY1 plays a predominant role in light-induced tuber greening and SGA elevation, functioning as a light-controlled transcriptional switch for genes involved in SGAs and chlorophyll biosynthesis. We show that the transcription factor StHY5 acts downstream of StCRY1 to coregulate both chlorophyll and SGA metabolism. However, StMYB4, a transcription factor regulated by StHY5, promotes SGA synthesis by directly binding to SGA biosynthetic genes without affecting chlorophyll homeostasis. Furthermore, StCRY1 employs a dual strategy by modulating StMYB4 expression and physically interacting with StMYB4 to regulate its transcriptional activity. Collectively, these findings uncover a modularly coordinated control of SGA accumulation and chlorophyll biosynthesis by bifurcation of the StCRY1–StHY5 axis, providing a promising strategy to concurrently curb light-induced tuber greening and glycoalkaloids accumulation.