miR156-StSPL9 regulating the biosynthesis of flavonoids and secondary metabolites in potato tubers

The colored potatoes exhibit enhanced nutritional value due to their rich flavonoid content. Flavonoids are a class of compounds that confer a wide range of colors to plants, significantly influencing the color and quality of various plant species. Elucidating the mechanisms underlying flavonoid biosynthesis will provide important insights applicable to enhancing flavonoid accumulation in potato varieties. Through transient expression assays, we confirmed that StSPL9 is a target of miR156a. Functional studies revealed that miR156a overexpression reduces flavonoid content, a phenotype reversed by STTM-miR156a. Expanding on this, integrated multi-omics analyses demonstrated that the miR156a-StSPL9 module plays a systematic regulatory role in the biosynthesis pathways of flavonoids and anthocyanins in potato tubers. These results suggest that key downstream flavonoid pathway genes (e.g., CHS2, F3H, HST, CHS1A, BEATH, CHIL2, F3'5'H, FGGT1, and U79B6) may be regulated by miR156a-StSPL9 module, potentially contributing to the increased accumulation of hesperetin, kaempferol, and quercetin in potato tubers. By elucidating miR156a-StSPL9 regulatory module, this work provides novel insights into the metabolic networks of Solanum species and thereby establishes a foundation for the enhancement of nutritional quality in potatoes.