The inhibition effect of high temperature stress on potato tuber skin coloring mainly occurred in the belowground part of the plant.

High temperature stress leads to a dramatic reduction of both the anthocyanin concentration and the appearance quality of colored potatoes. However, it remains uncertain if the high temperature impacts potato tuber skin coloring through only the aerial or belowground parts of the plant, or through their interaction; and it's underlying reason is still unclear. In this study, the red-skin cultivar Qingshu9 (Qs9) was exposed to the high-temperature (30 °C) treatment on the belowground part alone (BH), aerial part alone (AH) and entire plant (EH), and the normal-temperature treatment on entire plant (EN) as control. The results indicated that the total anthocyanin content in tuber skin of the BH treatment was significantly lower than the EN and AH treatment, and there was no accumulation of cyanidin and pelargonidin in BH treatment, only peonidin. Compared with the EN treatment, the decrease rate of total anthocyanin content of the AH treatment was much smaller than the BH treatment, and the composition of anthocyanin did not change. Transcriptome analysis showed the downregulated DEGs of BH vs EN, BH vs AH and AH vs EN were significantly associated with the anthocyanin synthesis and metabolism pathway. High temperature inhibited anthocyanin synthesis by reducing the expression of key genes (StPAL, StF3H, StF3'H, StF3'5'H, StDFR and StANS) in the anthocyanin synthesis pathway. In summary, high temperature inhibits anthocyanin synthesis in tuber skin by downregulating key genes, and this inhibitory effect mainly occurs through the belowground part of the plant.