Torreya grandis, a prominent tree species of the autochthonous subtropical region of China, possesses a drupe-like fruit containing a nut that is rich in nutrients and bioactive compounds. However, the effect of calcium (Ca2+) sugar alcohol (CSA), a newly developed chelated Ca2+-fertilizer, on the secondary metabolism of phenolics in T. grandis nuts is largely unknown, for which transcriptomic and metabolomic analysis was carried out.

Our results indicated that a new regulatory module, Ca2+-AP2-HCT, involved in the regulation of phenolic acid biosynthesis was revealed, expanding the understanding of the role of Ca2+ fertilizers in plant secondary metabolism.

Transcriptome sequencing detected 47,064 transcripts, and several phenolic acid biosynthesis pathway-related genes were identified. Correlation analysis showed that the four transcription factors, TgWRKY1, TgAP2-1, TgAP2-3, and TgAP2-4, were positively associated with the accumulation of phenolic acids. Furthermore, the binding of TgAP2-1 to the TgHCT promoter was confirmed using yeast one hybrid and dual-luciferase assays. Furthermore, the expression of TgHCT in Nicotiana enhanced the total flavonoid content. Conclusions: Our results indicated that a new regulatory module, Ca2+-AP2-HCT, involved in the regulation of phenolic acid biosynthesis was revealed, expanding the understanding of the role of Ca2+ fertilizers in plant secondary metabolism.