The qRT-PCR analysis was performed as described by Shi et al.38. Different tissues (root, stem, leaf, petiole, calyx, and petal tissues) were collected from a single one-year-old plant and from hairy roots treated with MeJA, abscisic acid (ABA), gibberellin (GA3), yeast extract (YE), salicylic acid (SA) and ethylene (Eth), after which the tissue samples were frozen in liquid nitrogen. Total RNA was extracted as described previously34. A qRT-PCR assay was performed using a GoTaq-qPCR Master Mix kit (Promega, China) on an Applied Biosystems StepOne Real-time PCR System (USA). The internal control was the S. miltiorrhiza Actin gene. All the primers used for qRT-PCR are listed in Supplementary Table S1. Gene expression levels were quantified using the comparative Ct method4,5.

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