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Abstract Background Light, an essential factor in plant development, exerts a significant impact on both primary and secondary metabolism in plants. Althaea officinalis, commonly known as marshmallow, offers versatile applications through its leaves and roots. With a plethora of identified bioactive compounds and their extensive use in food, health, and supplements, it is widely cultivated globally. This study aimed to demonstrate the definitive positive impact of dark and light irradiation on both primary and secondary metabolite production in A. officinalis hairy roots and to elucidate the light-responsive mechanism through integrated metabolome and transcriptome analysis. Results When exposed to light, significant changes with a greenish colour shift were observed in 60 metabolites. Multivariate statistical analysis revealed a distinct separation between light- and dark-treated hairy roots, likely attributed to metabolites such as glutamic acid, phenylalanine, catechin hydrate, and chlorophyll. Correspondingly, the pathways significantly impacted included galactose metabolism, alanine, aspartate, and glutamate metabolism, flavone and flavonol biosynthesis, and phenylalanine metabolism. Light-responsive differentially expressed genes associated with pigment and phenylpropanoid biosynthetic pathways were analysed and compared via RNA sequencing. Furthermore, among the light-related transcription factors, including CONSTANS-LIKE and double B-box zinc finger, which are responsible for photomorphogenic modulation, were upregulated. Moreover, light-responsive genes, such as ribulose bisphosphate carboxylase, photosystem II, and chlorophyll A-B binding family protein, were upregulated. Conclusions These findings emphasise that exposure of A. officinalis hairy root culture to light conditions is a useful method for enhancing most of the primary and secondary metabolites. Graphical abstract |
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