Transcriptome profiling reveals histone deacetylase 1 gene overexpression improves flavonoid, isoflavonoid, and phenylpropanoid metabolism in Arachis hypogaea hairy roots

The peanut ( ) is a crop plant of high economic importance, but the epigenetic regulation of its root growth and development has not received sufficient attention. Research on has shown that histone deacetylases (HDACs) are involved in cell growth, cell differentiation, and stress response. Few studies have focused on the role of HDACs in the root development of other plants, particularly crop plants. In earlier studies, we found large accumulations of histone deacetylase 1 ( ) mRNA in peanut roots. However, we did not explore the role of AhHDA1 in peanut root development. In this paper, we investigated the role of the peanut gene and focused on the effect of altered expression in hairy roots at both the phenotypic and transcriptional levels. We analyzed the transformation of hairy roots using Agrobacterium rhizogenes and RNA sequencing to identify differentially expressed genes that were assigned to specific metabolic pathways. Transgenic hairy roots were used as experimental material to analyze the downstream genes expression and histone acetylation levels. To thoroughly understand function, we also simultaneously screened the -interacting proteins using a yeast two-hybrid system. -overexpressing hairy roots were growth-retarded after 20 d in vitro cultivation, and they had a greater accumulation of superoxide anions and hydrogen peroxide than the control and RNAi groups. overexpression in hairy roots accelerated flux through various secondary synthetic metabolic pathways, as well as inhibited the primary metabolism process. overexpression also caused a significant upregulation of genes encoding the critical enzyme chalcone synthase ( , CHS) in the flavonoid biosynthesis pathway, hydroxyisoflavanone synthase ( ) in the isoflavonoid biosynthesis pathway, and caffeoyl-CoA O-methyltransferase ( ) in the phenylpropanoid biosynthesis pathway. In contrast, ferredoxin 1 ( ), the polypeptide of the oxygen-evolving complex of photosystem II ( ), and ribulose bisphosphate carboxylase ( ) in the photosynthetic pathway were significantly downregulated by overexpression. The expression levels of these genes had a positive correlation with histone acetylation levels. Our results revealed that the relationship between altered gene metabolism activities and overexpression was mainly reflected in flavonoid, isoflavonoid, and phenylpropanoid metabolism. overexpression retarded the growth of transgenic hairy roots and may be associated with cell metabolism status. Future s