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Basic leucine zipper (bZIP) transcription factors play crucial roles in various abiotic stress responses as well as anthocyanin accumulation. Anthocyanins are most abundant in colorful skin radish, which exhibit strong antioxidant activity that offers benefits for human health. Here, a total of 135 bZIP-encoding genes were identified from radish genome. Synteny analysis showed that 104 radish and 63 ArabidopsisbZIP genes were orthologous. Transcriptome analysis revealed that 10 RsbZIP genes exhibited high-expression levels in radish taproot (RPKM>10). Specifically, RsbZIP010 exhibited down-regulated expression under Cd, Cr and Pb stresses, whereas RsbZIP031 and RsbZIP059 showed significant down-regulation under heat and salt stresses, respectively. RT-qPCR analysis indicated that RsbZIP011 and RsbZIP102 were significantly up-regulated in the tissues of radish with high anthocyanin contents. Furthermore, the promoter sequences of 39 anthocyanin-related genes were found to contain G-box or ACE-box elements that could be recognized by bZIP family members. Taken together, several RsbZIPs might be served as critical regulators in radish taproot under Cd, Cr, Pb, heat and salt stresses. RsbZIP011 and RsbZIP102 were the potential participants in anthocyanin biosynthesis pathway of radish. These results facilitate further investigation on functional characterization of bZIP genes in response to abiotic stress and anthocyanin biosynthesis in radish. [ABSTRACT FROM AUTHOR]

• An efficient transformation system with A. rhizogenes was established in radish. • RsMYB90 promoted anthocyanin accumulation in transgenic hairy roots. • RsMYB90 - RsUFGT module positively regulated the biosynthesis of anthocyanin. Radish (Raphanus sativus L.) is recalcitrant to regeneration and genetic transformation, which has severely limited its gene function verification and germplasm innovation. To overcome the limitation, we have developed a rapid and stable regeneration and transformation of hairy roots in radish to explore the potential function of the critical genes involved in the anthocyanin biosynthesis via the optimization of explant selection, bacteria solution concentration, acetosyrinone (AS) concentration and strain types. The single factor experimental designing method was applied and each treatment was conducted for three independent biological replicates. The hairy roots induction rate was more than 90% when using cotyledon with petiole or rootless seedling as explants, while only 53.33% hypocotyls could induce hairy roots. Phenotypic observation and molecular identification indicated that the highest positive transgenic rate of hairy roots could reach approximately 17.51%, when employed optimal optical density (OD 600) and AS concentration at 1.0 and 300 μM, respectively, as well as the best strain of MSU440. Subsequently, RsMYB90 was found to play a positive role in the anthocyanin accumulation through the established hairy root transgenic system, and a number of anthocyanin-related genes, such as RsUFGT, RsCHS and RsF3H , were up-regulated by RNA-seq and RT-qPCR analysis. In addition, yeast one-hybrid (Y1H) and dual-luciferase assays (DLA) showed that the RsMYB90 could bind to the promoter of RsUFGT to activate its expression. Taken together, the stable A. rhizogenes -mediated transformation system provides an avenue for gene function assay, genetic engineering and study of secondary metabolisms in radish. [ABSTRACT FROM AUTHOR]