Integrated multi-omics analysis uncovers roles of mdm-miR164b-MdORE1 in strigolactone mediated inhibition of adventitious root formation in apple

Abstract

Adventitious root (AR) formation is important for the vegetative propagation. The effects of strigolactones (SLs) on AR formation have been rarely reported, especially in woody plants. In this study, we first verified the inhibitory effects of SLs on AR formation in apple materials. Transcriptome analysis identified 12,051 differentially expressed genes over the course of AR formation, with functions related to organogenesis, cell wall biogenesis or plant senescence. WGCNA suggests SLs might inhibit AR formation through repressing the expression of two core hub genes, MdLAC3 and MdORE1. We further verified that enhanced cell wall formation and accelerated senescence were involved in the AR inhibition caused by SLs. Combining small RNA and degradome sequencing, as well as a dual-luciferase sensor system, we identified and validated three negatively correlated miRNA–mRNA pairs, including mdm-miR397–MdLAC3 involved in secondary cell wall formation, and mdm-miR164a/b–MdORE1 involved in senescence. Finally, we have experimentally demonstrated the role of mdm-miR164b–MdORE1 in SLs-mediated inhibition of AR formation. Overall, our findings not only propose a comprehensive regulatory network for the function of SLs on AR formation, but also provide novel candidate genes for the potential genetic improvement of AR formation in woody plants using transgenic or CRISPR technology.

Strigolactone regulates adventitious root formation via the MdSMXL7‐MdWRKY6‐MdBRC1 signaling cascade in apple

“…We have generated RNA‐sequencing data based on basal sections of stem cuttings with no treatment, 10 μ m GR24 (rac‐GR24, a SLs synthetic analog) treatment and 1.48 μ m indole‐3‐butyric acid (IBA) treatment for 0, 1, 3 and 7 days during the rooting process in a previous study (BioProject ID PRJNA650149) (Fan et al., 2022). In the present study, we employed RNA‐sequencing data of the GR24 treated group (G) and non‐treated group (M) for weighted gene co‐expression network analysis (WGCNA) to detect gene co‐expression networks and identify the vital genes that specifically affect SL‐mediated inhibition of AR formation.…”

“…AR formation in cuttings is a multi‐phase developmental process dynamically regulated by various hormones. Exogenous SL treatment has been reported to inhibit the formation of ARs (Fan et al., 2022). In the present study, we identified the hub gene MdBRC1 , which integrates SL signaling and controls ARs formation through regulating auxin signaling in apple.…”