In silico identification of auxin-responsive genes through de novo transcriptome assembly and differential expression analysis during early adventitious root formation in contrasting genotypes of Melia dubia Cav

This study investigates the molecular basis of auxin-induced adventitious root (AR) formation in Melia dubia Cav., a commercially important tree species. Juvenile stem cuttings from a good rooter (MG) and a poor rooter (MP) were pulse-treated with indole-3-butyric acid (IBA), and basal tissues were sampled at 0, 12, 24, and 36 hours for RNA sequencing. De novo assembly of RNA-seq data yielded 94,337 and 79,103 unigenes for MG and MP, respectively. Functional annotation against NCBI, KEGG, COG, and GO databases revealed enrichment of hormone signal transduction pathways, metabolic processes, and secondary metabolite biosynthesis. Although MP exhibited a higher number of differentially expressed genes, MG showed earlier, coordinated, and pathway-specific activation, particularly in auxin-related signaling. AUX1/LAX influx carriers, TIR1/AFB receptors, AUX/IAA repressors, ARF transcription factors, GH3, and SAUR gene families—were more extensively and temporally regulated in MG. Positive regulators such as ARF7, ARF19, GH3-1, and several SAUR genes were preferentially expressed in the good-rooting genotype. KEGG enrichment highlighted plant hormone signal transduction, flavonoid biosynthesis, and ABC transporter pathways as central to efficient AR formation. Overall, superior rooting in M.dubia is associated with precise temporal regulation of auxin signalling and transport, providing molecular insights and potential markers for improving clonal propagation.