| Summary: | The primary determinants of apple (<i>Malus</i>) tree architecture include plant height and internode length, which are the significant criteria for evaluating apple dwarf rootstocks. Plant height and internode length are predominantly governed by phytohormones. In this study, we aimed to assess the mechanisms underlying dwarfism in a mutant of <i>Malus baccata</i>. <i>M. baccata</i> dwarf mutant (<i>Dwf</i>) was previously obtained through natural mutation. It has considerably reduced plant height and internode length. A comparative transcriptome analysis of wild-type (WT) and <i>Dwf</i> mutant was performed to identify and annotate the differentially expressed genes responsible for the <i>Dwf</i> phenotype using RNA-seq and GO and KEGG pathway enrichment analyses. Multiple DEGs involved in hormone signaling pathways, particularly auxin signaling pathways, were identified. Moreover, the levels of endogenous indole-3-acetic acid (IAA) were lower in <i>Dwf</i> mutant than in WT. The Aux/IAA transcription factor gene <i>MbIAA19</i> was downregulated in <i>Dwf</i> mutant due to a single nucleotide sequence change in its promoter. Genetic transformation assay demonstrated strong association between <i>MbIAA19</i> and the dwarf phenotype. <i>RNAi-IAA19</i> lines clearly exhibited reduced plant height, internode length, and endogenous IAA levels. Our study revealed that MbIAA19 plays a role in the regulation of dwarfism and endogenous IAA levels in <i>M. baccata</i>.
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