Morphological, transcriptomics and phytohormone analysis shed light on the development of a novel dwarf mutant of cabbage (Brassica oleracea)

•A spontaneous cabbage dwarf mutant 99–198dw was first discovered from the wild-type 99–198.•Expression of key genes related to IAA, BR and GA were down and those related to SA, JA, ABA and ET were up.•Change in GA4, JA, ET, SA and ABA measured by LC–MS/MS were consistent with the transcriptome results.•Change in phytohormones is due to but not the cause of the dwarf trait by hormone treatment•Deficiencies in cell division resulted in dwarfism in 99–198dw Plant dwarf mutants generally exhibit delayed growth, delayed development, short internodes, and abnormal leaves and flowers and are ideal materials to explore the molecular mechanism of plant growth and development. In the current study, we first discovered a spontaneous cabbage (Brassica oleracea) dwarf mutant 99–198dw, which exhibits a dwarf stature, wrinkled leaves, non-heading, and substantially reduced self-fertility compared with the wild-type 99–198; however, the underlying molecular mechanism of its dwarfism is unknown. Here, we performed comparative phenotype, transcriptome and phytohormone analyses between 99–198 and 99–198dw. Cytological analysis showed that an increase in cell size, a reduction in cell layers, chloroplast degradation and a reduction in mitochondria were observed in 99–198dw. RNA-Seq showed that a total of 3801 differentially expressed genes (DEGs) were identified, including 2203 upregulated and 1598 downregulated genes in the dwarf mutant. Key genes in stress-resistant pathways were mostly upregulated, including salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA), ethylene (ET), etc., while the DEGs reported to be related to plant height, such as those involved in the gibberellin (GA), brassinolide (BR), indole-3-acetic acid (IAA), and strigolactone (SL) pathways were mostly downregulated. In addition, the DEGs in the cell division pathway were all downregulated, which is consistent with the cytokinesis defects detected by cytological analysis. The changes in the GA4, JA, ET, SA and ABA contents measured by liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) absolute quantification were consistent with the transcriptome analysis. Further hormone treatment tests showed that the exogenous application of GA, BR, 6BA, paclobutrazol (PC), etc. did not rescue the phenotype, implying that the change in phytohormones is due to but not the cause of the dwarf trait. It was speculated that mutation of certain DEG related to cell division or participating in s