Comparative transcriptome analysis to identify the key genes and metabolic pathways involved in the Brassica napus semi-dwarf mutant zs-d

• The semi-dwarf rapeseed mutant zs-d was developed via EMS mutagenesis. • zs-d shows compact architecture, shorter internodes, and reduced height. • Semi-dwarfism in zs-d is controlled by a single, partially dominant gene. • Altered hormone levels (auxins) and anthocyanins contribute to the zs-d phenotype. • This study offers insights into rapeseed breeding and dwarfism mechanisms. Plant height is an important agronomic trait that affects the architecture of rapeseed, one of the most important oil crops worldwide. Reduced height can significantly improve rapeseed lodging resistance, which benefits mechanized harvesting of the crop. The semi-dwarf rapeseed mutant zs-d was obtained from the elite variety Zhongshuang11 (ZS11) by ethyl methylsulfonate mutagenesis. Compared with ZS11, zs-d had purple petioles and dark green leaves, a more compact architecture (due to a smaller branch angle), shorter internodes, and significantly lower plant height. This semi-dwarfism is controlled by a single, partially dominant gene. A comparison of the pigment content of zs-d and ZS11 in leaves revealed that the anthocyanin content of zs-d was dramatically higher; however, its total chlorophyll content was significantly lower. Observation of stem paraffin sections revealed that the number of zs-d cells was significantly higher than that of ZS11 cells in identical area fields of view. Furthermore, the length and area of cortical cells in zs-d were significantly reduced compared with those in ZS11 plants. Determining and analyzing endogenous hormone content showed that while the indole acetic acid content was significantly decreased, the 5-deoxystrigol content of strigolactone synthetic precursors was significantly increased in the zs-d hypocotyls. Integrative analysis of stem and leaf RNA-seq data for zs-d and ZS11 revealed that the mutant phenotype of zs-d may be attributed to phytohormones (especially auxins) and anthocyanins. Overall, this study lays a theoretical foundation for further elucidating the molecular mechanism of semi-dwarfism in zs-d , offering valuable insights for dwarfing in rapeseed breeding.