BnaSD.C3 is a novel major quantitative trait locus affecting semi- dwarf architecture in Brassica napus L

Plant height is a key plant architectural trait that affects the seed yield, harvest index and lodging resistance in Brassica napus L., although the genetic mechanisms affecting plant height remain unclear. Here, a semi-dwarf mutant, df34, was obtained by ethyl methanesulphonate-induced mutagenesis. Genetic analysis showed that the semi-dwarf phenotype is controlled by one semi-dominant gene, which was located on chromosome C03 using a bulked segregant analysis coupled with whole-genome sequencing, and this gene was named BnaSD.C3. Then BnaSD.C3 was fine-mapped to a 297.35-kb segment of the "Darmor-bzh" genome, but there was no potential candidate gene for the semi-dwarf trait underlying this interval. Furthermore, the interval was aligned to the Zhongshuang 11 reference genome. Finally, combining structural variation analysis, transcriptome sequencing, phytohormone analyses and gene annotation information, BnaC03G0466900ZS and BnaC03G0478900ZS were determined to be the most likely candidate genes affecting the plant height of df34. This study provides a novel major locus for breeding and new insights into the genetic architecture of plant height in B. napus.