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Background   Brassica napus  provides approximately 13–16% of global vegetable oil for human consumption and biodiesel production. Plant height (PH) is a key trait that affects plant architecture, seed yield and harvest index. However, the genetic mechanism of PH in  B. napus  is poorly understood.    Results  A dwarf mutant  df59  was isolated from a large-scale screening of an ethyl methanesulphonate-mutagenized rapeseed variety Ningyou 18. A genetic analysis showed that the dwarfism phenotype was controlled by one semi-dominant gene, which was mapped on C9 chromosome by quantitative trait loci sequencing analysis and designated as  BnaDwf.C9 . To fine-map  BnaDwf.C9 , two F 2  populations were constructed from crosses between conventional rapeseed cultivars (Zhongshuang 11 and Holly) and  df59 .  BnaDwf.C9  was fine-mapped to the region between single-nucleotide polymorphism (SNP) markers M14 and M4, corresponding to a 120.87-kb interval of the  B. napus  ‘Darmor- bzh ’ genome. Within this interval, seven, eight and nine annotated or predicted genes were identified in “Darmor- bzh ”, “Ningyou 7” and “Zhongshuang 11” reference genomes, respectively. In addition, a comparative transcriptome analysis was performed using stem tips from Ningyou 18 and  df59  at the stem elongation stage. In total, 3995 differentially expressed genes (DEGs) were identified. Among them, 118 DEGs were clustered in plant hormone-related signal transduction pathways, including 81 DEGs were enriched in auxin signal transduction. Combining the results of fine-mapping and transcriptome analyses,  BnaC09g20450D  was considered a candidate gene for  BnaDwf.C9 , which contains a SNP that co-segregated in 4746 individuals. Finally, a PCR-based marker was developed based on the SNP in  BnaC09g20450D .    Conclusions  The combination of quantitative trait loci sequencing, fine-mapping and genome-wide transcriptomic analysis revealed one candidate gene located within the confidence interval of 120.87-kb region. This study provides a new genetic resource for semi-dwarf breeding and new insights into understanding the genetic architecture of PH in  B. napus .

Fine-mapping and transcriptome analysis of a candidate gene controlling plant height in Brassica napus L.