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

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 F2 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 genome-wide transcriptomic analysis was performed using stem tips from NY18 and DF59 at the stem elongation stage. In total, 81 of the 118 differentially expressed genes were enriched in auxin signal transduction, suggesting that genes in this pathway are responsible for the dwarf phenotype of DF59. 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 4,746 individuals. Finally, a PCR-based marker was developed based on the SNP in BnaC09g20450D, and PCR products were easily and correctly detected using agarose gel electrophoresis.