Candidate gene prediction for a petal degeneration mutant, pdm, of the Chinese cabbage (Brassica campestris ssp pekinensis) by using fine mapping and transcriptome analysis

A stably inherited petal degeneration mutant pdm of the Chinese cabbage was obtained from its wild-type 'FT' by radiation treatment (Co-60 gamma-rays) and isolated microspore culture. Petals of the pdm mutant were observed to be shriveled, degenerated, not fully expanded, and darker at the flowering stage than those of 'FT.' The pdm mutant phenotype was found to be controlled by a single recessive nuclear gene. For linkage analysis and gene mapping, 1419 recessive homozygous individuals with the pdm phenotype of the F-2 generation were investigated as the mapping population. Results showed that the pdm was located between markers Indelhsn26 and SSRhsn123 at a genetic distance of 0.04 and 0.04 cM, respectively, on linkage group A01. Physical distance between Indelhsn26 and SSRhsn123, the two most closely linked markers, was estimated to be approximately 285.2 kb. Twenty-eight genes were predicted in the target region. Using RNA-seq, Bra040093 was predicted to be the most likely candidate gene for pdm. Based on gene annotation, Bra040093 encodes a peroxisomal acyl-coenzyme A oxidase 1 (ACX1). Comparison of the sequences in pdm and 'FT' revealed two single-nucleotide polymorphisms in pdm. Expression patterns of Bra040093 between pdm and 'FT' were analyzed using quantitative real-time PCR, and the expression level was dramatically higher in 'FT' than in pdm. These findings provide a solid foundation and valuable resources for map-based cloning, identification, and functional analysis of pdm and facilitate the understanding of floral development processes in the Chinese cabbage.