Comparative analysis of the orange versus yellow petal of rapeseed ( Brassica napus ) using UPLC‐HESI‐MS/MS and transcriptome analysis

Abstract The petal colour of rapeseed plants is usually yellow but can range from milky white to orange or pink, making petal colour a popular target in rapeseed breeding programmes. In this study, metabolites and RNA were extracted from the yellow (Bn‐Y) and orange (Bn‐O) petal colour lines in rapeseed. Chromatography analysis, RNA‐Seq and quantitative RT‐PCR analysis were conducted. A total of 89 differential metabolites including 64 down‐regulated and 25 up‐regulated metabolites were identified in the petals of orange versus yellow rapeseed by UHPLC‐ESI‐MS/MS. A total of 168 differentially expressed genes (DEGs) were detected in the petals of Bn‐O versus Bn‐Y plants. KEGG functional annotation and quantitative RT‐PCR analysis showed that BnaC08g39510D and BnaA09g10680D expression was significantly higher in orange petals than in yellow and that BnaC09g07880D and BnaC09g08690D were strongly expressed in yellow petals but were not expressed in orange petals. These results will be useful for further understanding the molecular mechanisms underlying petal colour and provide the theoretical and practical basis for breeding varieties with colourful petals.