Fine mapping and evolutionary relationship of genes controlling pigments accumulation in oilseed rapa (Brassica napus L.)

Purple/red appearance is one of common phenotypic variations in leaves, stems, and siliques of oilseed rapa (Brassica napus L.) but very rare in flowers. In this study, the causal genes for the purple/red traits in stems and flowers in two accessions of oilseed rapa (DH_PR and DH_GC001, respectively) derived from the wide hybridization were fine mapped and candidate genes were determined by methods combined with bulked segregant analysis (BSA) and RNA-seq analysis. Both purple stem trait and red flowers trait were mapped to the locus as the AtPAP2 homologous genes (BnaPAP2.C6a and BnaPAP2.A7b, respectively) belonging to R2R3-MYB family. Sequencing of the BnaPAP2.C6a gene in purple stem accession revealed several Indels and SNPs in its promoter region, intron 1 as well as exons. However, only a 211bp insertion was identified in promoter region of BnaPAP2.A7b of DH_GC001. In addition, other seven AtPAP2 homologous genes were identified in B. napus and five of which were in A7 and C6 chromosome. Combined with micro-collinear and gene expression analysis we revealed the evolutionary relationships of the nine genes and their function divergence. Our results not only contribute to a better understanding of anthocyanin inheritance in B. napus, but also provide useful toolbox for future breeding of cultivars with purple/red traits through combination of different functional alleles and homologs.