Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species

Yellow seed is one favorite trait for the breeding of Brassica oilseed crops, but the performance of seed coat color is very complicated due to the involvement of various pigments. The variation of the seed coat color of Brassica crops was related to the specific expression of transcription factors which regulated the up-regulated expression of catalytic enzymes in the anthocyanin synthesis pathway. Although there have been previous reports on the regulation mechanism of seed coat color from linkage marker development, gene fine-mapping and multi-omics association analysis, the seed coat color of Brassica crops is affected by events such as genome triploidization, the regulatory mechanism is still largely unknown. In this study, we identified genes related to anthocyanin synthesis in six Brassica crops in U-triangle at the genome-wide level and performed collinearity analysis. A total of 1119 anthocyanin-related genes were identified, the collinear relationship of anthocyanin-related genes on subgenomic chromosomes was the best in B.napus (AACC) and the worst in B.carinata (BBCC). The comparison of gene expression related to anthocyanin metabolic pathways in seed coats during seed development revealed differences in anthocyanin metabolism among these species. Interestingly, the R2R3-MYB transcription factors MYB5 and TT2 were differentially expressed at all eight stages of seed coat development, indicating that they might be the key genes that caused the variation of the seed coat color. The expression curve and trend analysis of the seed coat development period showed that the main reason for the unexpressed copies of MYB5 and TT2 may be gene silencing caused by gene structural variation. These results were valuable for the genetic improvement of Brassica seed coat color, and also provided new insights into gene multicopy evolution in Brassica polyploids.