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

Abstract

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 change of seed coat color of Brassica crops is related to the specific synthesis and accumulation of anthocyanin, and the expression level of structural genes in anthocyanin synthesis pathway is specifically regulated by transcription factors. Despite some previous reports on the regulations of seed coat color from linkage marker development, gene fine-mapping and multi-omics association analysis, the trait of Brassica crops is affected by the evolutionary 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 comparisons of gene expressions for anthocyanin metabolic pathways in seed coats during seed development revealed differences in its 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 analyses of the seed coat development period showed that the main reason for the unexpressed copies of MYB5 and TT2 was likely 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.

Molecular evolution analysis of MYB5 in Brassicaceae with specific focus on seed coat color of Brassica napus

“…Breeding yellow-seeded rapeseed is a significant objective within the realm of rapeseed breeding. Over the course of several decades, researchers have on ducted extensive investigations into the formation and regulatory mechanisms underlying the yellow seed coat [ 24 , 28 – 30 , 54 – 56 ]. The transition from yellow to black seed coat primarily occurs as a result of pigment deposition, particularly proPAs [ 57 ].…”

“…In our previous investigation, it was observed that MYB5 and TT2 exhibited differential expression patterns throughout the 8 stages of seed coat development in 6 distinct Brassica species. This finding implies that these genes may play a pivotal role in the modulation of seed coat color alteration [ 30 ]. Nonetheless, the precise mechanism by which MYB5 specifically participates in the regulation of seed coat color in B. napus remains unreported and necessitates further investigation.…”

The Essential Role of Proteoglycans and Glycosaminoglycans in Odontogenesis

“…Syndecan 2 appears to be more closely related to the initial stage of odontogenesis, as it is expressed only before the bud stage (Fujikawa et al 2022). Moreover, its spatiotemporal expression pattern showed high concordance with the odontogenic shift from E11.5 to E13.5, suggesting a potential role in early epithelium-mesenchyme interaction (Chen et al 2023). Unlike syndecan 2, syndecan 4 plays a critical role in amelogenesis, as suggested by its strong expression in preameloblasts.…”

“…demonstrated that the expression of GAG biosynthetic enzymes exerts remarkable spatiotemporal specificity during early odontogenesis, suggesting their potential role in mediating early epithelial-mesenchymal interactions (Chen et al 2023). Furthermore, recent evidence indicates that GAGs play an essential role in dental stem cell homeostasis via the regulation of signaling pathways.…”

Systematic identification of R2R3-MYB S6 subfamily genes in Brassicaceae and its role in anthocyanin biosynthesis in Brassica crops

“…Conversely, in B. napus, the presence of 10 homologous genes of PAP1 has led to the identi cation of distinct regulatory genes for anthocyanin production in different tissues. Speci cally, BnaPAP2.A7 serves as the primary regulatory factor in leaves and petals [32,42,43,48], while BnaPAP2.C6 exerts the primary regulatory function in stems and siliques [49]. In this study, we have conducted a comprehensive analysis of the transcriptional regulatory mechanism of anthocyanin biosynthesis in various organs of B. napus, including leaves, stems, owers, and siliques.…”