Seed coat color is an important quality and domestication trait. The adzuki bean has more than a dozen seed coat colors closely associated with the anthocyanin and flavonoid metabolism pathways. In this study, we explored the pigment composition of 10 different seed coat color adzuki beans including red, black mottle on red, black mottle on gray, golden, green, black, ivory, brown, and light brown. The results showed that anthocyanins are the main pigment in adzuki bean seed coat. There were no carotenoid or pelargonidin derivatives in the seed coats of any accessions. Different colors of adzuki bean seed coat have different pigment compositions and the combination of procyanidins and anthocyanins affected seed coat color. The ivory seed coat had an extremely low proanthocyanidin and anthocyanin content. Only the green adzuki bean seed coats contained chlorophyll. Our results explain the pigment composition of the different seed coat colors and the combination of proanthocyanidins and anthocyanins affected seed coat color in adzuki bean. These results can provide a theoretical basis for the study of adzuki bean coloring mechanism.

Blueberries are recognized worldwide as one of the most important healthy foods due to their anthocyanins, which have special antioxidant properties. They have become a highly produced and valuable fruit crop. Most blueberry varieties are rich in anthocyanins, which impart a beautiful blue color; however, there are currently several blueberry varieties with different colors worldwide, and these special-colored varieties are the key to analyzing the coloring mechanism of blueberry fruit. Fruit color could be seen as an important nutritional quality trait in terms of marketing. In this study, a combination of transcriptomic and metabolomic analyses was performed on three representative blueberry varieties (‘Pink Popcorn’, ‘Chandler’, and ‘Black Pearl’) with pink, blue, and black fruits, respectively. The metabolomic results showed that the delphinium pigment is the dominant anthocyanin, which is the prerequisite for the formation of fruit color in blueberries. We identified 18 candidate structural genes in the anthocyanin biosynthesis pathway that were significantly up-regulated during three stages of fruit ripening in ‘Black Pearl’ and ‘Chandler’, but these were not found to be significantly expressed in ‘Pink Popcorn’ after combining the transcriptomic analysis results. The non-expression of the VcANS gene may lead to the pink color of the mature fruit of ‘Pink Popcorn’. The phylogenetic tree, heatmap analysis, and WGCNA analysis identified a candidate transcription factor, VcMYBA, which may regulate the differences between black and blue fruits in blueberries by regulating the expression level of multiple structural genes in the anthocyanin biosynthesis pathway. These results provide new insights into the mechanisms of anthocyanin accumulation and coloration in blueberries during fruit ripening and can help support production practices to improve fruit quality characteristics. The key candidate genes that regulate the fruit color differences among different blueberry varieties have the potential to enhance the antioxidant properties and quality characteristics of blueberries through future genomic editing.

Dendrobium (Orchidaceae, Epidendoideae) plants have flowers with a wide variety of colors that persist for a long period throughout the year. The yellow coloration of Dendrobium flowers is mainly determined by the flavonol pathway and the flavone pathway, but the relevant biosynthesis mechanisms during vernalization remain unclear. To explore the similarities and differences in flavonoid biosynthesis in different tissues during vernalization, we selected two species of Dendrobium for a flower color study: Dendrobium capillipes Rchb (which has yellow flowers) and Dendrobium nobile Lindl (which has white flowers). We collected a total of 36 samples from six tissue types and both Dendrobium species during vernalization and subjected the samples to metabolic profiling and transcriptome sequencing. A total of 31,504 differentially expressed genes (DEGs) were identified between different tissues of the two Dendrobium species by transcriptomic analysis. However, many differentially accumulated metabolites (DAMs) and DEGs were enriched not only in the general pathway of “flavonoid biosynthesis” but also in multiple subpathways of “flavone and flavonol biosynthesis”. According to a combined transcriptome and metabolome analysis, Putrescine hydroxycinnamoyl transferase 1 (LOC110093422) may be the main gene responsible for the differences in flavonoid accumulation during vernalization, which is closely associated with yellow flowers. Taken together, the results of our study preliminarily revealed the metabolites responsible for and the key genes regulating flavonoid biosynthesis during vernalization. These results provide a basis for the further study of the molecular mechanism of flavonoid synthesis during vernalization.

Summary: Adzuki bean (Vigna angularis) is an important legume crop cultivated in over 30 countries worldwide. We developed a high‐quality chromosome‐level reference genome of adzuki bean cultivar Jingnong6 by combining PacBio Sequel long‐read sequencing with short‐read and Hi‐C technologies. The assembled genome covers 97.8% of the adzuki bean genome with a contig N50 of approximately 16 Mb and a total of 32 738 protein‐coding genes. We also generated a comprehensive genome variation map of adzuki bean by whole‐genome resequencing (WGRS) of 322 diverse adzuki beans accessions including both wild and cultivated. Furthermore, we have conducted comparative genomics and a genome‐wide association study (GWAS) on key agricultural traits to investigate the evolution and domestication. GWAS identified several candidate genes, including VaCycA3;1, VaHB15, VaANR1 and VaBm, that exhibited significant associations with domestication traits. Furthermore, we conducted functional analyses on the roles of VaANR1 and VaBm in regulating seed coat colour. We provided evidence for the highest genetic diversity of wild adzuki (Vigna angularis var. nipponensis) in China with the presence of the most original wild adzuki bean, and the occurrence of domestication process facilitating transition from wild to cultigen. The present study elucidates the genetic basis of adzuki bean domestication traits and provides crucial genomic resources to support future breeding efforts in adzuki bean.