Integrated transcriptomic and metabolomic analyses reveals anthocyanin biosynthesis in leaf coloration of quinoa (Chenopodium quinoa Willd.)

Abstract

Abstract Quinoa leaves demonstrate a diverse array of colors, offering a potential enhancement to landscape aesthetics and the development of leisure-oriented sightseeing agriculture in semi-arid regions. This study utilized combined transcriptomic and metabolomic analyses to investigate the mechanisms underlying anthocyanin synthesis in both emerald green and pink quinoa leaves. Differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were analyzed between two different germplasms at different periods. Several key genes, including 4CL, C3'H, HCT, CHS, CHI, ANR, CYP75B1, UGT79B1, FG3, FG2, CYP73A, MYC2, bHLH14, HY5, and TGA, were identified in anthocyanin biosynthesis using DEG analysis. GO enrichment analysis revealed seven closely related GO Terms. KEGG enrichment analysis identified six metabolic pathways that were significantly associated with anthocyanin biosynthesis, with flavonoid biosynthesis (ko00941) emerging as the most pivotal. Metabolomic analysis confirmed cyanidin 3-O-(3'',6''-O-dimalonyl glucoside) and naringenin as key DAMs in pink leaves. Combined transcriptomic and metabolomic analyses indicated that both the flavonoid biosynthesis pathway (ko00941) and anthocyanin biosynthesis pathway (ko00942) were involved in the anthocyanin biosynthesis pathway. Ten DEGs, including PAL, CHI, CYP75B1, F3H, FG3, CYP73A, HCT, C3'H, 4CL, and CHS, were verified through qRT-PCR, with the results across the nine comparison groups consistent with that from transcriptomic sequencing. These findings provide a foundation for elucidating the molecular regulatory mechanisms governing flavonoid synthesis in quinoa leaves.