Integrated metabolome and transcriptome analyses reveal the formation of seed albinism in Nelumbo nucifera

Abstract Background Albinism in plants causes slow growth, dwarfing and even death. Most albinism is mainly focused on leaf albinism. Studies of seed albinism are still lacking and scarcely studied in higher plants with asexual reproduction. Results In this study, two seed albinism mutations (AM1 and AM2) in lotus were unable to survive in normal condition, exhibiting a decline in carotenoid and chlorophyll contents compared with wild type (WT). Metabolome analyses illustrated a total of 51 differentially changed metabolites (DCMs) in embryo of AM1 (AM1‐E), AM2 (AM2‐E) and WT (WT‐E), along with 94 DCMs in cotyledon of AM1 (AM1‐C), AM2 (AM2‐C) and WT (WT‐C). Forty‐four DCMs were associated with metabolic pathways including flavonoid, lipid, photosynthesis and starch metabolism. Additionally, transcriptome analysis was performed to screen a total of 2060 differentially expressed genes (DEGs) in WT‐E, AM1‐E and AM2‐E, as well as 104 DEGs in WT‐C, AM1‐C and AM2‐C. These DEGs were highly enriched in metabolic pathways of flavonoid biosynthesis, lipid biosynthesis, chlorophyll biosynthesis, carotenoid biosynthesis and the tricarboxylic acid cycle. Conclusions A total of 21 key genes encoding transcription factors, 100 DEGs and 44 DCMs were selected to construct correlation networks. The results suggested that combined effects of basic helix–loop–helix, myeloblastosis viral oncogene homologs, basic leucine zipper and APETALA2/ethylene‐responsive factor regulated the DEGs involved in carotenoid synthesis, flavonoid biosynthesis, photosynthesis and fatty acid synthesis, which further resulted in the etiolation of N. nucifera . © 2025 Society of Chemical Industry.