The LncRNA401-LrWRKY70 Module Regulates the Blue-Purple Flower Color Formation in Lycoris

Lycoris plants are known for their diverse flower colors, but the molecular mechanisms behind these variations remain unclear. In this study, we first used the CIELAB system to precisely measure flower color. We objectively defined the petals of Lycoris sprengeri as blue-purple (Bp) and compared them with the white petals of Lycoris longituba (W) and the red petals of Lycoris radiata var. pumila (R). Metabolomic analysis showed that specific kaempferol glycosides, including kaempferol-3-O-sophoroside and lonicerin, accumulated significantly in the blue-purple petals. Transcriptomic analysis revealed that genes related to flavonoid biosynthesis were generally more active in the colored petals (Bp and R). However, different expression patterns of key hydroxylase genes created a metabolic split. Specifically, the blue-purple petals showed high expression of LrF3′5′H (directing synthesis toward delphinidin) and LrFLS (promoting kaempferol accumulation), whereas the red petals mainly expressed LrF3′H (leading to cyanidin synthesis). Further investigation identified LrWRKY70 as a core transcription factor highly correlated with these flavonoid pathway genes. Crucially, we discovered a new long non-coding RNA, LncRNA401, located downstream of the LrWRKY70 antisense strand. It showed a strong positive correlation with LrWRKY70. Functional verification through transient overexpression demonstrated that LncRNA401 significantly increased the expression of LrWRKY70. This, in turn, broadly activated downstream flavonoid biosynthesis genes, including LrCHS, LrF3′5′H, LrFLS, and LrDFR. This cascade ultimately promoted the synthesis of anthocyanins and kaempferol derivatives, resulting in the unique blue-purple phenotype. Our results reveal a novel LncRNA401-LrWRKY70 regulatory module. This module plays a key role in metabolic reprogramming for flower color formation in Lycoris, providing important insights into plant secondary metabolism and valuable targets for breeding specific flower colors.