Comparative transcriptome analysis of leaves and roots revealed organ-specific defense strategies of pearl millet under multiple abiotic stresses

Abiotic stresses induced by environmental changes severely constrain crop production. Pearl millet (Pennisetum glaucum (L.) R. Br.), an important forage crop for marginal lands, exhibits broad-spectrum stress tolerance, yet its common molecular mechanisms in response to multiple stresses remain unclear. This study analyzed transcriptome data from leaves and roots under six stresses (CdCl2, NaCl, PEG, WL, Heat, Cold) to identify organ-specific and common defence mechanisms. Results indicate leaves lack cross-stress common pathways, activating carotenoid biosynthesis only under water and temperature stresses. In contrast, roots exhibited stronger transcriptional reorganization and more consistent strategies across stresses. Phenylpropanoid biosynthesis and flavonoid biosynthesis pathways were significantly enriched under all stresses, with differential expression of key enzyme genes coupled to cell wall reinforcement and oxidative stress defense functions. Interaction network analysis further revealed the MYB transcription factor family as a central hub coordinating these pathways, with key nodes like PMF4G04191 and PMF5G01787 exhibiting the highest interaction frequencies with pathway genes. This study elucidates pearl millet's organ-specific strategy for coping with complex environments, highlighting how roots achieve broad-spectrum stress tolerance by regulating conserved phenylpropane and flavonoid metabolic networks. It provides key target genes for multi-stress-tolerant forage breeding research.