Comparative Transcriptome Analysis of Leaves and Roots Revealed Organ-Specific and Cross-Stress Defense Strategies of Pearl Millet Under Different Abiotic Stresses

Pearl millet (Pennisetum glaucum (L.) R. Br.) is widely recognized for its high tolerance to marginal environments. However, a systematic understanding of its organ-specific transcriptional adaptation mechanisms under individually applied abiotic stresses remains limited. In this study, we conducted a comparative transcriptome analysis of leaves and roots subjected to six distinct stress treatments (Ion stress: CdCl2/NaCl; Water stress: PEG/Waterlogging; Temperature stress: Heat/Cold), revealing fundamental differences in defense strategies between the two organs. Across all stresses, leaves showed more differentially expressed genes (DEGs) (213) than roots (118), yet the transcriptional responses were largely stress-specific. Carotenoid biosynthesis was the only pathway co-activated in leaves under both water and temperature stress. In contrast, roots exhibited a robust and conserved strategy, with significant enrichment of phenylpropanoid and flavonoid biosynthesis pathways consistently observed across all six stresses. This cross-stress synergistic response involved more than 300 enzyme genes in roots, including key enzymes such as peroxidases (128) and shikimate O-hydroxycinnamoyltransferases (33), which collectively contribute to root-specific cell wall reinforcement and oxidative stress defense. Interaction network analysis further revealed that the MYB transcription factor family serves as a central regulatory hub in root stress responses, with key nodes PMF4G04191 and PMF5G01787 frequently interacting with pathway genes under all stress conditions. This study elucidates the organ-specific and cross-stress defense mechanisms in pearl millet, providing valuable transcriptomic resources and candidate genes for molecular-assisted breeding of multi-stress-tolerant varieties.