SRP341504 PRJNA771486 Cotton transcriptome sequencing In order to understand the molecular mechanism of cotton's response to drought during the flowering and boll periods, transcriptomics and metabolomics were carried out for two introgression lines (drought-tolerant line: T307; drought-sensitive line: S48) which were screened from G. hirsutum cv. 'Emian22' with some gene fragments imported from G. barbadense acc. 3-79. Results showed that the basic drought response in cotton included a series of broad-spectrum responses, such as amino acid synthesis, hormone (ABA) signal transduction, MAPK signal transduction pathway, which activated in both drought-tolerant and drought-sensitive line. However, the difference of their imported fragments and missing sequences, which triggers endoplasmic reticulum (ER) protein processing, photosynthetic-related pathways (in leaves) and membrane solute transport (in roots) in drought-tolerant line T307, while these are missed or not activated in drought-sensitive line S48, reflecting the different drought tolerance of the two genotypes. VIGS assay of drought-tolerant differentially expressed HSP genes (mainly in leaf) and ABC transporter genes (mainly in roots) indicated that those genes play important role in cotton drought tolerant. Combined analysis of transcriptomics and metabolomics highlighted the important roles of ER-stress related HSP genes and root specific ABC transporter genes in plants drought tolerance.