Integrated transcriptome and proteome analysis reveals complex regulatory mechanism of cotton in response to salt stress

Abstract Background Soil salt stress seriously restricts the yield and quality of cotton worldwide. To investigate molecular mechanism response to stress, a main cultivated variety Gossypium hirsutum L. acc. Xinluzhong 54 was used perform transcriptome proteome integrated analysis. Results Through analysis in leaves under for 0 h (T0), 3 (T3) 12 (T12), we identified 8 436, 11 628 6 311 differentially expressed genes (DEGs) T3 vs. T0, T12 T0 T3, respectively. A total 459 proteins (DEPs) were by proteomic analysis, which 273, 99 260 DEPs Metabolic pathways, biosynthesis secondary metabolites, photosynthesis plant hormone signal transduction enriched among DEGs or DEPs. Detail revealed that complex signaling such as abscisic acid (ABA) jasmonic (JA) signaling, calcium mitogen-activated protein kinase (MAPK) cascade, transcription factors, activation antioxidant ion transporters, participated regulating cotton. Conclusions Our research not only contributed understand but also nine candidate genes, might be useful breeding improve salt-tolerance