Molecular mechanism that underlies cotton response to salt and drought stress revealed by complementary transcriptomic and iTRAQ analyses

Abstract

Drought and salinity severely retard cotton growth and development, resulting in a substantial reduction in global cotton production. To investigate the molecular mechanisms underlying plant response, we compared the transcriptomic and proteomic expression profiles of cotton seedlings exposed to drought or salt stress using RNA-sequencing and iTRAQ sequencing, respectively, to gain a comprehensive understanding of the common and specific responses of cotton plants to salt and drought stress. The complexity of transcriptional and post-transcriptional regulations of salt and drought stress-responsive mechanisms was manifested most obviously by the tenuous yet intertwined relationships between the number of transcripts and the profile of protein expression. Intron retention was found to be the most prevalent alternative splicing type, suggesting a significant regulatory function at the transcriptional level. Enrichment analysis revealed that the majority of differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were involved in the MAPK signaling pathway, phenylpropanoid biosynthesis, plant hormone signal transduction, and flavonoid biosynthesis. In particular, a number of MAPK cascade genes, including GhMEKK36, GhMAPKK3, GhMAPKK4, GhMAPK1, and GhMAPK5 were prominently upregulated by both the drought and salt stress treatments, and the functional role of these genes was investigated by ectopic expression in transgenic Arabidopsis, which exhibited significantly enhanced stress tolerance. This study advances our understanding of the molecular mechanisms that underpin cotton responses to drought and salt stress, offering crucial insights for further elaboration of the genes and pathways that are involved in cotton drought and salt tolerance.