Dynamic transcriptome and co-expression network analysis of the cotton (Gossypium hirsutum) root response to salinity stress at the seedling stage

Upland cotton (Gossypium hirsutum) is a salt-tolerant crop that can endure high salt concentrations without apparent damage. However, the plant’s response to salinity stress is a complex biological process. An analysis of the dynamic changes in transcript profiles will provide a global picture of the cotton response to salinity stress. Here, we monitored the transcriptome changes in two cotton genotypes, the salt-tolerant H15, and sensitive ZM12, at 0, 0.25, 1, 3, 6, 12, 24, and 48 h in roots exposed to 200-mM NaCl. In total, 13,894 and 5057 differentially expressed genes were identified as being involved in salt-stress tolerance in H15 and ZM12, respectively. Of these, 3825 genes were common to both genotypes. A differential expression analysis revealed that the number of differentially expressed genes increased significantly during the first 24 h after the salt-stress treatment and then significantly decreased at 48 h in both genotypes. A transcription factor (TF) analysis revealed three different patterns based on the expression of 45 TFs’ families, with the majority of differentially expressed TFs increasing rapidly after the salt-stress treatment in both genotypes. A weighted gene co-expression network analysis showed that two gene modules were related to salinity, and genes in these modules were mainly involved in plant–pathogen interactions, the plant MAPK signaling pathway, and diterpenoid biosynthesis. Our results increase the understanding of cotton metabolic pathways involved in responses to salt stress.