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.

陆地棉（陆地棉））是一种耐盐作物，可以忍受高盐浓度而不会受到明显损害。但是，植物对盐分胁迫的反应是一个复杂的生物过程。成绩单动态变化的分析将提供棉花对盐分胁迫响应的全局图。在这里，我们在暴露于200mM NaCl的根中的0、0.25、1、3、6、12、24和48 h时，监测了两种棉花基因型，耐盐H15和敏感ZM12的转录组变化。总共鉴定出13894个和5057个差异表达的基因分别与H15和ZM12的盐胁迫耐受性有关。其中，3825个基因是两种基因型共有的。差异表达分析表明，两种基因型中，差异表达基因的数量在盐胁迫处理后的最初24小时内显着增加，然后在48小时时显着减少。转录因子（TF）分析揭示了基于45个TF家族的表达的三种不同模式，两种基因型经过盐胁迫处理后，大多数差异表达的TF迅速增加。加权基因共表达网络分析表明，两个基因模块与盐度有关，这些模块中的基因主要涉及植物-病原体相互作用，植物MAPK信号通路和二萜类生物合成。我们的结果增加了对盐胁迫响应中涉及的棉花代谢途径的了解。