Transcriptome analysis reveals differentially expressed ERF transcription factors associated with salt response in cotton

•Transcriptome of cotton response to salt stress revealed disturbance in the molecular, cellular, and biological processes.•The differentially expressed transcription factor genes may be the key mediators of salt stress regulation in cotton.•ERFs may emerge as key players of salt tolerance in cotton.•Silencing of GhERF4L and GhERF54L significantly reduced salt tolerance of cotton seedlings. Salinity is a major abiotic stress limiting plant growth and development that has caused severe damage to yield and quality of cotton fiber. Uncovering the mechanisms of response to salt stress is important in breeding salt-tolerant cotton varieties. Transcriptome analysis identified 2356 differentially expressed genes in cotton under salt stress, of which 9.4% were predicted transcription factors (TFs). Approximately 17.6% (39 out of 222) of the differentially expressed TFs belonged to the ethylene response factor (ERF) family. Expression pattern analysis showed significant changes in these ERFs during salt stress. Moreover, the number of down-regulated ERFs was more than that of the up-regulated ERFs. Two of the ERFs, GhERF4L and GhERF54L, showed increased (12–15 times) expression after 12 h of salt treatment. Silencing of GhERF4L and GhERF54L significantly reduced salt tolerance of cotton seedlings, indicating their role in regulating cotton response to salt stress. This study revealed the essential role of ERF transcription factors in the salt response mechanism of plants, and provided important genetic resources for breeding salt-tolerant cotton.