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Background  Salt stress is one of the most damaging abiotic stresses in production of Upland cotton ( Gossypium hirsutum ). Upland cotton is defined as a medium salt-tolerant crop. Salinity hinders root development, shoots growth, and reduces the fiber quality.    Results  Our previous study verified a  GhCIPK6a  gene response to salt stress in  G. hirsutum . The homologs of  GhCIPK6a  were analyzed in A 2  ( G. arboreum ), D 5  ( G .  raimondii ), and AD 1  ( G. hirsutum ) genomes. GhCIPK6a localized to the vacuole and cell membrane. The GhCBL1-GhCIPK6a and GhCBL8-GhCIPK6a complexes localized to the nucleus and cytomembrane. Overexpression of  GhCIPK6a  enhanced expression levels of co-expressed genes induced by salt stress, which scavenged ROS and involved in MAPK signaling pathways verified by RNA-seq analysis. Water absorption capacity and cell membrane stability of seeds from  GhCIPK6a  overexpressed lines was higher than that of wild-type seeds during imbibed germination stage. The seed germination rates and seedling field emergence percentages of  GhCIPK6a  overexpressed lines were higher than that of control line under salt stress. Moreover, overexpressing of  GhCIPK6a  in cotton increased lint percentage, and fiber length uniformity under salt stress.    Conclusions  We verified the function of  GhCIPK6a  by transformation and RNA-seq analysis.  GhCIPK6a  overexpressed lines exhibited higher tolerance to abiotic stresses, which functioned by involving in ROS scavenging and MAPK pathways. Therefore,  GhCIPK6a  has the potential for cotton breeding to improve stress-tolerance.

GhCIPK6a increases salt tolerance in transgenic upland cotton by involving in ROS scavenging and MAPK signaling pathways