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To properly understand cotton responses to potassium (K⁺) deficiency and how its shoot feedback regulates K⁺ uptake and root growth, we analyzed the changes in root transcriptome induced by low K⁺ (0.03 mM K⁺, lasting three days) in self-grafts of a K⁺ inefficient cotton variety (CCRI41/CCRI41, scion/rootstock) and its reciprocal grafts with a K⁺ efficient variety (SCRC22/CCRI41). Compared with CCRI41/CCRI41, the SCRC22 scion enhanced the K⁺ uptake and root growth of CCRI41 rootstock. A total of 1968 and 2539 differently expressed genes (DEGs) were identified in the roots of CCRI41/CCRI41 and SCRC22/CCRI41 in response to K⁺ deficiency, respectively. The overlapped and similarly (both up- or both down-) regulated DEGs in the two grafts were considered the basic response to K⁺ deficiency in cotton roots, whereas the DEGs only found in SCRC22/CCRI41 (1954) and those oppositely (one up- and the other down-) regulated in the two grafts might be the key factors involved in the feedback regulation of K⁺ uptake and root growth. The expression level of four putative K⁺ transporter genes (three <i>GhHAK5s</i> and one <i>GhKUP3</i>) increased in both grafts under low K⁺, which could enable plants to cope with K⁺ deficiency. In addition, two ethylene response factors (ERFs), <i>GhERF15</i> and <i>GhESE3</i>, both down-regulated in the roots of CCRI41/CCRI41 and SCRC22/CCRI41, may negatively regulate K⁺ uptake in cotton roots due to higher net K⁺ uptake rate in their virus-induced gene silencing (VIGS) plants. In terms of feedback regulation of K⁺ uptake and root growth, several up-regulated DEGs related to Ca²⁺ binding and CIPK (CBL-interacting protein kinases), one up-regulated <i>GhKUP3</i> and several up-regulated <i>GhNRT2.1s</i> probably play important roles. In conclusion, these results provide a deeper insight into the molecular mechanisms involved in basic response to low K⁺ stress in cotton roots and feedback regulation of K⁺ uptake, and present several low K⁺ tolerance-associated genes that need to be further identified and characterized.