The working model for csi-miR171c-CsSCLs mediated regulation of SE in citrus callus. csi-miR171c suppresses the expression of 2 target CsSCL genes (CsSCL2 and CsSCL3), CsSCLs exert feedback regulation on csi-miR171c expression. CsClot was identified as interacting protein of CsSCL2/3, and overexpression of CsClot disturbed ROS homeostasis and enhanced SE capability in citrus callus. Moreover, CsSCL2/3 proteins directly bind and inhibit the expression of downstream regeneration-related genes including CsWOX2, CsWOX13, and CsLBD40 and inhibit biological processes such as auxin response and cell wall organization, thereby reducing SE capability in citrus callus.