BackgroundVerticillium wilt is one of the most devasting diseases for many plants, leading to global economic loss. Cotton is known to be vulnerable to its fungal pathogen,Verticillium dahliae, yet the related genetic mechanism remains unknown.ResultsBy genome-wide association studies of 419 accessions of the upland cotton,Gossypium hirsutum, we identify ten loci that are associated with resistance against Verticillium wilt. Among these loci,SHZDI1/SHZDP2/AYDP1from chromosome A10 is located on a fragment introgressed fromGossypium arboreum. We characterize a large cluster of Toll/interleukin 1 (TIR) nucleotide-binding leucine-rich repeat receptors in this fragment. We then identify a dual-TIR domain gene from this cluster,GhRVD1, which triggers an effector-independent cell death and is induced byVerticillium dahliae. We confirm thatGhRVD1is one of the causal gene forSHZDI1. Allelic variation in the TIR domain attenuates GhRVD1-mediated resistance againstVerticillium dahliae. Homodimerization between TIR1-TIR2 mediates rapid immune response, while disruption of its αD- and αE-helices interface eliminates the autoactivity and self-association of TIR1-TIR2. We further demonstrate that GhTIRP1 inhibits the autoactivity and self-association of TIR1-TIR2 by competing for binding to them, thereby preventing the resistance toVerticillium dahliae.ConclusionsWe propose the first working model for TIRP1 involved self-association and autoactivity of dual-TIR domain proteins that confer compromised pathogen resistance of dual-TIR domain proteins in plants. The findings reveal a novel mechanism onVerticillium dahliaeresistance and provide genetic basis for breeding in future.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13059-023-02950-9.