In plants, large numbers of R genes, which segregate as loci with alternative alleles conferring different resistance to pathogens, have been maintained over a long evolutionary time. In theory, there seem to be no reason for hosts to harbor susceptible alleles in view of their null contribution to resistance. As such, why should populations support disease-susceptible individuals along with disease-resistant individuals? In rice, a single copy gene Pi-at segregates for two expressed clades of alleles, one resistant and the other susceptible. We simulated loss-of-function of the Pi-ta susceptible allele using the CRISPR/Cas9 system to detect subsequent fitness changes and obtained insights into fitness effects on retention of the Pi-ta susceptible allele. Our creation of artificial knockout of the Pi-ta susceptible allele suffered a fitness decline of up to 49% in term of filled grains yield upon the loss of Pi-ta's function. The Pi-ta susceptible alleles might serve as an off-switch to the downstream immune signaling, thus contributing to fine-tuning of plant defense response. These findings highlight the interplay between genetic architecture and fitness effects of segregating R gene alleles and also provide a plausible explanation how host genomes can tolerate the possible genetic load associated with a vast repertoire of R genes. This attempt to evaluate the fitness effect of the R gene in crop will bring some clues to researchers and breeders that not all disease resistant genes will bring fitness cost as universally acknowledged.