Fitness benefit plays a vital role in the retention of the Pi-ta susceptible alleles

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.