Soybean maintained immunodiversity during domestication despite a significant loss in genetic diversity

Soybean (Glycine max (L.) Merr.) is one of the most economically important crops in the world, but every year, pathogens cause billions of dollars' worth of losses worldwide. The domestication of this critical crop was associated with several severe genetic bottlenecks that resulted in a dramatic loss of genetic diversity (∼50%) relative to its wild progenitor. Although domestication selected for favorable agricultural traits, it is unclear how the reduced genetic diversity affected the immunity landscape of cultivated soybean relative to its wild ancestors. We performed a comprehensive screen for effector-triggered immune (ETI) responses of both cultivated soybean (Glycine max) and wild soybean (Glycine soja) against the bacterial speck pathogen Pseudomonas syringae. We uncovered an extensive ETI landscape in both species, with 121/529 alleles (22.9%) from 32/65 effector families (49.2%) eliciting ETI in G. max and 125/529 alleles (23.6%) from 23/65 effector families (35.4%) eliciting ETI in G. soja. Interestingly, soybean recognized all three effectors encoded in the conserved effector locus (CEL) of P. syringae (AvrE, HopM, and HopAA), providing pervasive and stacked resistance against this common soybean pathogen. Finally, we demonstrate that pretreatment of soybean with the CEL effectors can immunize soybean against subsequent infection. Overall, we have defined the ETI landscape of soybean against P. syringae and demonstrated that domestication has not compromised soybean immunodiversity despite a dramatic loss in genetic diversity.