Leaf rust, caused by the fungus Puccinia triticina, continues to be the most damaging disease of wheat globally. The resistance (R) - avirulence (Avr) interaction model is widely exploited in wheat breeding of leaf rust resistance because this simple mode of action can be selected based on clear phenotypes in specific wheat cultivars and Pt isolates and mostly offers resistance at all plant growth stages.

The lack of knowledge of resistance mechanisms and the host and pathogen R and Avr genes that modulate pathogen ingress has often led to “blind” selection of disease resistance, and due to fast adaptation of pathogens in one-on-one relationships, rapid breakdown of resistance. Till now, more than 80 loci conferring resistance to Pt (“Lr” genes) have been designated in wheat, however, few of the actual Lr genes have been identified and no corresponding Avr gene has been isolated from Pt.

This study identified a race-specific all-stage wheat R gene Lr41, which is among the first known alien introgression from Aegilops tauschii on chromosome 2DS. The presence of Lr41 as a non-NLR gene was confirmed with comparative genomics and transcriptomics, mutagenesis and functional validation.

We further showed that Pt virulence on Lr41 was due to haplotype sequence variations in a specific genomics region affecting AvrLr41. Experimentally confirmed with native- and hetero-expression, this study provided the first model illustrating direct and unconventional R-Avr interaction in wheat leaf rust resistance.

We anticipate the current findings would help understand how wheat recognises Pt or even other pathogens through race-specific modes. Identification of the paired Lr41 and AvrLr41 may be directly fed into wheat breeding programs for engineering disease resistance.