An unusual tandem kinase fusion protein confers leaf rust resistance in wheat

<p>The introgression of chromosome segments from wild relatives is an established strategy to enrich crop germplasm with novel disease-resistance genes. Here, we use mutagenesis and transcriptome sequencing to clone the leaf rust resistance gene <em>Lr9</em>, which was introduced into bread wheat from the wild grass species <em>Aegilops</em> <em>umbellulata</em>. We establish that <em>Lr9</em> encodes an unusual tandem kinase fusion protein. Long-read sequencing of a wheat <em>Lr9</em> introgression line and the putative <em>Ae</em>. <em>umbellulata</em> <em>Lr9</em> donor enabled us to assemble the ~28.4-Mb <em>Lr9</em> translocation and to identify the translocation breakpoint. We likewise cloned <em>Lr58</em>, which was reportedly introgressed from <em>Ae</em>. <em>triuncialis</em>, but has an identical coding sequence compared to <em>Lr9</em>. Cytogenetic and haplotype analyses corroborate that the two genes originate from the same translocation event. Our work sheds light on the emerging role of kinase fusion proteins in wheat disease resistance, expanding the repertoire of disease-resistance genes for breeding.</p>