We cloned wheat leaf rust resistance gene Lr9 using MutIsoSeq. Lr9 encodes unusual tandem kinase fusion protein

The introgression of chromosome segments from wild wheat relatives is an established strategy to enrich the bread wheat gene pool with novel disease resistance genes. Here, we use mutagenesis and transcriptome sequencing to clone the leaf rust resistance genes Lr9 and Lr58, which were introduced into bread wheat from the wild grass species Aegilops umbellulata (UU genome) and Ae. triuncialis (UtUtCtCt genome), respectively. We established that the Lr9 and Lr58 coding sequences are identical, encoding an unusual wheat tandem kinase (WTK) fusion protein. Cytogenetic and haplotype analyses corroborate a common origin for Lr9 and Lr58 from Ae. umbellulata. Long-read sequencing of an Lr9-carrying wheat line and the putative Ae. umbellulata Lr9 donor allowed us to assemble the historically important Lr9 translocation. Our work sheds light on the emerging role of unusual kinase fusion proteins in wheat disease resistance, expanding the repertoire of disease resistance genes for breeding.