Improved reannotations of Aegilops umbellulata (PI 554389) genome and transcriptomics data provide candidates for leaf rust resistance for wheat improvement

Leaf rust caused by Puccinia triticina is a yield limiting disease of cultivated wheat throughout the world. Ae. umbellulata is a diploid species of wheat wild relatives containing high genetic diversity for resistance to multiple races of leaf rust. Here, we used short-read data along with long-read transcript data to reannotate (version 2) the Ae. umbellulata acc. PI 554389 reference genome. In this annotation, we reported 62,434 gene models consisting of 41,906 high confidence (HC) gene models and 20,992 low confidence (LC) gene models. Comparative transcriptome profiling of resistant (PI 554389) and susceptible (PI 554417) accessions challenged with TNBJS revealed distinct temporal patterns of defense activation. The resistant accession exhibited an early and stronger transcriptional response at 6 h after inoculation, whereas the susceptible accession showed delayed expression changes. In comparisons between treated and mock samples of the resistant accession, we identified two candidate resistance genes—one encoding a leucine-rich repeat and another with a kinase domain—that were differentially expressed at early infection stages, suggesting potential roles in pathogen recognition or downstream signaling. This integrative genomic and transcriptomic framework enhances the functional characterization of Ae. umbellulata and identifies promising candidate genes for functional validation and deployment in wheat improvement programs aimed at achieving durable leaf rust resistance.