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

Authors: SINGH, JATINDER - North Dakota State University; GUDI, SANTOSH - North Dakota State University; MAUGHAN, JEFF - Brigham Young University; Gupta, Rajeev; GILL, UPINDER - North Dakota State University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/14/2025
Publication Date: 12/29/2025
Citation: Singh, J., Gudi, S., Maughan, J., Gupta, R., Gill, U. 2025. Improved reannotations of Aegilops umbellulata (PI 554389) genome and transcriptomics data provides candidates for leaf rust resistance for wheat improvement. Scientific Reports. 15:Article 44930. https://doi.org/10.1038/s41598-025-29241-6.
DOI: https://doi.org/10.1038/s41598-025-29241-6

Interpretive Summary: Wheat is one of the most consumed staple foods by the human population. Significant production losses are incurred annually in wheat due to various abiotic and biotic stresses. Global yield losses due to biotic factors are estimated to range from 20-40% annually, depending on the region and year. Among the three rusts, leaf rust is widely distributed and found commonly in almost all wheat growing areas. Indeed, leaf rust is reported to cause the largest crop losses in wheat globally among all the wheat pathogens. In the current study, we presented an improved annotations of the reference genome of wheat wild relative, Ae. umbellulata to provide more accurate gene models and resistance gene analog prediction. Further, we used transcriptomics data from two contrasting Ae. umbellulata accessions to determine the underlying mechanism of leaf rust resistance and to identify candidate resistance genes for further characterization and to be used in future wheat improvement programs to develop resilient germplasm.

Technical Abstract: 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 perform a transcriptomics study to discover the underlying disease resistance mechanism in Ae. umbellulata against P. triticina. The experiment included two contrasting accessions, PI 554389 (resistant) and PI 554417 (susceptible) inoculated with the highly virulent P. triticina race TNBJS. The time series experiment was performed at four time point, 0 hour, 6 hours after inoculation (HAI), 24 HAI and 72 HAI in three biological replications. 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 annotaiton, we reported 62434 gene models consisting of 41906 high confidence (HC) gene models and 20992 low confidence (LC) gene models. The gene expression analysis showed highly differentially expression genes (DEGs) in resistant vs susceptible comparison at all time points. In treated vs mock comparisons of resistant accession, we observed fewer DEGs, likely due to the constitutive expression of resistance genes. We found two candidate resistance genes, one containting leucine rich repeat and other with kinase domain, differentially expressing at early stages of the infection (i.e. 6 HAI). The functional validation of these genes will be invaluable for future wheat improvement efforts for leaf rust resistance.