Improved reannotations of Aegilops umbellulata (PI 554389) genome and transcriptomics data provides 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 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.