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Leaf rust (LR) caused by Puccinia recondita f. sp. secalis (Prs) is a highly destructive disease in rye. However, the genetic mechanisms underlying the rye immune response to this disease remain relatively uncharacterised. In this study, we analysed the expression of four genes in 12 rye inbred lines inoculated with Prs at 20 and 36 h post-treatment (hpt): DXS (1-deoxy-D-xylulose 5-phosphate synthase), Glu (β-1,3-glucanase), GT (UDP-glycosyltransferase) and PR-1 (pathogenesis-related protein 1). The RT-qPCR analysis revealed the upregulated expression of the four genes in response to Prs in all inbred lines and at both time-points. The gene expression data were supported by microscopic and macroscopic examinations, which revealed that eight lines were susceptible to LR and four lines were highly resistant to LR. A relationship between the infection profiles and the expression of the analysed genes was observed: in the resistant lines, the expression level fold changes were usually higher at 20 hpt than at 36 hpt, while the opposite trend was observed in the susceptible lines. The study results indicate that DXS, Glu, GT and PR-1 may encode proteins crucial for the rye defence response to the LR pathogen. [ABSTRACT FROM AUTHOR]

The genetic background of the immune response of rye to leaf rust (LR), although extensively studied, is still not well understood. The recent publication of the genome of rye line Lo7 and the development of efficient transcriptomic methods has aided the search for genes that confer resistance to this disease. In this study, we investigated the potential role of rye orthologs of wheat Lr genes (Lr1, Lr10, Lr21, Lr22a, and RGA2/T10rga2-1A) in the LR seedling-stage resistance of inbred rye lines D33, D39, and L318. Bioinformatics analysis uncovered numerous Lr orthologs in the Lo7 genome, namely, 14 ScLr1, 15 ScRga2, and 2 ScLr21 paralogs, and 1 each of ScLr10 and ScLr22a genes. The paralogs of ScLr1, ScRga2, and ScLr21 were structurally different from one another and their wheat counterparts. According to an RNA sequencing analysis, only four wheat Lr gene orthologs identified in the Lo7 genome (ScLr1_3, ScLr1_4, ScLr1_8, and ScRga2_6) were differentially expressed; all four were downregulated after infection with compatible or incompatible isolates of Puccinia recondita f. sp. secalis (Prs). Using a more precise tool, RT-qPCR, we found that two genes were upregulated at 20 h post-infection, namely, ScLr1_4 and ScLr1_8 in lines D33 and D39, respectively, both of which have been found to be resistant to LR under field conditions and after treatment with a semi-compatible Prs strain. We were unable to discern any universal pattern of gene expression after Prs infection; on the contrary, all detected relationships were plant genotype-, Prs isolate-, or time-specific. Nevertheless, at least some Lr orthologs in rye (namely, ScLr1_3 ScLr1_4, ScLr1_8, and ScRga2_6), even though mainly downregulated, may play an important role in the response of rye to LR. [ABSTRACT FROM AUTHOR]