Fig 1.
Phenotypic expression of stem rust of wheat.
Comparison of stem rust infection in susceptible (C306, Sr24-) and resistant (HW2004, Sr24+) wheat near isogenic lines (NILs) differing in Sr24 stem rust resistance gene at multiple time-points up to14 dpi (days post inoculation): (A) 0 dpi, (B) 5 dpi, (C) 9 dpi, (D) 14 dpi.
Fig 2.
Global expression profile of DEGs in response to Pgt infection.
Overview of transcriptomic response at three time-points (0 hpi, 10 hpi and 72 hpi) in (A) HW2004 and (B) C306 based on hierarchal clustering. Up refers to upregulated and Down to downregulated DEGs in the respective NILs, R1 & R2 refer to the two independent biological replicates.
Fig 3.
Number of DEGs at early (10 hpi) and late (72 hpi) stages of infection in the two NILS.
(A) Number of DEGs at 10 hpi and 72 hpi compared to 0 hpi time-point in HW2004. (B) Venn diagram representation of common and unique upregulated DEGs at 10 hpi and 72 hpi in HW2004. (C) Common and unique downregulated DEGs at 10 hpi and 72 hpi in HW2004. (D) Number of DEGs at 10 hpi and 72 hpi compared to 0 hpi time-point in C306. (E) Venn diagram representation of common and unique upregulated DEGs at 10 hpi and 72 hpi in C306. (F) Common and unique downregulated DEGs at 10 hpi and 72 hpi in C306. Numbers in the Venn diagram represent number of DEGs in the respective stage of infection.
Fig 4.
Comparative transcriptomics of wheat NILs for Sr24.
(A) Number of DEGs in HW2004 compared to C306 at three stages of infection (0, 10 and 72 hpi). Venn diagram representation of number of unique and shared DEGs at different stages of infection: (B) Upregulated and (C) Downregulated genes in HW2004 at basal, early and late stages of infection. Common and unique DEGs among the two NILs at early (10 hpi) stage of infection: (D) upregulated and (E) downregulated genes. Numbers in the Venn diagram represent number of DEGs in the respective category.
Table 1.
Functional annotation of representative differentially expressed genes in HW2004 at early infection stage.
Table 2.
Functional annotation of representative differentially expressed genes in HW2004 at late infection stage.
Fig 5.
Gene Ontology (GO) characterization of upregulated genes.
Overview of GO terms in (A) HW2004 and (B) C306. BP refers to Biological Process, MF to Molecular Function and CC to Cellular Compartment. The GO IDs of the respective GO terms are indicated in the parenthesis.
Fig 6.
Heatmap representation for temporal expression pattern of representative disease response genes.
Heat map profiles of several categories of stem rust responsive genes in (A) HW2004 and (B) C306. Labels in the middle represent broad biological function of the DEGs and colour scale represent the log2 fold-change of DEGs. R1 and R2 refer to the two independent biological replicates. Important biological categories of upregulated genes in HW2004 upon Pgt infection: (C) at early and (D) late stage, and downregulated genes at (E) early and (F) late stages.
Table 3.
Biological function GO terms enriched in HW2004 in response to Pgt.
Table 4.
Pathways upregulated in HW2004 in response to Pgt.
Table 5.
Functional annotation of representative important differentially expressed genes in HW2004 compared to C306 at early infection stage.
Fig 7.
Expression pattern of representative DEGs, belonging to important defence responsive biological categories by RT-qPCR.
Transcript response of key stem rust responsive genes at early (10 hpi) and late (72 hpi) stages of infection in top panel (A) for HW2004 and bottom panel (B) for C306. The functional categories in indicated on the top and the transcript IDs are given on the bottom side (TC373972: LRR containing kinase, CA637923: receptor protein kinase—like protein, TC436787: BHLH family protein-like, TC447183: WRKY45, TC418450: PR4, CA699240: β-1,3-glucanase, TC453213: Cytochrome P450, TC381007: Antifungal zeamatin-like protein, TC426838: Acetone-cyanohydrin lyase, TC398331: Caffeic acid O-methyltransferase, TC426094: Chalcone synthase, TC378627: Peroxidase-2, TC381069: α-ketoglutarate dehydrogenase). Fold changes were normalized to basal (0 hpi) stage. Error bars indicate SD of three independent biological replicates.
Fig 8.
Characteristics of the DEGs in Wheat NIL HW2004 (post Pgt 7G11 infection) mapped on the 70 Mbp region of the translocated fragment (spanning the Sr24-linked marker, Xbarc71) corresponding to the chromosome 3E of Thinopyrum elongatum.
A) Relative positions of Sr24-linked marker Xbarc71 and DEGs mapped across the 70 Mbp region of the translocated fragment. B) Relative expression levels (log2FC) of the DEGs. C) Biological functional categorization based on the Uniprot/TC ID information. D) Indication of post-infection time-course expression response (early/late and up/down) of the mapped DEGs. The scale on the bottom is indicative of the position of the DEGs in the 70 Mbp region, while the information about the functional categories (and colour codes) are indicated on the right-hand side panel.
Table 6.
Pgt induced representative DEGs from HW2004 showing similarity to Thinopyrum elongatum chromosome 3E, in vicinity to region linked with marker of Sr24.
Fig 9.
Schematic representation of probable mechanism of Sr24-mediated resistance in wheat upon Pgt infection.
Black coloured lines represent sequence of events and candidates involved in pathogen detection and activation of defence responses. Red coloured lines and shapes represent upregulated pathways and processes upon Pgt infection, while blue coloured lines represent pathways which are repressed upon Pgt infection.