The conserved bacterial flagellin subunit, flg22, is recognized by the host membrane- localized pattern recognition receptor (PRR) FLS2, and the conserved fungal cell wall component chitin is recognized by another host PRR receptor, CERK1. Well-characterized examples of MAMPs are bacterial flagellin, which is required for motility and the structural molecule chitin found in fungal cell walls. The MAMPs are essential for survival and conserved across diverse genera, thus cannot be shed by the pathogen and are under purifying selection. The first tier involves the recognition of conserved microbe-derived molecules known as pathogen- associated molecular patterns (PAMPs) or more appropriately as microbe- associated molecular patterns (MAMPs) by cell surface receptors. Plants are subjected to a diverse array of microbes that can trigger a two-tiered immune response ). Barley transcript analysis after colonization with 9 RMRL virulent and 15 RMRL avirulent isolates inoculated on the susceptible line Harrington showed significantly lower expression of host biotic stress responses specific to RMRL virulent isolates suggesting virulent isolates harbor effectors that suppress resistance responses. Comparative transcriptomics between the 9 RMRL virulent -vs- the 15 RMRL avirulent Pgt isolates identified 44 differentially expressed genes encoding candidate secreted effector proteins (CSEPs), among which 38 were expressed at lower levels in virulent isolates suggesting that they may represent RMRL avirulence genes. Transcriptome wide association analysis identified 33 variants across 28 genes that were associated with dominant RMRL virulence, thus, representing candidate suppressors of resistance. The transcripts were mapped to the Pgt race SCCL reference genome identifying 114 K variants in predicted genes that would result in nonsynonymous amino acid substitutions. In planta RNAseq was conducted with the 24 diverse isolates on the susceptible barley variety Harrington, 5 days post inoculation. Thirty-seven Pgt isolates showing differential responses on RMRL were genotyped using Restriction Site Associated DNA-Genotyping by Sequencing (RAD-GBS), identifying 24 diverse isolates that were used for transcript analysis during the infection process. Variants associated with Pgt virulence on rpg4/5. Identification of Pgt Candidate Secreted Effector Protein (CSEP) and their classification based on level of expression. List of gene that are differentially regulated in rpg4/5 virulent isolates compared to rpg4/5 avirulent isolates. List of gene that are differentially regulated in Rpg1 virulent isolates compared to Rpg1 avirulent isolates. Gene enrichment analysis of differentially expressed gene in virulent vs avirulent rpg4/5 inoculated Harrington in R bioconductor package TopGO, Table S10. Differentially expressed gene in between virulent rpg4/5 and avirulent rpg4/5 inoculated sampled and its comparison with the non-inoculated controls. RNAseq read mapping statistics for the non-inoculated Harrington samples. RNAseq read mapping statistics for the Pgt inoculated Harrington samples. Read and mapping statistics of RAD-GBS data of Pgt Samples. Infection type of group3 Pgt isolates on barley differential lines. Infection type of group2 Pgt isolates on barley differential lines.
Infection type of group1 Pgt isolates on barley differential lines. Group of Pgt isolates based on their virulence on barley lines containing stem rust resistance gene rpg4/5 and/or Rpg1. Microsoft Excel Workbook containing 13 tables. Additional file 1: Contains supplementary tables Table S1-S13.
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