Thomas NC, Schwessinger B, Liu F, Chen H, Wei T, Nguyen YP, Shaker IW, Ronald PC.

PeerJ. 2016 Sep 28;4:e2446. eCollection 2016.

Abstract

The rice XA21 receptor kinase confers robust resistance to the bacterial pathogen Xanthomonas oryzaepv. oryzae (Xoo). We developed a detached leaf infection assay to quickly and reliably measure activation of the XA21-mediated immune response using genetic markers. We used RNA sequencing of elf18 treated EFR:XA21:GFP plants to identify candidate genes that could serve as markers for XA21 activation. From this analysis, we identified eight genes that are up-regulated in both in elf18 treated EFR:XA21:GFP rice leaves and Xoo infected XA21 rice leaves. These results provide a rapid and reliable method to assess bacterial-rice interactions.

See: https://www.ncbi.nlm.nih.gov/pubmed/27703843

Figure 1: The transcriptomic profile of elf18 treated EFR:XA21:GFP rice is enriched for stress response related and photosynthesis-related genes.

(A) Multi-dimensional scaling comparing biological coefficients of variance between each sample. Samples labeled Kit0 are Kitaake rice leaf samples without treatment. Samples labeled Kitaake represent untreated Kitaake samples at 0 h, EFRX represent EFR:XA21:GFP untreated samples (EFRX0) and samples treated with 500 nM elf18 at 0.5 h (EFRX0.5), 1 h (EFRX1), 3 h (EFRX3), 6 h (EFRX6), and 12 h (EFRX12). Groups of technical replicates are circled and sample color codes are indicated in upper left legend. (B) A five-way Venn diagram indicating number of total (indicated in parentheses), unique and overlapping differentially regulated genes between time points. (C) Heatmap representing expression levels of differentially regulated genes (DRGs) for EFR:XA21:GFP samples treated with elf18 for indicated durations. The three major DRG clades, determined by expression profile, are labeled 1, 2 and 3 and are indicated to the right of the heatmap. Significantly enriched gene ontology terms with a false discovery rate less than 0.5, compared to the reference, for each clade are shown on the right under the respective clade number. The heatmap color key indicates log₂ fold change values compared with untreated, EFR:XA21:GFP 0 h samples.