XA21-specific induction of stress-related genes following Xanthomonas infection of detached rice leaves

Nicholas C Thomas; Benjamin Schwessinger; Furong Liu; Huamin Chen; Tong Wei; Yen P Nguyen; Isaac WF Shaker; Pamela C Ronald

doi:10.7287/peerj.preprints.2289v1

XA21-specific induction of stress-related genes following Xanthomonas infection of detached rice leaves

Nicholas C Thomas^1,2, Benjamin Schwessinger^1,2,3, Furong Liu^1,2, Huamin Chen^1,4, Tong Wei^1,2, Yen P Nguyen¹, Isaac WF Shaker¹, Pamela C Ronald ^1,2

1 Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA, United States

2 Joint BioEnergy Institute, Emeryville, CA, United States

3 Research School of Biology, Australian National University, Acton, Australia

4 State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Bejing, China

DOI: 10.7287/peerj.preprints.2289v1

Published: 2016-07-13
Accepted: 2016-07-13

Subject Areas: Agricultural Science, Plant Science
Keywords: XA21, Xanthomonas, EFR, Rice, RNAseq

Copyright: © 2016 Thomas et al.
Licence: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.

Cite this article: Thomas NC, Schwessinger B, Liu F, Chen H, Wei T, Nguyen YP, Shaker IW, Ronald PC. 2016. XA21-specific induction of stress-related genes following Xanthomonas infection of detached rice leaves. PeerJ Preprints 4:e2289v1 https://doi.org/10.7287/peerj.preprints.2289v1

Abstract

The rice XA21 receptor kinase confers robust resistance to the bacterial pathogen Xanthomonas oryzae pv. 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 8 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.

Author Comment

This is a preprint submission to PeerJ Preprints.

Supplemental Information

RNA sequencing sample treatment summary

Table summarizes the experimental setup including the genotypes, time of treatment, and type of treatment used for samples used in RNA sequencing. There were three replicates for each sample for a total of 21 sequenced samples.

DOI: 10.7287/peerj.preprints.2289v1/supp-1
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Differentially regulated gene expression table with clade number and putatuve function

DOI: 10.7287/peerj.preprints.2289v1/supp-2
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Differentially regulated gene clade groups and GO term analysis

DOI: 10.7287/peerj.preprints.2289v1/supp-3
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Marker gene summary and primer information

DOI: 10.7287/peerj.preprints.2289v1/supp-4
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Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Nicholas C Thomas performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Benjamin Schwessinger conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Furong Liu performed the experiments, reviewed drafts of the paper.

Huamin Chen performed the experiments, reviewed drafts of the paper.

Tong Wei analyzed the data, reviewed drafts of the paper.

Yen P Nguyen performed the experiments, reviewed drafts of the paper.

Isaac WF Shaker performed the experiments, reviewed drafts of the paper.

Pamela C Ronald conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

The National Center for Biotechnology Information Sequence Read Archive (SRA)

BioProject ID PRJNA250865

http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA250865

Funding
This work was part of the DOE Joint BioEnergy Institute (http://www.jbei.org) and the DOE Joint Genome Institute and were supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. B. S. was supported by a Human Frontiers Science Program long-term postdoctoral fellowship (LT000674/2012) and a Discovery Early Career Award (DE150101897). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.