Small RNA and mRNA Profiling of Arabidopsis in Response to Phytophthora Infection and PAMP Treatment

  • Yingnan Hou
  • Wenbo MaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1578)


Small non-coding RNAs (smRNAs) regulate gene expression at both transcriptional and post-transcriptional levels. Well known for their roles in development, smRNAs have emerged as important regulators of plant immunity. Upon pathogen perception, accumulation of specific smRNAs are found to be altered, presumably as a host defense response. Therefore, identification of differentially accumulated smRNAs and their target genes would provide important insight into the regulation mechanism of immune responses. Here, we describe the detailed experimental procedure using Illumina sequencing to analyze the expression profiles of smRNAs and mRNAs in Arabidopsis. We focus on a newly developed pathosystem using Phytophthora capsici as the pathogen and include the treatment of Arabidopsis leaves with pathogen-associated molecular patterns (PAMPs) of Phytophthora.

Key words

Small RNA-Seq RNA-Seq Next-generation sequencing Small RNA-regulated defense response Pattern-triggered immune response Phytophthora infection 



This research is supported by grants from USDA-NIFA (2014-67013-21554) and NSF-PGRP (IOS-1340001) for W. Ma.


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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Department of Plant Pathology and MicrobiologyUniversity of CaliforniaRiversideUSA
  2. 2.Center for Plant Cell BiologyUniversity of CaliforniaRiversideUSA

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