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Open Access Highly Accessed Research article

Antagonistic, overlapping and distinct responses to biotic stress in rice (Oryza sativa) and interactions with abiotic stress

Reena Narsai126*, Chuang Wang34, Jie Chen5, Jianli Wu5, Huixia Shou34 and James Whelan23

Author Affiliations

1 Centre for Computational Systems Biology, Bayliss Building M316 University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia

2 ARC Centre of Excellence in Plant Energy Biology, Bayliss Building M316 University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia

3 Joint Research Laboratory in Genomics and Nutriomics, Zhejiang University, Hangzhou 310058, China

4 College of Life Sciences, Zhejiang University, Hangzhou 310058, China

5 China National Rice Research Institute, Hangzhou 310006, China

6 ARC Centre of Excellence in Plant Energy Biology, Centre for Computational Systems Biology, MCS Building M316 University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia

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BMC Genomics 2013, 14:93  doi:10.1186/1471-2164-14-93

Published: 12 February 2013

Abstract

Background

Every year, substantial crop loss occurs globally, as a result of bacterial, fungal, parasite and viral infections in rice. Here, we present an in-depth investigation of the transcriptomic response to infection with the destructive bacterial pathogen Xanthomonas oryzae pv. oryzae(Xoo) in both resistant and susceptible varieties of Oryza sativa. A comparative analysis to fungal, parasite and viral infection in rice is also presented.

Results

Within 24 h of Xoo inoculation, significant reduction of cell wall components and induction of several signalling components, membrane bound receptor kinases and specific WRKY and NAC transcription factors was prominent, providing a framework for how the presence of this pathogen was signalled and response mounted. Extensive comparative analyses of various other pathogen responses, including in response to infection with another bacterium (Xoc), resistant and susceptible parasite infection, fungal, and viral infections, led to a proposed model for the rice biotic stress response. In this way, a conserved induction of calcium signalling functions, and specific WRKY and NAC transcription factors, was identified in response to all biotic stresses. Comparison of these responses to abiotic stress (cold, drought, salt, heat), enabled the identification of unique genes responsive only to bacterial infection, 240 genes responsive to both abiotic and biotic stress, and 135 genes responsive to biotic, but not abiotic stresses. Functional significance of a number of these genes, using genetic inactivation or over-expression, has revealed significant stress-associated phenotypes. While only a few antagonistic responses were observed between biotic and abiotic stresses, e.g. for a number of endochitinases and kinase encoding genes, some of these may be crucial in explaining greater pathogen infection and damage under abiotic stresses.

Conclusions

The analyses presented here provides a global view of the responses to multiple stresses, further validates known resistance-associated genes, and highlights new potential target genes, some lineage specific to rice, that play important roles in response to stress, providing a roadmap to develop varieties of rice that are more resistant to multiple biotic and abiotic stresses, as encountered in nature.