Abstract
BackgroundEvery 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.ResultsWithin 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.ConclusionsThe 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.
Highlights
Every year, substantial crop loss occurs globally, as a result of bacterial, fungal, parasite and viral infections in rice
Bacterial leaf blight is a common problem seen in rice species infected with Xanthomonas oryzae pv. oryzae (Xoo) and these infections are known to result in significant crop loss, ranging up to 60% of potential yield, or several billions in direct economic terms [2]
In this study we examine global transcriptomic responses to a variety of biotic stresses in parallel, revealing the specific pathways e.g. calcium signalling and WRKY and NAC transcription factors that have a conserved response across multiple pathogen infections in rice
Summary
Substantial crop loss occurs globally, as a result of bacterial, fungal, parasite and viral infections in rice. Given the ever-increasing demand for food, prevention of losses from abiotic and biotic stresses offers a resource neutral avenue in terms of resource transgenic plants, resulting in greater tolerance to a given stress imposition While this is promising there are several barriers translating laboratory based experiments to field situations, including the use of model plants compared to crop plants and the impositions of single stresses compared to multiple stresses [1]. In addition to recognition and signalling functions being crucial to resistance, a number of WRKY transcription factors have been observed to result in greater resistance when over-expressed/knockedout, indicating that these have an important role in the regulation of gene expression following pathogen infection [8,9,10] One example of this is for WRKY13, which has been found to be an important regulator of rice interaction with Xoo as well as the fungus, M.grisea, where activation of this gene resulted in increased resistance of rice to these infections [11]. Given the crucial role of transcription factors that have been shown to have a direct effect on resistance, as well as the findings that transcriptomic changes are characteristic of responses to infection [12,13,14,15], the examination of global transcriptomic responses provide great insight into the mode of response to infection
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