How stress affects rice: a characterization of the rice transcriptome during single and simultaneous abiotic and biotic stresses
Date
2019
Authors
Cohen, Stephen Philip, author
Leach, Jan E., advisor
Argueso, Cristiana T., advisor
Snow, Christopher D., committee member
Antunes, Mauricio S., committee member
Journal Title
Journal ISSN
Volume Title
Abstract
Environmental stresses, both abiotic and biotic, are large contributors to pre-harvest crop loss. Abiotic stresses, such as drought, salinity, non-optimal temperature and others, are non-living factors in the environment that have a negative effect on plants. Biotic stresses are biological factors that can harm plants, including pathogens, pests and competition from other plants. With climate change increasing the incidence of abiotic stresses and the constant pressures of pests and pathogens, it is critical to world agriculture that varieties of plants broadly tolerant to stresses are developed. For this, it is necessary to understand how plants respond to multiple simultaneous stresses. The goal of this work is to characterize the stress response of the global staple food plant rice. Here, I present the results of two comprehensive transcriptome studies. In the first, I characterize how the rice transcriptome changes in response to simultaneous heat stress and infection by the bacterial pathogen Xanthomonas oryzae (Xo). Xo includes the causal agent for the economically important bacterial blight disease of rice, Xo pathovar oryzae (Xoo). Bacterial blight is more severe during abiotic stresses such as high temperature and drought. Most rice resistance (R) genes that target Xoo lose function at high temperature; however, function of the R-gene Xa7 is enhanced when the host is subjected to abiotic stresses. Understanding why Xa7 is more effective during heat stress gives insight into host processes that are important during combined abiotic and biotic stresses. The major finding of this study was that the abscisic acid (ABA) pathway is a node of cross-talk in the interactions between heat stress and pathogen attack, during both susceptible and resistant interactions. In the second comprehensive study, I characterize how the rice transcriptome is universally regulated by all stresses. Understanding universalities in rice stress response transcriptomes provides insight into how plants endure a wide variety of stresses in the field. To explore the universal rice transcriptome response, I developed a custom workflow to analyze publicly available RNA-Seq data from rice stress response studies, including the abiotic stresses drought, salinity, heat and cold, and the biotic stresses bacterial leaf streak, bacterial blight, rice blast, and two viral diseases. From this study, I concluded that the rice stress response is a robust system with many overlapping features. This core response includes down-regulation of photosynthetic processes and up-regulation of downstream signaling of the hormones ABA, salicylic acid and jasmonic acid. Within this dissertation, I present networks of gene regulation in four major rice responses: (1) response to a susceptible interaction with Xo during high temperature, (2) response to a resistant interaction with Xo during high temperature, (3) core response to abiotic stresses and (4) core response to biotic stresses. Common among all of these pathways are the pathways upstream and downstream of the plant hormone ABA. ABA-related processes are universally up-regulated by abiotic and biotic stresses, and are only repressed during the enhanced Xa7 response at high temperature. Because ABA signaling is critical for stress response, we need a thorough understanding of how genes in the ABA response network interact to most efficiently improve rice to be tolerant to multiple and simultaneous stresses. The gene networks I have characterized can be integrated with genome and transcriptome data from stress-tolerant rice varieties. By having a complete understanding of the rice stress response, we can develop an informed approach for developing new varieties of rice that are resistant to stress.
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Zip file contains data spreadsheets.
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Subject
biotic stresses
plant stress response
Xanthomonas oryzae
high temperature
abiotic stresses
rice transcriptome