Introduction
Rice (Oryza sativa ) is one of the main staple food crops for over half of the world’s population. Rice blast disease, caused by the blast fungus Magnaporthe oryzae, is the most devastating rice disease, causing from 10-30% annual yield losses worldwide (Deng et al., 2017; Liu et al., 2013; Liu, Liu, Triplett, Leach, & Wang, 2014). Due to its importance in rice production, the rice-M. oryzae interaction has been studied for decades and has become a model system in the study of plant-fungal interactions. The infection starts when fungal spores, called conidia, land on the surface of rice leaf (Talbot, 2003). Conidia attach to the leaf cuticle, germinate rapidly and form a dome-shaped infection cell called an appressorium within 8 h (Dagdas et al., 2012). The appressorium produces a specialized hypha, a penetration peg, pierces the leaf cuticles and invades epidermal cells, where the peg expands to form invasive hyphae by 24 h postinoculation (hpi) (Dagdas et al., 2012; Kankanala, Czymmek, & Valent, 2007). During fungal invasion, rice cells first mount a less specific immune response upon recognition of pathogen-associated molecular patterns (PAMPs), named PAMPs-triggered immunity (PTI). In the compatible interaction, M. oryzae secrete a large number of effector proteins to counteract the PTI in susceptible rice plants (Liu et al., 2014). While in the incompatible interaction, certain fungal effector/effectors is/are recognized by cognate nucleotide-binding, leucine-rich-repeat (NLR) proteins, resulting in robust immune responses, called effector-triggered immunity (ETI) in resistant rice plants (Jones & Dangl, 2006; Liu et al., 2014; Tang, Wang, & Zhou, 2017; W. Wang, Feng, Zhou, & Tang, 2020). PTI and ETI trigger many similar immune responses, including the activation of mitogen-activated protein kinases, transient calcium influx, a rapid burst of reactive oxygen species (ROS), deposition of callose, transcriptional reprogramming and phytohormone regulation (Cui, Tsuda, & Parker, 2015; W. Wang et al., 2020).
Currently, although more than 70 defense regulators in rice blast resistance have been identified, many more defense regulators in rice blast resistance remain to be identified (Li, Chern, Yin, Wang, & Chen, 2019). The immune signaling pathways and networks in rice are elusive. Large-scale approaches have been used to study the transcriptome profile of rice in response to M. oryzae , including microarrays and RNA-sequencing. Due to technical limits of microarrays, previous studies have only identified a small number of DEGs in the rice response toM. oryzae. For instance, Wei et al identified 551 and 131 DEGs at 24 hpi in resistant and susceptible rice cultivars, respectively (Wei et al., 2013). Within the limit number of DEGs, functional analysis indicated that genes involved in signaling pathways were upregulated during the rice early response to M. oryzae (Wei et al., 2013). In recent years, RNA-sequencing (RNA-seq) technology has provided a powerful and effective tool to study the transcriptome profile in plant-microbe interactions. A comprehensive transcriptome analysis using time-series RNA-seq on Arabidopsis challenged with virulent or avirulent Pseudomonas syringae strains discovered thatArabidopsis activates very similar transcriptome responses in compatible and incompatible interactions but with different speeds, and the phytohormone network is required for achieving high-amplitude transcriptional reprogramming within the early infection stage (Mine et al., 2018). However, to date, full time-series RNA-seq data on rice -M. oryzae interactions have not been reported.
In this study, we present a high-resolution time-series transcriptome data at 12, 24, 36 and 48 hpi of both compatible and incompatible rice-M. oryzae interactions using RNA-seq. We found that the resistant rice cultivar activated high-amplitude transcriptional responses at 12 hpi, which is much earlier than 24 hpi, as suggested in previously studies. A group of core genes involved in both compatible and incompatible rice-M. oryzae interactions were identified. Functional pathway analysis of DEGs revealed that the protein translation machinery was regulated at the early stage in rice immune responses to M. oryzae . Furthermore, we identified and verified three new genes that are involved in rice resistance to blast disease. Collectively, these findings provide a comprehensive overview of transcriptional reprogramming during rice immune responses to M. oryzae and potential gene resources for functional characterization of the rice immune system.