Transcriptome Analysis of Early Defenses in Rice against Fusarium fujikuroi

Abstract

Background Bakanae is a seedborne disease caused by Fusarium fujikuroi. Rice seedlings emerging from infected seeds can show diverse symptoms such as elongated and slender stem and leaves, pale coloring, a large leaf angle, stunted growth and even death. Little is known about rice defense mechanisms at early stages of disease development. Results This study focused on investigating early defenses against F. fujikuroi in a susceptible cultivar, Zerawchanica karatals (ZK), and a resistant cultivar, Tainung 67 (TNG67). Quantitative PCR revealed that F. fujikuroi colonizes the root and stem but not leaf tissues. Illumina sequencing was conducted to analyze the stem transcriptomes of F. fujikuroi-inoculated and mock-inoculated ZK and TNG67 plants collected at 7 days post inoculation (dpi). More differentially expressed genes (DEGs) were identified in ZK (n = 169) than TNG67 (n = 118), and gene ontology terms related to transcription factor activity and phosphorylation were specifically enriched in ZK DEGs. Among the complex phytohormone biosynthesis and signaling pathways, only DEGs involved in the jasmonic acid (JA) signaling pathway were identified. Fourteen DEGs encoding pattern-recognition receptors, transcription factors, and JA signaling pathway components were validated by performing quantitative reverse transcription PCR analysis of individual plants. Significant repression of jasmonate ZIM-domain (JAZ) genes (OsJAZ9, OsJAZ10, and OsJAZ13) at 3 dpi and 7 dpi in both cultivars, indicated the activation of JA signaling during early interactions between rice and F. fujikuroi. Differential expression was not detected for salicylic acid marker genes encoding phenylalanine ammonia-lyase 1 and non-expressor of pathogenesis-related genes 1. Moreover, while MeJA did not affect the viability of F. fujikuroi, MeJA treatment of rice seeds (prior to or after inoculation) alleviated and delayed bakanae disease development in susceptible ZK. Conclusions Different from previous transcriptome studies, which analyzed the leaves of infected plants, this study provides insights into defense-related gene expression patterns in F. fujikuroi–colonized rice stem tissues. Twelve out of the 14 selected DEGs were for the first time shown to be associated with disease resistance, and JA-mediated resistance was identified as a crucial component of rice defense against F. fujikuroi. Detailed mechanisms underlying the JA-mediated bakanae resistance and the novel defense-related DEGs are worthy of further investigation.

Leaf Transcriptome Analysis of Broomcorn Millet Uncovers Key Genes and Pathways in Response to Sporisorium destruens

“…It was inferred that invasion by Sporisorium destruens increased the JA content in the leaves of diseased broomcorn millet to resist Sporisorium destruens invasion. However, Cheng's research results showed that the genes associated with the JA biosynthetic process were up-regulated in the resistant cultivar, Selenio, and down-regulated in the susceptible Dorella cultivar [32], which was contrary to our result. Research on the role of JA in the interaction between broomcorn millet and smut needs further investigation.…”

“…Sequencing analysis identified 514 and 5452 DEGs in the resistant and susceptible cultivars, respectively. This result was consistent with the study by Cheng et al [32], in which inoculation of Tainung 67 (resistant rice cultivar) and Zerawchanica karatals (susceptible rice cultivar) with Fusarium fujikuroi resulted in the appearance of 118 and 169 DEGs, respectively. Hence, susceptible varieties tend to activate gene expression in response to stress.…”

OsWRKY114 Is a Player in Rice Immunity against Fusarium fujikuroi

“…JA-dependent defense responses are important factors in resistance to F. fujikuroi in rice [ 14 , 16 ]. To determine whether OsWRKY114 is also involved in JA responses, we analyzed the expression levels of various JA-related genes in OsWRKY114 OX .…”

“…High-performance liquid chromatography-mass spectrometry and comparative transcriptome profiling showed that increasing GA and decreasing JA levels in infected plants are important for plant susceptibility to F. fujikuroi [ 14 , 15 ]. Transcriptome analysis revealed that the expression levels of JAZ genes decrease during the early stages of F. fujikuroi infection and that JA-dependent immunity is crucial for the resistance of rice to F. fujikuroi [ 16 ]. However, the signaling components and regulatory mechanisms of GA and JA signaling involved in rice– F. fujikuroi interactions are largely unknown.…”

Gene Expression in the Developing Seed of Wild and Domesticated Rice

“…A few studies have aimed to better understand the dynamics of key genes and regulatory mechanisms in rice associated with morphology [ 22 ], physiology [ 23 ], abiotic and biotic stress mechanisms [ 24 , 25 , 26 ]. Transcriptional control of nutrients during grain filling in rice has been studied by designing a GeneChip microarray covering half of the rice genome to understand the effect of genes participating in nutrient partitioning on starch quality [ 27 ].…”