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.

Bananas lie among the world’s most important cash and staple crops but are threatened by various devastating pathogens. The phytohormone salicylic acid (SA) plays a key role in the regulation of plant immune response. Tracking the expression of SA-responsive marker genes under pathogen infection is important in pathogenesis elucidation. However, the common SA-responsive marker genes are not consistently induced in different banana cultivars or different organs. Here, we conducted transcriptome analysis for SA response of a banana cultivar, ‘Pei-Chiao’ (Cavendish, AAA genome), and identified three genes, MaWRKY40, MaWRKY70, and Downy Mildew Resistant 6 (DMR6)-Like Oxygenase 1 (MaDLO1) that are robustly induced upon SA treatment in both the leaves and roots. Consistent induction of these three genes by SA treatment was also detected in both the leaves and roots of bananas belonging to different genome types such as ‘Tai-Chiao No. 7’ (Cavendish, AAA genome), ‘Pisang Awak’ (ABB genome), and ‘Lady Finger’ (AA genome). Furthermore, the biotrophic pathogen cucumber mosaic virus elicited the expression of MaWRKY40 and MaDLO1 in infected-leaves of susceptible cultivars. The hemi-biotrophic fungal pathogen Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) also consistently induced the expression of MaWRKY40 and MaDLO1 in the infected-roots of the Foc TR4-resistant cultivar. These results indicate that MaWRKY40 and MaDLO1 can serve as reliable SA-responsive marker genes for the study of plant immunity in banana. Revealing SA-responsive marker genes provides a stepping-stone for further studies in banana resistance to pathogens.

Small RNAs act as fungal pathogen effectors that silence host target genes to promote infection, a virulence mechanism termed cross-kingdom RNA interference (RNAi). The essential pathogen factors of cross-kingdom small RNA production are largely unknown. We here characterized the RNA-dependent RNA polymerase (RDR)1 in the fungal plant pathogen Botrytis cinerea that is required for pathogenicity and cross-kingdom RNAi. B. cinerea bcrdr1 knockout (ko) mutants exhibited reduced pathogenicity and loss of cross-kingdom small RNAs. We developed a novel "switch-on" GFP reporter to study cross-kingdom RNAi in real-time within the living plant tissue which highlighted that bcrdr1 ko mutants were compromised in cross-kingdom RNAi. Moreover, blocking seven pathogen cross-kingdom small RNAs by expressing a short-tandem target mimic RNA in transgenic Arabidopsis thaliana led to reduced infection levels of the fungal pathogen B. cinerea and the oomycete pathogen Hyaloperonospora arabidopsidis. These results demonstrate that cross-kingdom RNAi is significant to promote host infection and making pathogen small RNAs an effective target for crop protection.

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Background: Banana, an important cash and staple crop worldwide, suffers from various biotrophic and hemi-biotrophic pathogens. In plants’ defense against these pathogens, the phytohormone salicylic acid (SA) plays a key role in the regulation of immune response. Using a specific set of SA-responsive genes as markers is frequently adopted to monitor the onset of SA-mediated immune response. However, reliable SA-responsive genes marker genes have not been well established in bananas. Results: From the transcriptome analysis of SA-treated ‘Pei-Chiao’ banana roots, we identified 19 up-regulated and 3 down-regulated genes. Four of the up-regulated genes previously reported to play crucial roles in SA-mediated immunity in other species were further analyzed for their applicability in different tissues and cultivars of bananas using real-time quantitative reverse-transcription PCR. The analysis showed that WRKY40, WRKY70, and Downy Mildew Resistant 6 (DMR6)-Like Oxygenase 1 (DLO1) were significantly induced upon SA treatment in both the leaves and roots of ‘Pei-Chiao’ (AAA genome), ‘Pisang Awak’ (ABB genome), and ‘Lady Finger’ (AA genome) bananas.Conclusions: The uncovering of common marker genes WRKY40, WRKY70, and DLO1 for SA response in different banana genome types provides the stepping stone for studies towards understanding of SA-mediated immune response in bananas.