Rice blast caused by Magnaporthe oryzae is the most severe and devastating disease in rice results in serious losses worldwide. Based on this, the interaction between rice and M. oryzae has been studied extensively for decades, but the pathogen always has a negative effect on the new and emerging rice varieties. The present study employed comparative transcriptome strand-specific RNA sequencing and genome approaches of Diantun rice susceptible (D502) and resistance (D506) lines (leaves) in the presence of blast fungus, M. oryzae. Overall differential expression genes (DEGs) displayed 5838 and 3719 DEGs in D502 and D506, respectively 24hpi, however, the expression of DEGs in the former line was 5113, and in later line it was 4794 after 48hpi. Interestingly, only 2493 and 2418 DEGs were similar at both time hour points in both lines, respectively. Among DEGs, mostly exhibited down-regulated expression only in D502 major pathways, including plant hormones signal transduction and starch and sucrose metabolism at both time hours, suggesting susceptibility D502 on upon pathogen infection. Additionally, protein-protein interaction network analysis based on DEGs was performed between both varieties to find possible connections and increase interaction network complexity at 24h to 48h in D506, that might result in resistance to M. oryzae. We found many up and down-regulated DEGs only in D506 after pathogen infection, which might have a significant role in PTI and ETI immunity response. Next, through genomic analysis, different non-synonymous single nucleotide polymorphisms (nsSNPs) were identified between both D502 and D506 rice varieties. Here, four up-regulated genes, including WAK1, WAK4, WAK5, and OsDja9 harboring nsSNPs were found only in resistant D506 variety. Following alignment of open reading frame (ORF) region sequences revealed that the exonic SNPs lead the amino acid variation. Our study proved that SNPs in these four genes were related to providing resistance in D506 line upon pathogen infection. In summary, we conclude that above-targeted rice defense and resistance genes identified through gene transcripts and modern genomic approaches could help us provide robust rice breeding and agricultural practices in future.

Fusarium oxysporum f. sp. capsici (Foc) poses a significant position in agriculture that has a negative impact on chili plant in terms of growth, fruit quality, and yield. Biological control is one of the promising strategies to control this pathogen in crops. Chili is considered as one of the most important crops in the Hyderabad region that is affected by Fusarium wilt disease. The pathogen was isolated from the infected samples in the region and was confirmed by morphological characteristics and PCR with a band of 488 bp. The bacterial strains were isolated from the rhizosphere soil of healthy plant and also confirmed by PCR with a band of 1,542 bp.The molecular characterization of the fungal and bacterial strain has shown 99.9% homology with the retrieved sequences of Fusarium oxysporum f. sp. capsici and Bacillus subtilis from NCBI. The 1-month-old Ghotki chili plants were inoculated with 1×10⁵ cfu spore/ml⁻¹ suspension and confirmed that the FOC-1 is responsible for chili Fusarium wilt disease. Subsequently, among the 33 screened Bacillus strains, only 11 showed antagonistic activity against F. oxysporum. Out of these, only two strains (AM13 and AM21) have shown maximum antagonistic activity against the pathogen by reducing the infection and promoting growth parameters of chili plants under both in vitro and greenhouse conditions. The study suggested that biological control is the most promising control strategy for the management of Fusarium wilt of chili in the field.

Nitrogen fertilization is essential for crop yield but can increase susceptibility to rice blast, a phenomenon known as Nitrogen-Induced Susceptibility (NIS). The genetic architecture governing natural variation in NIS remains poorly characterized. To address this, we performed a genome-wide association study (GWAS) using a diverse panel of 268 rice accessions from the rice diversity panel 2, under controlled nitrogen regimes 0N (control), 1N (100 mg/L NH ₄ NO ₃ ), 2N (200 mg/L NH ₄ NO ₃ ). Our analyses defined a NIS Index (NISI), which revealed extensive phenotypic polymorphism in nitrogen responsiveness across the rice diversity panel. GWAS identified several significant loci, including a novel locus on chromosome 8 (NIS4) harboring F-box protein genes within a stress-responsive gene cluster containing eight F-box genes, a drought resistance gene, and a heat shock protein 70 gene. Physiological dissection showed that a ‘negative NIS’ phenotype (enhanced resistance under high nitrogen) correlated with a rapid, pathogen-triggered defense response, characterized by immediate induction of peroxidase activity and lignin biosynthesis. Conversely, susceptible lines exhibited delayed defense. Gene expression analysis linked active nitrogen assimilation (GS/GOGAT cycle) to susceptibility. We conclude that NIS polymorphism has a genetic component and may involve the host’s ability to redirect nitrogen resources toward early defense activation during pathogen invasion.

Magnaporthe oryzae, the causal agent of rice blast disease, produces devastating damage to global rice production. It is urgent to explore novel strategies to overcome the losses caused by this disease. 9-phenanthrol is often used as a transient receptor potential melastatin 4 (TRPM4) channel inhibitor for animals, but we found its fungal toxicity to M. oryzae. Thus, we explored the antimicrobial mechanism through transcriptome and metabolome analyses. Moreover, we found that overexpression of a gene encoding 4-hydroxyphenylpyruvate dioxygenase involved in the tyrosine degradative pathway enhanced the tolerance of 9-phenanthrol in M. oryzae. Thus, our results highlight the potential fungal toxicity mechanism of 9-phenanthrol at metabolic and transcriptomic levels and identify a gene involving 9-phenanthrol alleviation. Importantly, our results demonstrate the novel mechanism of 9-phenanthrol on fungal toxicity that will provide new insights of 9-phenanthrol for application on other organisms.

Magnaporthe oryzae is one of the most devastating pathogens of rice, causing significant economic losses worldwide. Despite extensive studies on the M. oryzae-rice interaction, particularly focusing on the underlying resistance mechanisms, the molecular basis of rice resistance remains poorly understood. This study employed an integrated metabolomic, transcriptomic, and genomic approach to compare the response of Diantun susceptible (D502) and resistant (D506) rice lines to M. oryzae infection at 48 h post-inoculation. A total of 588 and 595 differentially accumulated metabolites (DAMs) were identified in D502 and D506, respectively. Notably, 55% of these metabolites exhibited similar expression patterns across both lines, while 9 DAMs displayed contrasting patterns at 48 h in response to pathogen infection. Pathway analysis revealed significant regulation of flavonoid, nucleotide derivatives, phenylpropanoid and polyketide, and vitamin biosynthesis pathways, with specific metabolites from these pathways potentially contributing to resistance in D506. KEGG enrichment analysis further identified key pathways in D506, including linoleic acid metabolism, plant hormone signal transduction, α-linolenic acid metabolism, and the pentose phosphate pathway. Network analysis based on DAMs and differentially expressed genes (DEGs) highlighted eight up-regulated metabolites and their key genes responsible for resistance, which are associated with flavonoid, tryptophan, and phytohormone, resulting in suppressed M. oryzae infection in D506. The content of sakuranetin was significantly higher, and the peak in expression of their key gene OMT-9 after M. oryzae infection at 48 h, lead to an increase in phytoalexin production in the D506 line. Subsequently, exonic non-synonymous single nucleotide polymorphisms (nsSNPs) within abscisic acid synthesis (NCED1) gene, identified through genome-wide analysis, were associated with amino acid substitutions potentially affecting protein function. This finding suggests that the ABA and their key genes are essential for the resistance in D506 against M. oryzae. In last, we conclude that our findings underscore the power of integrating metabolomics, transcriptomics, and genomics to identify key metabolites and genes underlying resistance to M. oryzae. The insights gained from this study offer valuable resources for enhancing rice breeding strategies and improving disease management in agriculture.

Manganese, as an essential trace element, participates in many physiological reactions by regulating Mn associated enzymes. Magnaporthe oryzae is a serious pathogen and causes destructive losses for rice production. We identified a cytochrome P450 gene, MoMCP1, involving the alleviation of manganese toxin and pathogenicity. To identify the underlying mechanisms, transcriptomics were performed. The results indicated that many pathogenicity related genes were regulated, especially hydrophobin related genes in ∆Momcp1. Furthermore, the Mn²⁺ toxicity decreased the expressions of genes involved in the oxidative phosphorylation and energy production, and increased the reactive oxygen species (ROS) levels, which might impair the functions of mitochondrion and vacuole, compromising the pathogenicity and development in ∆Momcp1. Additionally, our results provided further information about Mn associated the gene network for Mn metabolism in cells.