Unraveling the transcriptional network regulated by miRNAs in blast-resistant and blast-susceptible rice genotypes during Magnaporthe oryzae interaction

[Display omitted] •Differentially expressed seventy unique miRNAs were identified in the resistant rice variety, while 106 unique miRNAs were identified in the susceptible rice variety during Magnaporthe invasion.•Inverse expression patterns were observed between miRNAs and their target genes, with a total of 838 target genes showing inverse expression in the resistant variety and 1091 target genes in the susceptible variety.•Twelve novel miRNAs were discovered, demonstrating their pivotal role in plant defense.•The expression of novel miRNAs, including Chr8_26996, Chr12_40110, and Chr12_41899, showed negative correlation with the expression of Cyt-P450 monooxygenase, serine carboxypeptidase, and zinc finger A20 domain-containing stress-associated protein, respectively.•miRNAChr10_39610, involved in the mRNA surveillance pathway, was identified. The plant pathogen Magnaporthe oryzae poses a significant threat to global food security, and its management through the cultivation of resistant varieties and crop husbandry practices, including fungicidal sprays, has proven to be inadequate. To address this issue, we conducted small-RNA sequencing to identify the roles of miRNAs and their target genes in both resistant (PB1637) and susceptible (PB1) rice genotypes. We confirmed the expression of differentially expressed miRNAs using stem-loop qRT-PCR analysis and correlated them with rice patho-phenotypic and physio-biochemical responses. Our findings revealed several noteworthy differences between the resistant and susceptible genotypes. The resistant genotype exhibited reduced levels of total chlorophyll and carotenoids compared to the susceptible genotype. However, it showed increased levels of total protein, callose, H2O2, antioxidants, flavonoids, and total polyphenols. Additionally, among the defense-associated enzymes, guaiacol peroxidase and polyphenol oxidase responses were higher in the susceptible genotypes. In our comparative analysis, we identified 27 up-regulated and 43 down-regulated miRNAs in the resistant genotype, while the susceptible genotype exhibited 44 up-regulated and 62 down-regulated miRNAs. Furthermore, we discovered eight up-regulated and five down-regulated miRNAs shared between the resistant and susceptible genotypes. Notably, we also identified six novel miRNAs in the resistant genotype and eight novel miRNAs in the susceptible genotype. These novel miRNAs, namely Chr8_26996, Chr12_40110, and Chr12_41899, were found to negatively co