Abstract
MicroRNAs regulate plant responses to fungal infections and immunity. In this study, miRNAs were identified in six rice cultivars during a Rhizoctonia solani Kühn AG1-IA infection using a deep sequencing approach. Known and novel miRNAs were analyzed in these rice cultivars, and a set of fungal infection/immunity-associated miRNAs and target genes were quantified by reverse transcription (RT)-qPCR in six rice cultivars. Additionally, the relative expression of these miRNAs was analyzed in different time points of the infection, wild species of rice, and in response to different strains of R. solani. Osa-miR1320-5p showed preferential expression during the fungal infection in all the six rice genotypes, while Osa-miR156d, Osa-miR159b, Osa-miR820c, and Osa-miR1876 were differentially regulated in susceptible and resistant genotypes. A greater degree of downregulation of miRNAs was observed during the initial time points of infection (24–72 h), suggesting a maximum molecular activity of rice-R. solani interaction and resistance response of the host during the early phase of infection. After R. solani infection, the expression of Osa-miR820c and Osa-miR156d was downregulated in Oryza rufipogon, O. alta, O. latifolia, and O. minuta, while Osa-miR397b was downregulated in all the wild rice species except O. officinalis. This study provided comprehensive information on the repertoire of miRNAs expressed in six sheath blight disease-susceptible and resistant indica and aus rice cultivars.
Highlights
Rice is the most widely consumed staple food crop of the world, especially in Asian countries
Beside analyzing the genome-wide known and novel miRNAs in these rice cultivars, 14 of these miRNAs reported to be involved in fungal infection and immunity were quantified by reverse transcription (RT)-qPCR to decipher the fold change regulation of these miRNAs during R. solani infection
To identify the rice microRNAs induced by R. solani infection, we analyzed the small RNA sequencing data obtained from control and infected rice tissues of susceptible (TN1, BPT5204, N22, and Vandana) and resistant (Tetep and Pankaj) genotypes
Summary
Rice is the most widely consumed staple food crop of the world, especially in Asian countries. Wenlei et al [27] analyzed the expression of rice miRNAs in a susceptible (Xudao 3, a japonica cultivar) and a resistant (YSBR1, a hybrid progeny of japonica/indica) rice cultivar in response to R. solani infection They reported miRNAs expression after 5, 10, and 20 h of fungal inoculation. The expressed miRNAs were mapped to known sheath blight-resistant QTLs. Beside analyzing the genome-wide known and novel miRNAs in these rice cultivars, 14 of these miRNAs reported to be involved in fungal infection and immunity were quantified by reverse transcription (RT)-qPCR to decipher the fold change regulation of these miRNAs during R. solani infection. This is a most comprehensive effort to analyze the miRNAs that adds significant information on gene regulation during rice-R. solani interactions
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