Genome-Wide Characterization of Rice Black Streaked Dwarf Virus-Responsive MicroRNAs in Rice Leaves and Roots by Small RNA and Degradome Sequencing

Abstract

MicroRNAs (miRNAs) are small, non-coding RNAs which typically function by guiding cleavage of target mRNAs. They play important roles in development, abiotic stress and responses to pathogens. Four small RNA libraries and four degradome libraries were constructed from the leaves and roots of healthy rice and plants infected with Rice black streaked dwarf virus (RBSDV). Analysis of the deep sequencing results showed that the expression patterns of 14 miRNAs in leaves and 16 miRNAs in roots changed significantly in response to RBSDV infection. Some responses were similar in roots and leaves, but many miRNAs responded differently in different tissues. The results were confirmed for selected miRNAs by quantitative real-time PCR. By using degradome sequencing, a total of 104 target transcripts for 17 conserved and 16 non-conserved miRNAs were shown to be responsive to RBSDV infection. Fifteen novel miRNAs were also identified by small RNA and degradome sequencing. The results provide new insights into the regulatory networks of miRNAs and their targets in different plant tissues in response to virus infection.

Suppression of auxin signalling promotes rice susceptibility to Rice black streaked dwarf virus infection

“…The RT‐qPCR assay was performed using the ABI7900HT Sequence Detection System (Applied Biosystems, CA, USA) with ChamQTM SYBR qPCR Master Mix (Low ROX Premixed). OsUBQ5 (AK061988) was used as an internal control (Sun et al , ). The relative expression levels of genes were determined using the 2 ‐ΔΔC (t) method.…”

Abscisic acid negatively modulates plant defence against rice black‐streaked dwarf virus infection by suppressing the jasmonate pathway and regulating reactive oxygen species levels in rice

“…The OsUBQ5 gene (AK061988) was used for the internal control and normalization to calculate fold changes in gene expression (Z. Sun, He, Li, Wang, & Chen, ), and the fold changes were analysed via the 2 ‐ΔΔC(t) method. All gene‐specific primers for qRT‐PCR are shown in Table S1.…”

“…Total RNA was extracted from rice seedlings with TRIzol reagent Sun, He, Li, Wang, & Chen, 2015), and the fold changes were analysed via the 2 -ΔΔC(t) method. All gene-specific primers for qRT-PCR are shown in Table S1.…”

Jasmonic acid‐mediated defense suppresses brassinosteroid‐mediated susceptibility to Rice black streaked dwarf virus infection in rice

“…The RT-qPCR was performed under the following conditions: 95°C for 3 min; and 40 cycles of 95°C for 15 s, 60°C for 15 s, and 72°C for 20 s. Relative gene expression was analyzed by the comparative Ct method (2 ÀDDCt method) (Livak & Schmittgen, 2001). The mRNA expression levels were normalized against the expression of UBQ5 (Sun et al, 2015). At least three biological replicate samples were used.…”