Construction and characterisation of a knock-down RNA interference line of OsNRPD1 in rice (Oryza sativa ssp japonica cv Nipponbare)

Seeds of osnrpd1 lines are available from the corresponding author on reasonable request. Scripts to identify TEs insertions are available at github (https://github.com/EricUPVD/sam2ins) under the Unlicence, a license with no conditions. Sequences have been deposited at NCBI under the SRA bioproject accession PRJNA535389. All other relevant data have been provided within the main text, figures and additional files.

International audience

English. In plants, RNA-directed DNA Methylation (RdDM) is a mechanism of silencing that relies on the production of 24-nt siRNAs by RNA POLYMERASE IV (Pol IV) to trigger methylation and thus inactivation of transposable elements (TEs). We present the construction and characterisation of osnrpd1, a knock-down RNA interference line of OsNRPD1 gene that encodes the largest subunit of Pol IV in rice (Oryza sativa ssp japonica cv Nipponbare). We show that osnrpd1 displays a lower accumulation of OsNRPD1 transcripts, associated to an overall reduction of 24-nt siRNAs and DNA methylation level in all three contexts, CG, CHG and CHH. We uncovered new insertions of known active TEs, the LTR retrotransposons Tos17 and Lullaby and the LINE-type retrotransposon Karma. However, we did not observe any clear developmental phenotype, contrary to what was expected for a mutant severily affected in RdDM. In addition, despite the presence of many putatively functional TEs in the rice genome, we found no evidence of in planta global reactivation of transposition. This knock-down of OsNRPD1 likely led to a weakly affected line, with no effect on development and a limited effect on transposition. We discuss the possibility that a knockout mutation of OsNRPD1 would cause sterility in rice.This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.