DOC analysis from Construction and characterization of a knock-down RNA interference line of <i>OsNRPD1</i> in rice (<i>Oryza sativa</i> ssp <i>japonica</i> cv Nipponbare)

In plants, RNA-directed DNA methylation (RdDM) is a silencing mechanism relying on the production of 24-nt small interfering RNAs (siRNAs) by RNA POLYMERASE IV (Pol IV) to trigger methylation and inactivation of transposable elements (TEs). We present the construction and characterization of <i>osnrpd1</i>, a knock-down RNA interference line of <i>OsNRPD1</i> gene that encodes the largest subunit of Pol IV in rice (<i>Oryza sativa</i> ssp <i>japonica</i> cv Nipponbare). We show that <i>osnrpd1</i> displays a lower accumulation of <i>OsNRPD1</i> transcripts, associated with 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 <i>Tos17</i> and <i>Lullaby</i> and the long interspersed nuclear element-type retrotransposon <i>Karma.</i> However, we did not observe any clear developmental phenotype, contrary to what was expected for a mutant severely affected in RdDM. In addition, despite the presence of many putatively functional TEs in the rice genome, we found no evidence of <i>in planta</i> global reactivation of transposition. This knock-down of <i>OsNRPD1</i> likely led to a weakly affected line, with no effect on development and a limited effect on transposition. We discuss the possibility that a knock-out mutation of <i>OsNRPD1</i> would cause sterility in rice.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.