Genome-Wide Identification of Dicer-Like, Argonaute, and RNA-Dependent RNA Polymerase Gene Families in Brassica Species and Functional Analyses of Their Arabidopsis Homologs in Resistance to Sclerotinia sclerotiorum

Abstract

RNA silencing is an important mechanism to regulate gene expression and antiviral defense in plants. Nevertheless, RNA silencing machinery in the important oil crop <i>Brassica napus</i> and function in resistance to the devastating fungal pathogen <i>Sclerotinia sclerotiorum</i> are not well-understood. In this study, gene families of RNA silencing machinery in <i>B. napus</i> were identified and their role in resistance to <i>S. sclerotiorum</i> was revealed. Genome of the allopolyploid species <i>B. napus</i> possessed 8 <i>Dicer-like</i> (<i>DCL</i>), 27 <i>Argonaute</i> (<i>AGO</i>), and 16 <i>RNA-dependent RNA polymerase</i> (<i>RDR</i>) genes, which included almost all copies from its progenitor species <i>B. rapa</i> and <i>B. oleracea</i> and three extra copies of <i>RDR5</i> genes, indicating that the <i>RDR5</i> group in <i>B. napus</i> appears to have undergone further expansion through duplication during evolution. Moreover, compared with Arabidopsis, some <i>AGO</i> and <i>RDR</i> genes such as <i>AGO1, AGO4, AGO9</i>, and <i>RDR5</i> had significantly expanded in these <i>Brassica</i> species. Twenty-one out of 51 <i>DCL, AGO</i>, and <i>RDR</i> genes were predicted to contain calmodulin-binding transcription activators (CAMTA)-binding site (CGCG box). <i>S. sclerotiorum</i> inoculation strongly induced the expression of <i>BnCAMTA3</i> genes while significantly suppressed that of some CGCG-containing RNA silencing component genes, suggesting that RNA silencing machinery might be targeted by CAMTA3. Furthermore, Arabidopsis mutant analyses demonstrated that <i>dcl4-2, ago9-1, rdr1-1, rdr6-11</i>, and <i>rdr6-15</i> mutants were more susceptible to <i>S. sclerotiorum</i>, while <i>dcl1-9</i> was more resistant. Our results reveal the importance of RNA silencing in plant resistance to <i>S. sclerotiorum</i> and imply a new mechanism of CAMTA function as well as RNA silencing regulation.