Small RNA-mediated regulation of cross-kingdom gene expression in sugar beet genotypes resistant and susceptible to rhizomania

Rhizomania in sugar beet causes significant yield and sucrose loss worldwide. The disease is caused by Beet necrotic yellow vein virus (BNYVV) and vectored by the plasmodiophorid, <i>Polymyxa betae</i>. Resistance to rhizomania in commercial cultivars is currently dependent upon the use of <i>Rz1</i> and <i>Rz2</i> resistant genes in sugar beet. We have developed an ethyl methanesulphonate mutant breeding line (KEMS12; PI672570) that is highly resistant to rhizomania. Using rhizomania-resistant (R) and susceptible (S) sugar beet breeding lines, natural infection and comprehensive RNA sequencing, we have identified the accumulation of a unique set of small non-coding RNAs (sncRNAs) derived from both the sugar beet plant and the BNYVV virus during active infection that may have possible regulatory roles in the resistance and/or susceptibility to rhizomania. Examples of target genes that are differentially expressed in the roots and leaves at early and late infection stages in sugar beet by plant-derived microRNAs (miRNAs) include <i>Bevul.9G209500</i> (cytoplasm-related catalytic activity), <i>Bevul.2G095700</i> (potassium transporter) and <i>Bevul.9G160600</i> (zinc finger), which were up-regulated in the R line (vs. S). Viral-derived sncRNAs predominantly originated from RNA1 and RNA2 and targeted a subset of 69 sugar beet genes with overall expression that showed a strong negative correlation with higher sncRNA abundance. The results presented here for the first time demonstrate putative roles of sugar beet miRNAs in rhizomania resistance and BNYVV-derived sncRNAs and small peptides as potential pathogenicity factors.