Genome-wide identification and expression analyses of the Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in onion (Allium cepa L.)

Abstract

ABSTRACT RNA silencing is a highly conserved gene expression regulatory mechanism participating in plant development and stress responses. Dicer-like protein (DCL), Argonaute protein (AGO) and RNA-dependent RNA polymerase (RDR) are directly involved in RNA silencing. So far, the characterisation and expression analysis of RDR, AGO and DCL proteins have not been performed in onion. A genome-wide analysis identified eight AcAGO, four AcDCL and four AcRDR putative genes in onion. Their cis-acting elements were investigated. The transcript levels of genes in different onion tissues and response to abiotic stress were studied. The results demonstrated that AcAGOs, AcDCLs and AcRDRs showed various tissue expression patterns. AcAGO2 and AcAGO4b were highly expressed in onion bulbs. AcDCLs and AcRDRs showed the highest transcript levels in inflorescence. AcAGO1, AcAGO5 and AcDCL1 were constitutively expressed in leaf and bulb during onion bulb expansion. AcRDR1 and AcRDR6 were upregulated during bulb expansion. AcAGOs were upregulated with salinity treatment, whereas AcDCLs and AcRDRs showed different expression patterns in abiotic stress response. Our results provided a basis for further clarification of RNA silencing-mediated environment stimulation response and development in onion.