The integrative expression and co-expression analysis of the AGO gene family in rice.

Argonautes (AGOs) play crucial roles in RNAi and related pathways in several species and regulate plant growth and development. However the investigation in rice argonautes (OsAGOs) remains elusive. Here we focused on the expression pattern and co-expression profiles of OsAGO genes. Microarray-based and qRT-PCR expression profiling of 19 OsAGO genes indicated that most OsAGOs expressed specifically and preferentially during stages of reproductive development, and exhibited preferential up-regulation in panicle stages. Six OsAGO genes showed specific up/down-regulation in response to Gibberellin A3 (GA3), Kinetin (KT), or 1-Naphthaleneacetic acid (NAA) treatments. And three OsAGOs presented specific up-regulation in response to light and dark treatments. Ten OsAGOs were co-expressed with Dicer-like (DCL), Double-stranded RNA Binding (DRB) and RNA-dependent RNA polymerase (RDR) genes, which were related with RNA processing including RNAi pathways. Twelve OsAGOs were correlated with 17 kinds of transcription factors involving diverse functions. Four OsAGOs RNAi plants were constructed, the expression level of co-expression genes, including DCL3, DRB2, RDR4 etc., were changed while OsAGOs were down-regulated in RNAi lines, providing experimental evidence for co-expression networks. The results provide new insights in understanding the biological pathways of OsAGO genes, as well as in selecting the candidate genes involved in RNA silencing mechanisms.