Genome-wide analysis of RNA-interference pathway in Brassica napus, and the expression profile of BnAGOs in response to Sclerotinia sclerotiorum infection

Plants have developed a fine-tuned RNA interference (RNAi) pathway to regulate multitude of cellular processes, including development, stress responses, metabolism and maintenance of genome integrity. Successful activation of the RNAi pathway involves the deployment of Argonaute (AGO) protein, Dicer-like protein (DCL) and RNA-dependent RNA polymerase (RDR). These efficient and indispensable components of the RNAi pathway has not been identifying and characterizing in one of the most important oil crops, Brassica napus, which provides edible oil for human, feeds for livestock and raw materials for bioenergy generation. In this study, 28 BnAGO, eight BnDCL and 13 BnRDR genes were identified in B. napus. We subsequently analyzed their structures, conserved domains and chromosomal localization. Further phylogenetic analyses conducted with Arabidopsis and rice revealed that BnAGO, BnDCL and BnRDR gene families are classified into seven, four and four clades, respectively. They are also associated with gene loss and duplication events, which apparently occur in the course of evolution. More so, the expression level of BnAGO genes in various tissues were also investigated and the result showed that 15 BnAGO genes exhibited much higher expression levels in flowers and siliques than leaves, suggesting that they may play tissue-specific roles in B. napus. Additionally, BnAGO2, BnAGO3 and BnAGO5 were strongly induced in both susceptible and resistant cultivars during infection by the pathogen Sclerotinia sclerotiorum, whereas BnAGO7 was significantly suppressed, suggesting these genes are likely involved in different immune responses. Our results provide useful information for further elucidation of the RNAi machinery in B. napus.