Identification of Arabidopsis thaliana small RNAs responsive to the fungal pathogen Botrytis cinerea at an early stage of interaction

Small RNAs are widely involved in the regulation of gene expression in eukaryotes. In plants, small RNAs (sRNAs) have been described as key components in the regulation of plant growth, development and stress responses, including abiotic and biotic stresses. Here, we showed that different types of small RNAs were differentially expressed in Arabidopsis thaliana at an early stage of its interaction with Botrytis cinerea, a necrotrophic fungal pathogen that causes the gray mold disease. In this study, we found mainly conserved microRNAs and other classes of sRNAs such as heterochromatic siRNAs and secondary siRNAs with high abundance and response to B. cinerea. In particular, the upregulated microRNAs (miR167, miR159 and miR319) and the regulation of their target transcripts may be involved in the fine-turning of plant hormones during B. cinerea infection. We also found that miR173, which triggers the production of secondary siRNAs from TAS1 and TAS2 genes, was upregulated and we found the secondary siRNAs upregulation of some TAS1c and TAS2 transcripts during B. cinerea infection. Furthermore, GO analysis revealed that target genes were involved in different biological processes. Interestingly, transcripts of small RNA-related enzymes and a subset of the PPR gene superfamily mediated by sRNAs regulation may be important for an appropriate immune response to B. cinerea at an early stage of infection. A better understanding of the mechanisms that operate during B. cinerea-plant interaction is key to developing more effective strategies for its control.