In an attempt to identify novel and apoptosis/pathogen-regulated microRNAs (miRNAs) and small interfering RNAs, we performed a robust microarray screening of small RNA population from Vitis vinifera L. cv. Limberger cell suspension exposed to apoptosis activators (e.g. methyl jasmonate) or elicitors (botrycin and cinerein) derived from necrotrophic fungus Botrytis cinerea Pers. et Fries. Using a microarray expression profiling approach, we identified 22 miRNAs. We found that a majority of these miRNAs were predicted to target stress/defense-related genes of plants. Of the 22 V. vinifera miRNAs, 11 have sequence conservation in Arabidopsis thaliana but exhibited species-specific developmental and/or stress/defense-related expression patterns. Ten of the miRNAs are highly conserved in other plant species, suggesting that even conserved miRNAs may have different regulatory roles in various species. Our results show that these grapevine miRNAs can be also induced by various apoptosis inducers. Fifty-one potential targets were predicted to the newly identified miRNAs based on sequence complementarity. In addition to miRNAs, we identified 102 other novel endogenous small RNAs in Vitis, indicating that a large number of miRNAs and other small regulatory RNAs are encoded by the Vitis vinifera genome.
