Identification of Differentially Expressed miRNAs and Target Genes in a Highly Pungent Pepper (Capsicum chinense Jacq.)

MicroRNAs (miRNAs) are a class of small non-coding RNAs, which play a crucial role in regulating genes involved in plant growth, development, and secondary metabolite production. Capsaicinoids are pepper-specific amides responsible for the pungency in peppers, as well as for the different pharmacological activities of peppers. Comparison of the small RNA libraries generated by deep sequencing of RNA from placental tissue samples of a highly pungent chilli cultivar (Capsicum chinense Jacq. cv. ‘Umorok’) and a non-pungent cultivar (C. annuum cv. ‘Bell pepper’) revealed a total of 69 known miRNAs belonging to 28 families differentially expressed in the placenta of the two pepper cultivars. The GO terms of the majority of the differentially expressed miRNAs are “defense response to other organisms”, “regulation of DNA-templated transcription”, “transport”, “protein metabolic process”, and “phosphorylation”. Many of the target proteins identified in this study, including MYB transcription factors, gibberellin response elements, and transcripts involved in the immune response against fungal pathogens might be involved in regulating capsaicinoids biosynthesis. Significant differential expression of miRNAs targeting conserved genes with known role in regulating capsaicinoids biosynthesis, such as miR162, miR168-3p.1.1, miR166a-5p, miR167-5p, miR6027-3p, miR482a-3p, miR482d-3p.1, and miR6024-3p, indicate their potential involvement in regulating capsaicinoids biosynthesis. These findings thus, identified the differentially expressed miRNAs in C. chinense, which may be selected for future studies to explore the miRNA-mediated mechanism of capsaicinoid accumulation.