Characterization of miRNA-mediated auxin signaling during banana (Musa spp.) fruit ripening

Auxin signaling is essential for the whole plant life cycle and the core components of auxin signaling include the auxin receptor TIR/AFB, corepressor Aux/IAA, and transcription factor ARF. They jointly modulate a variety of biological processes through regulating the expression of auxin-responsive genes. In the past decades, microRNAs (miRNAs) have been well documented as vital regulators of gene expression. A group of miRNA families have been found to target genes associated with auxin signal transduction, such as TIR/AFBs and ARFs. Banana is a typical climacteric fruit that undergo dramatic physiological and biochemical changes during ripening process. However, the role of auxin itself and miRNAs in auxin signaling during fruit ripening remain largely unknown in banana. In this study, we comprehensively characterized three key gene families of auxin signaling pathways in banana. There are 15 TIR/AFB, 50 Aux/IAA, and 49 ARF genes in the banana genome. Also, we identified multiple miRNAs that can target members of auxin-related gene families, and the targeting relationship and inhibitory effect of miR393, miR160 and miR167 on specific TIR/AFB and ARF family members were further experimentally validated. In addition, the expression analysis of banana pulp after ethylene treatment revealed the specific response of these auxin-related miRNAs to ethylene. Finally, a mode of action of miRNA-mediated auxin signaling in ethylene-induced banana fruit ripening was proposed. Our results not only unraveled the regulation of miRNA on banana auxin response, but also provided a reference for the study of miRNA-mediated auxin signaling in the ripening of climacteric fruit.