Comparative analysis of fruit ripening-related miRNAs and their targets in blueberry using small RNA and degradome sequencing

Citation

Hou, Y., Zhai, L., Li, X., Xue, Y., Wang, J., Yang, P., Cao, C., Li, H., Cui, Y., Bian, S. (2017). Comparative analysis of fruit ripening-related miRNAs and their targets in blueberry using small RNA and degradome sequencing. International Journal of Molecular Sciences, [online] 18(12), http://dx.doi.org/10.3390/ijms18122767

Plain language summary

MicroRNAs (miRNAs) are unique cellular RNAs which supress gene expression and ultimately halt protein production in cells of plants, animals and some viruses. miRNAs play vital roles in the regulation of fruit development and ripening. This study focussed on blueberry, a small berry fruit crop with economical and nutritional value. At the present time, not much is known about the miRNAs and their targets involved in blueberry fruit ripening. In this study we examined several families of miRNAs belonging to white as well as blue fruits. It was found that during fruit maturation, many miRNAs are shown to be differentially expressed such that the biochemical processes are determined by which genes are active and which proteins are made, in a cell, as a response to certain signals or triggers. These findings will certainly facilitate future investigations of the miRNA-mediated mechanisms that regulate fruit development and ripening in blueberry.

Abstract

MicroRNAs (miRNAs) play vital roles in the regulation of fruit development and ripening. Blueberry is an important small berry fruit crop with economical and nutritional value. However, nothing is known about the miRNAs and their targets involved in blueberry fruit ripening. In this study, using high-throughput sequencing of small RNAs, 84 known miRNAs belonging to 28 families and 16 novel miRNAs were identified in white fruit (WF) and blue fruit (BF) libraries, which represent fruit ripening onset and in progress, respectively. Among them, 41 miRNAs were shown to be differentially expressed during fruit maturation, and 16 miRNAs representing 16 families were further chosen to validate the sRNA sequencing data by stem-loop qRT-PCR. Meanwhile, 178 targets were identified for 41 known and 7 novel miRNAs in WF and BF libraries using degradome sequencing, and targets of miR160 were validated using RLM-RACE (RNA Ligase-Mediated (RLM)-Rapid Amplification of cDNA Ends) approach. Moreover, the expression patterns of 6 miRNAs and their targets were examined during fruit development and ripening. Finally, integrative analysis of miRNAs and their targets revealed a complex miRNA-mRNA regulatory network involving a wide variety of biological processes. The findings will facilitate future investigations of the miRNA-mediated mechanisms that regulate fruit development and ripening in blueberry.

Publication date

2017-12-19

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