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Int. J. Mol. Sci. 2017, 18(12), 2767; https://doi.org/10.3390/ijms18122767

Comparative Analysis of Fruit Ripening-Related miRNAs and Their Targets in Blueberry Using Small RNA and Degradome Sequencing

1
College of Plant Science, Jilin University, Changchun 130062, China
2
College of Life Sciences, Jilin University, Changchun 130012, China
3
Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON N5V 4T3, Canada
These authors contributed equally to the work.
*
Author to whom correspondence should be addressed.
Received: 20 November 2017 / Revised: 11 December 2017 / Accepted: 18 December 2017 / Published: 19 December 2017
(This article belongs to the Section Molecular Plant Sciences)
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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. View Full-Text
Keywords: blueberry; fruit ripening; miRNA; sRNA sequencing; targets; degradome sequencing blueberry; fruit ripening; miRNA; sRNA sequencing; targets; degradome sequencing
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Hou, Y.; Zhai, L.; Li, X.; Xue, Y.; Wang, J.; Yang, P.; Cao, C.; Li, H.; Cui, Y.; Bian, S. Comparative Analysis of Fruit Ripening-Related miRNAs and Their Targets in Blueberry Using Small RNA and Degradome Sequencing. Int. J. Mol. Sci. 2017, 18, 2767.

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