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.
Highlights
Blueberry is an economically and nutritionally important small fruit crop, and commercially harvested blueberry species include lowbush (Vaccinium angustifolium), highbush (V. corymbosum), and rabbiteye bluberry (V. ashei or V. virgatum)
To identify miRNAs involved in the ripening of blueberry fruits, two small RNA libraries were constructed for sequencing from samples of white (WF) and blue
Blueberries are fleshy berry fruits recognized for various phenolic compounds, especially anthocyanin pigments, which are involved in a wide variety of health benefits. It is totally unknown about the miRNAs and their targets involved in blueberry fruit development and maturation
Summary
Blueberry is an economically and nutritionally important small fruit crop, and commercially harvested blueberry species include lowbush (Vaccinium angustifolium), highbush (V. corymbosum), and rabbiteye bluberry (V. ashei or V. virgatum). The developmental process of blueberry fruit after fruit ripening onset can be conceptually divided into two sequential phases: expansion and maturation. RNA sequencing has become a powerful technology to profile the transcriptome and has provided much valuable information for gene identification and their potential roles during blueberry fruit development and maturation [3,4,5,6]. Emerging evidence has demonstrated that miRNAs play an important role in the regulation of fruit development and maturation. A combinatorial analysis of miRNAome and degradome sequencing was conducted to identify and characterize the miRNAs and their targets that act during blueberry fruit maturation, a key developmental phase for fruit quality and biosynthesis of anthocyanin. The findings provide new insights into understanding the regulatory network that controls fruit ripening in blueberry
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