Abstract

BackgroundA long juvenile period between germination and flowering is a common characteristic among fruit trees, including Malus hupehensis (Pamp.) Rehd., which is an apple rootstock widely used in China. microRNAs (miRNAs) play an important role in the regulation of phase transition and reproductive growth processes.ResultsM. hupehensis RNA libraries, one adult and one juvenile phase, were constructed using tree leaves and underwent high-throughput sequencing. We identified 42 known miRNA families and 172 novel miRNAs. We also identified 127 targets for 25 known miRNA families and 168 targets for 35 unique novel miRNAs using degradome sequencing. The identified miRNA targets were categorized into 58 biological processes, and the 123 targets of known miRNAs were associated with phase transition processes. The KEGG analysis revealed that these targets were involved in starch and sucrose metabolism, and plant hormone signal transduction. Expression profiling of miRNAs and their targets indicated multiple regulatory functions in the phase transition. The higher expression level of mdm-miR156 and lower expression level of mdm-miR172 in the juvenile phase leaves implied that these two small miRNAs regulated the phase transition. mdm-miR160 and miRNA393, which regulate genes involved in auxin signal transduction, could also be involved in controlling this process. The identification of known and novel miRNAs and their targets provides new information on this regulatory process in M. hupehensis, which will contribute to the understanding of miRNA functions during growth, phase transition and reproduction in woody fruit trees.ConclusionsThe combination of sRNA and degradome sequencing can be used to better illustrate the profiling of hormone-regulated miRNAs and miRNA targets involving complex regulatory networks, which will contribute to the understanding of miRNA functions during growth, phase transition and reproductive growth in perennial woody fruit trees.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1125) contains supplementary material, which is available to authorized users.

Highlights

  • A long juvenile period between germination and flowering is a common characteristic among fruit trees, including Malus hupehensis (Pamp.) Rehd., which is an apple rootstock widely used in China. microRNAs play an important role in the regulation of phase transition and reproductive growth processes

  • Our results showed that leaves in the juvenile phase were much smaller and had higher miRNA156 expression levels and lower SQUAMOSA promoter binding protein (SBP), SPL2 and SPL9 expression levels compared with adult leaves, implying that miRNA156 and its targets may play important roles in the juvenile to adult transition, leaf development and the transition to flowering

  • Our results showed that the AUX content and the expression of the targets (ARF16, ARF17, TIR1, AFB2 and AFB3) of miRNA160 and miRNA393 were significantly higher in A leaves than in J leaves (Figure 7C and D), indicating an important contribution of hormone-mediated responses to leaf maturation, reproductive growth and the flowering transition

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Summary

Introduction

A long juvenile period between germination and flowering is a common characteristic among fruit trees, including Malus hupehensis (Pamp.) Rehd., which is an apple rootstock widely used in China. microRNAs (miRNAs) play an important role in the regulation of phase transition and reproductive growth processes. Studies of the mechanisms involved in juvenile development and the juvenile to adult phase transition are vital for shortening the juvenile phase and accelerating the breeding of economically beneficial traits in woody plants, Many species have long juvenile vegetative phases. This may be associated with the biological processes involved in hormone synthesis and metabolism, carbohydrate synthesis and metabolism, and photosynthesis [1,6]. Other genes, including the MADS-box family of transcription factor (TF) genes in citrus, are involved in the juvenile to adult transition [11]. These control mechanisms represent a preliminary understanding of the molecular base of the transition from juvenile to adult phase in plants

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