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Open Access Research article

Identification and characterization of microRNAs in the flag leaf and developing seed of wheat (Triticum aestivum L.)

Ran Han12, Chao Jian12, Jinyang Lv12, Yan Yan12, Qing Chi12, Zhanjie Li12, Qian Wang12, Jin Zhang12, Xiangli Liu12 and Huixian Zhao12*

Author Affiliations

1 State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling 712100, Shaanxi, China

2 College of Life Sciences, Northwest A & F University, Yangling 712100, Shaanxi, China

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BMC Genomics 2014, 15:289  doi:10.1186/1471-2164-15-289

Published: 16 April 2014

Abstract

Background

MicroRNAs (miRNAs) regulate various biological processes in plants. Considerable data are available on miRNAs involved in the development of rice, maize and barley. In contrast, little is known about miRNAs and their functions in the development of wheat. In this study, five small RNA (sRNA) libraries from wheat seedlings, flag leaves, and developing seeds were developed and sequenced to identify miRNAs and understand their functions in wheat development.

Results

Twenty-four known miRNAs belonging to 15 miRNA families were identified from 18 MIRNA loci in wheat in the present study, including 15 miRNAs (9 MIRNA loci) first identified in wheat, 13 miRNA families (16 MIRNA loci) being highly conserved and 2 (2 MIRNA loci) moderately conserved. In addition, fifty-five novel miRNAs were also identified. The potential target genes for 15 known miRNAs and 37 novel miRNAs were predicted using strict criteria, and these target genes are involved in a wide range of biological functions. Four of the 15 known miRNA families and 22 of the 55 novel miRNAs were preferentially expressed in the developing seeds with logarithm (log2) of the fold change of 1.0 ~ 7.6, and half of them were seed-specific, suggesting that they participate in regulating wheat seed development and metabolism. From 5 days post-anthesis to 20 days post-anthesis, miR164 and miR160 increased in abundance in the developing seeds, whereas miR169 decreased, suggesting their coordinating functions in the different developmental stages of wheat seed. Moreover, 8 known miRNA families and 28 novel miRNAs exhibited tissue-biased expression in wheat flag leaves, with the logarithm of the fold changes of 0.1 ~ 5.2. The putative targets of these tissue-preferential miRNAs were involved in various metabolism and biological processes, suggesting complexity of the regulatory networks in different tissues. Our data also suggested that wheat flag leaves have more complicated regulatory networks of miRNAs than developing seeds.

Conclusions

Our work identified and characterised wheat miRNAs, their targets and expression patterns. This study is the first to elucidate the regulatory networks of miRNAs involved in wheat flag leaves and developing seeds, and provided a foundation for future studies on specific functions of these miRNAs.

Keywords:
MicroRNA; Triticum aestivum; Flag leaf; Seed development; Small RNA sequencing; Expression profile; miRNA target