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Open Access Research article

Grapevine microRNAs responsive to exogenous gibberellin

Jian Han1, Jinggui Fang1*, Chen Wang1*, Yanlei Yin2, Xin Sun1, Xiangpeng Leng1 and Changnian Song1

Author Affiliations

1 College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China

2 Institute of Pomology, Taian 210038, Shandong, China

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BMC Genomics 2014, 15:111  doi:10.1186/1471-2164-15-111

Published: 8 February 2014

Abstract

Background

MicroRNAs (miRNAs), involving in various biological and metabolic processes, have been discovered and analyzed in quite a number of plants species, such as Arabidopsis, rice and other plants. However, there have been few reports about grapevine miRNAs in response to gibberelline (GA3).

Results

Solexa technology was used to sequence small RNA libraries constructed from grapevine berries treated with GA3 and the control. A total of 122 known and 90 novel grapevine miRNAs (Vvi-miRNAs) were identified. Totally, 137 ones were found to be clearly responsive to GA3, among which 58 were down-regulated, 51 were up-regulated, 21 could only be detected in the control, and seven were only detected in the treatment. Subsequently, we found that 28 of them were differentially regulated by GA3, with 12 conserved and 16 novel Vvi-miRNAs, based on the analysis of qRT-PCR essays. There existed some consistency in expression levels of GA3-responsive Vvi-miRNAs between high throughput sequencing and qRT-PCR essays. In addition, 117 target genes for 29 novel miRNAs were predicted.

Conclusions

Deep sequencing of short RNAs from grapevine berries treated with GA3 and the control identified 137 GA3-responsive miRNAs, among which 28 exhibited different expression profiles of response to GA3 in the diverse developmental stages of grapevine berries. These identified Vvi-miRNAs might be involved in the grapevine berry development and response to environmental stresses.

Keywords:
Grapevine; Berry; microRNAs; Exogenous gibberellin; High throughput sequencing