Identification of novel and conserved microRNAs related to drought stress in potato by deep sequencing

Ning Zhang; Jiangwei Yang; Zemin Wang; Yikai Wen; Jie Wang; Wenhui He; Bailin Liu; Huaijun Si; Di Wang

doi:10.1371/journal.pone.0095489

Identification of novel and conserved microRNAs related to drought stress in potato by deep sequencing

PLoS One. 2014 Apr 18;9(4):e95489. doi: 10.1371/journal.pone.0095489. eCollection 2014.

Authors

Ning Zhang¹, Jiangwei Yang², Zemin Wang¹, Yikai Wen³, Jie Wang¹, Wenhui He¹, Bailin Liu², Huaijun Si¹, Di Wang²

Affiliations

¹ Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China.
² Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China.
³ College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China.

Abstract

MicroRNAs (miRNAs) are a group of small, non-coding RNAs that play important roles in plant growth, development and stress response. There have been an increasing number of investigations aimed at discovering miRNAs and analyzing their functions in model plants (such as Arabidopsis thaliana and rice). In this research, we constructed small RNA libraries from both polyethylene glycol (PEG 6,000) treated and control potato samples, and a large number of known and novel miRNAs were identified. Differential expression analysis showed that 100 of the known miRNAs were down-regulated and 99 were up-regulated as a result of PEG stress, while 119 of the novel miRNAs were up-regulated and 151 were down-regulated. Based on target prediction, annotation and expression analysis of the miRNAs and their putative target genes, 4 miRNAs were identified as regulating drought-related genes (miR811, miR814, miR835, miR4398). Their target genes were MYB transcription factor (CV431094), hydroxyproline-rich glycoprotein (TC225721), quaporin (TC223412) and WRKY transcription factor (TC199112), respectively. Relative expression trends of those miRNAs were the same as that predicted by Solexa sequencing and they showed a negative correlation with the expression of the target genes. The results provide molecular evidence for the possible involvement of miRNAs in the process of drought response and/or tolerance in the potato plant.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology
Droughts*
Gene Expression Regulation, Plant
Gene Library
High-Throughput Nucleotide Sequencing
MicroRNAs / genetics*
Molecular Sequence Annotation
Solanum tuberosum / genetics*
Stress, Physiological / genetics*

Substances

MicroRNAs

Grants and funding

This work was sponsored by the Specialized Research Fund for the Doctoral Program of Higher Education of China (No. 20106202120003), the Gansu Key Laboratory of Arid land Crop Science of Gansu Agricultural University (No. GSCS-2010-01), and the Fund for Creative Research Groups of Gansu Province (No. 130RJIA005). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.