Research Article: Identification of microRNAs in Response to Drought in Common Wild Rice (Oryza rufipogon Griff.) Shoots and Roots

Date Published: January 20, 2017

Publisher: Public Library of Science

Author(s): Jing-wen Zhang, Yan Long, Man-de Xue, Xing-guo Xiao, Xin-wu Pei, Yun Zheng.

http://doi.org/10.1371/journal.pone.0170330

Abstract

Drought is the most important factor that limits rice production in drought-prone environments. Plant microRNAs (miRNAs) are involved in biotic and abiotic stress responses. Common wild rice (Oryza rufipogon Griff.) contains abundant drought-resistant genes, which provide an opportunity to explore these excellent resources as contributors to improve rice resistance, productivity, and quality.

In this study, we constructed four small RNA libraries, called CL and CR from PEG6000-free samples and DL and DR from PEG6000-treated samples, where ‘R’ indicates the root tissue and ‘L’ indicates the shoot tissue. A total of 200 miRNAs were identified to be differentially expressed under the drought-treated conditions (16% PEG6000 for 24 h), and the changes in the miRNA expression profile of the shoot were distinct from those of the root. At the miRNA level, 77 known miRNAs, which belong to 23 families, including 40 up-regulated and 37 down-regulated in the shoot, and 85 known miRNAs in 46 families, including 65 up-regulated and 20 down-regulated in the root, were identified as differentially expressed. In addition, we predicted 26 new miRNA candidates from the shoot and 43 from the root that were differentially expressed during the drought stress. The quantitative real-time PCR analysis results were consistent with high-throughput sequencing data. Moreover, 88 miRNAs that were differentially-expressed were predicted to match with 197 targets for drought-stress.

Our results suggest that the miRNAs of O. rufipogon are responsive to drought stress. The differentially expressed miRNAs that are tissue-specific under drought conditions could play different roles in the regulation of the auxin pathway, the flowering pathway, the drought pathway, and lateral root formation. Thus, the present study provides an account of tissue-specific miRNAs that are involved in the drought adaption of O. rufipogon.

Partial Text

To respond to changes in the environment, plants have developed remarkable capabilities to adapt to extreme environments, such as high temperature, drought, and salt stress [1]. Abiotic stress is an important factor that limits plants geographic distribution and yield. Therefore, one central goal is the improvement of stress tolerance in crops.

Four libraries were constructed and sequenced for shoot and root tissues from 3-week-old common wild rice seedlings that were exposed to solutions with and without 16% PEG6000 for 24h. In total, 77 known miRNAs that belong to 23 families, including 40 up-regulated and 37 down-regulated in the shoot (Fig 2A; S2 File), and 85 known miRNAs that belong to 46 families, including 65 up-regulated and 20 down-regulated in the root (Fig 2A; S3 File), were identified as differentially expressed. In addition, we predicted 26 new miRNA candidates from the shoot and 43 from the root that were differentially expressed during drought stress.

 

Source:

http://doi.org/10.1371/journal.pone.0170330