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

Abstract

BackgroundDrought 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.ResultsIn 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.ConclusionOur 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.

Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources

“…It is also known to interact with MADS-box transcription factors, which is associated with stress response 79 . Besides, miR444 responded to drought stress in Dongxiang wild rice 80 . miR169d plays role in fighting drought stress in cotton 81 as well as sorghum 82 .…”

Differential Expression of Maize and Teosinte microRNAs under Submergence, Drought, and Alternated Stress

“…The growth and development processes are driven by hormonal signaling pathways that are fundamental in the response to submergence and drought in plants [ 41 ], where transcription factors and miRNAs participate. Several differentially expressed miRNAs identified in this work are known to act over target genes encoding transcription factors such as miR156 (squamosa promoter-binding protein like, SPL) [ 42 , 43 , 44 ], miR159 (giberellic acid-MYB transcription factor, GAMYB [ 28 , 29 ]), miR164 (NAM-ATAF-CUC domain transcription factor NAC, MYB [ 45 ]), miR166 (basic leucine zipper transcription factor, HD-ZIP III [ 46 , 47 ]), miR167 (auxin-responsive factor, ARF [ 30 , 35 , 48 ]), miR169 (nuclear transcription factor Y subunit alpha, NFYA [ 49 , 50 , 51 , 52 ]), miR319 (teosinte branched1/cycloidea/proliferating cell nuclear antigen factor, TCP [ 53 ]), and miR396 (growth-regulating factor, GRF [ 54 , 55 ]). Other target genes predicted in this study are listed in Table S6 .…”

Transcription Factors and microRNA Genes Regulatory Network Construction Under Drought Stress in Sesame (Sesamum indicum L.)

“…miR171 family was identified as drought-responsive microRNAs which regulate plant response during the stress [105,106,107]. miR529 also has been shown that involved in drought stress responses [105,107,108]. The relation of miR169 and miR395 with drought responses have been previously discussed.…”