Abstract
BackgroundDeveloping drought-tolerant rice varieties with higher yield under water stressed conditions provides a viable solution to serious yield-reduction impact of drought. Understanding the molecular regulation of this polygenic trait is crucial for the eventual success of rice molecular breeding programmes. microRNAs have received tremendous attention recently due to its importance in negative regulation. In plants, apart from regulating developmental and physiological processes, microRNAs have also been associated with different biotic and abiotic stresses. Hence here we chose to analyze the differential expression profiles of microRNAs in three drought treated rice varieties: Vandana (drought-tolerant), Aday Sel (drought-tolerant) and IR64 (drought-susceptible) in greenhouse conditions via high-throughput sequencing.ResultsTwenty-six novel microRNA candidates involved in the regulation of diverse biological processes were identified based on the detection of miRNA*. Out of their 110 predicted targets, we confirmed 16 targets from 5 novel microRNA candidates. In the differential expression analysis, mature microRNA members from 49 families of known Oryza sativa microRNA were differentially expressed in leaf and stem respectively with over 28 families having at least a similar mature microRNA member commonly found to be differentially expressed between both tissues. Via the sequence profiling data of leaf samples, we identified osa-miR397a/b, osa-miR398b, osa-miR408-5p and osa-miR528-5p as being down-regulated in two drought-tolerant rice varieties and up-regulated in the drought-susceptible variety. These microRNAs are known to be involved in regulating starch metabolism, antioxidant defence, respiration and photosynthesis. A wide range of biological processes were found to be regulated by the target genes of all the identified differentially expressed microRNAs between both tissues, namely root development (5.3–5.7 %), cell transport (13.2–18.4 %), response to stress (10.5–11.3 %), lignin catabolic process (3.8–5.3 %), metabolic processes (32.1–39.5 %), oxidation-reduction process (9.4–13.2 %) and DNA replication (5.7–7.9 %). The predicted target genes of osa-miR166e-3p, osa-miR166h-5p*, osa-miR169r-3p* and osa-miR397a/b were found to be annotated to several of the aforementioned biological processes.ConclusionsThe experimental design of this study, which features rice varieties with different drought tolerance and tissue specificity (leaf and stem), has provided new microRNA profiling information. The potentially regulatory importance of the microRNA genes mentioned above and their target genes would require further functional analyses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1851-3) contains supplementary material, which is available to authorized users.
Highlights
Developing drought-tolerant rice varieties with higher yield under water stressed conditions provides a viable solution to serious yield-reduction impact of drought
Overview of sequence pre-processing, length distributions and database mapping Leaf and stem tissues were harvested at the vegetative stage of three rice varieties with different drought tolerance levels grown under control and drought stress conditions for the construction and sequencing of 12 small RNA libraries
Post pre-processing of the raw reads, an average of 16847232, 15403441 and 18622662 clean reads were retrieved for Vandana, Aday Sel and IR64 small RNA libraries respectively (Additional file 2)
Summary
Developing drought-tolerant rice varieties with higher yield under water stressed conditions provides a viable solution to serious yield-reduction impact of drought. Most of the rice varieties presently cultivated in rainfed areas are developed for irrigated conditions. These varieties are highly popular among farmers because of their high yield potential and good grain quality but are highly susceptible to drought, causing substantial yield losses during years of drought [1]. Due to the increasing threat from water shortage and drought in many rice-growing areas of Asia, the rainfed areas, the development of drought-tolerant varieties with increased yield under drought is a priority area of rice research for sustainable rice production [3]. To ensure the success of these breeding programmes, understanding the molecular regulation of this polygenic trait in rice is crucial
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