Abstract
The first 24 hours after imbibition (HAI) is pivotal for rice seed germination, during which embryo cells switch from a quiescent state to a metabolically active state rapidly. MicroRNAs (miRNAs) have increasingly been shown to play important roles in rice development. Nevertheless, limited knowledge about miRNA regulation has been obtained in the early stages of rice seed germination. In this study, the small RNAs (sRNAs) from embryos of 0, 12, and 24 HAI rice seeds were sequenced to investigate the composition and expression patterns of miRNAs. The bioinformatics analysis identified 289 miRNA loci, including 59 known and 230 novel miRNAs, and 35 selected miRNAs were confirmed by stem-loop real-time RT-PCR. Expression analysis revealed that the dry and imbibed seeds have unique miRNA expression patterns compared with other tissues, particularly for the dry seeds. Using three methods, Mireap, psRNATarget and degradome analyses, 1197 potential target genes of identified miRNAs involved in various molecular functions were predicted. Among these target genes, 39 had significantly negative correlations with their corresponding miRNAs as inferred from published transcriptome data, and 6 inversely expressed miRNA-target pairs were confirmed by 5ʹ-RACE assay. Our work provides an inventory of miRNA expression profiles and miRNA-target interactions in rice embryos, and lays a foundation for further studies of miRNA-mediated regulation in initial seed germination.
Highlights
Rice is the staple food for over half of the world population, and an ideal plant model for monocot seed germination as it has an annotated genome and a well-developed germination system
Previous study has shown that large-scale rearrangement of transcripts mediated by RNA synthesis and degradation occurs in the first 24 h of rice seed germination [5]
Using an experimental system similar to that utilized in the previous study [5], the miRNA composition and dynamic expression patterns were investigated in the early stages of rice seed germination
Summary
Rice is the staple food for over half of the world population, and an ideal plant model for monocot seed germination as it has an annotated genome and a well-developed germination system. Classical studies have defined seed germination as a sequential process following a triphasic model based on water uptake, namely, rapid water uptake in the first 20 hours after imbibition (HAI) (phase I), lag phase for metabolism reactivation (phase II, 20–48 HAI), and PLOS ONE | DOI:10.1371/journal.pone.0145424. Albeit no significant change has been observed in phenotypes of the 24 HAI seed, the oxygen uptake was found to be enhanced in parallel with seed wet weight increase [3]. During this period, the pro-mitochondria are converted to the typical cristae-rich mitochondrial structures following recovery of the aerobic respiration for seedling establishment [2,4]. The first 24 HAI greatly determines the recovery of metabolism activity in rice seed during the germination progress
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