Abstract
MicroRNAs (miRNAs) have been shown to play crucial roles in the regulation of plant development. In this study, high-throughput RNA-sequencing technology was used to identify novel miRNAs, and to reveal miRNAs expression patterns at different developmental stages during rice (Oryza sativa L.) grain filling. A total of 434 known miRNAs (380, 402, 390 and 392 at 5, 7, 12 and 17 days after fertilization, respectively.) were obtained from rice grain. The expression profiles of these identified miRNAs were analyzed and the results showed that 161 known miRNAs were differentially expressed during grain development, a high proportion of which were up-regulated from 5 to 7 days after fertilization. In addition, sixty novel miRNAs were identified, and five of these were further validated experimentally. Additional analysis showed that the predicted targets of the differentially expressed miRNAs may participate in signal transduction, carbohydrate and nitrogen metabolism, the response to stimuli and epigenetic regulation. In this study, differences were revealed in the composition and expression profiles of miRNAs among individual developmental stages during the rice grain filling process, and miRNA editing events were also observed, analyzed and validated during this process. The results provide novel insight into the dynamic profiles of miRNAs in developing rice grain and contribute to the understanding of the regulatory roles of miRNAs in grain filling.
Highlights
Rice (Oryza sativa L.) grain filling is a highly coordinated developmental process
Known rice miRNAs accounted for 3.82%, 8.82%, 15.45% and 11.36% of the sequence reads in the 5 days after fertilization (DAF), 7 DAF, 12 DAF and 17 DAF libraries, respectively, indicating that mature miRNAs were relatively enriched in the 12 DAF library
Due to the relatively stable base pairs at its 59 end, miRNA* is usually thought to degrade rapidly when the cognate miRNA is selectively incorporated into effector complexes for target recognition [29], but a recent study in plants has shown that both miRNA and miRNA* can be selected and can silence different targets regardless of their thermodynamic stability [30]
Summary
Rice (Oryza sativa L.) grain filling is a highly coordinated developmental process. During this period, large amounts of storage compounds are synthesized and transported into the rice endosperm, which are major determinants of the economic value of rice grain and provide nutrients and calories for humans and many other animals. Proteomic and cDNA microarray analyses revealed that the products of grain filling-related genes are associated with several important processes, including biosynthesis, metabolism, transportation, the response to stimuli and signal transduction [3,6]. These findings, together with observations of the morphological changes that occur rice grain during the filling process [6,7], suggest that the accumulation of reserves involves multiple metabolic and regulatory pathways, and the expression of the genes in different pathways is coordinately regulated in a timely manner between different developmental stages during grain filling. The genes and underlying molecular mechanisms controlling rice grain filling remain elusive
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