Identification and Functional Analysis of Flowering Related microRNAs in Common Wild Rice (Oryza rufipogon Griff.)

Abstract

BackgroundMicroRNAs (miRNAs) is a class of non-coding RNAs involved in post- transcriptional control of gene expression, via degradation and/or translational inhibition. Six-hundred sixty-one rice miRNAs are known that are important in plant development. However, flowering-related miRNAs have not been characterized in Oryza rufipogon Griff. It was approved by supervision department of Guangdong wild rice protection. We analyzed flowering-related miRNAs in O. rufipogon using high-throughput sequencing (deep sequencing) to understand the changes that occurred during rice domestication, and to elucidate their functions in flowering.ResultsThree O. rufipogon sRNA libraries, two vegetative stage (CWR-V1 and CWR-V2) and one flowering stage (CWR-F2) were sequenced using Illumina deep sequencing. A total of 20,156,098, 21,531,511 and 20,995,942 high quality sRNA reads were obtained from CWR-V1, CWR-V2 and CWR-F2, respectively, of which 3,448,185, 4,265,048 and 2,833,527 reads matched known miRNAs. We identified 512 known rice miRNAs in 214 miRNA families and predicted 290 new miRNAs. Targeted functional annotation, GO and KEGG pathway analyses predicted that 187 miRNAs regulate expression of flowering-related genes. Differential expression analysis of flowering-related miRNAs showed that: expression of 95 miRNAs varied significantly between the libraries, 66 are flowering-related miRNAs, such as oru-miR97, oru-miR117, oru-miR135, oru-miR137, et al. 17 are early-flowering -related miRNAs, including osa-miR160f, osa-miR164d, osa-miR167d, osa-miR169a, osa-miR172b, oru-miR4, et al., induced during the floral transition. Real-time PCR revealed the same expression patterns as deep sequencing. miRNAs targets were confirmed for cleavage by 5′-RACE in vivo, and were negatively regulated by miRNAs.ConclusionsThis is the first investigation of flowering miRNAs in wild rice. The result indicates that variation in miRNAs occurred during rice domestication and lays a foundation for further study of phase change and flowering in O. rufipogon. Complicated regulatory networks mediated by multiple miRNAs regulate the expression of flowering genes that control the induction of flowering.

Genome-wide changes in microRNA expression during short and prolonged heat stress and recovery in contrasting rice cultivars

“…Similar to other reports of deep sequencing of microRNAs in rice, the expression of conserved miRNA families was significantly higher than that of non-conserved miRNAs (Sunkar et al , 2008; Zhu et al , 2008; Li et al , 2011; Chen et al , 2013). MicroRNA166 was most abundantly present across the 16 rice libraries sequenced in this study.…”

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

“…In fact, the cleaveage sites could be diverse. For instance, the cleavage site in the AK106348 mRNA by osa-miR3981-5p located at 13 th to 14 th [39]; Os09g03610 was cleaved by osa-miR819 at 12 th to 13 th and 16 th to 17 th [23]. Furthermore, osa-miR1848 could regulate OsCYP51G3 transcript, wherea the 5’ RLM-RACE test revealed that OsCYP51G3 mRNA was cleaved downstream of the osa-miR1848/OsCYP51G3 mRNA complementary site [40].…”

“…Moreover, Oryza coarctata grows normally in saline water, and 338 known miRNAs and 95 novel miRNAs were found to respond to salt stress [22]. In 2013, we also identified flowering-related miRNAs in CWR [23]. …”

Identification and Characterization of microRNAs in the Developing Seed of Linseed Flax (Linum usitatissimum L.)

“…Previous studies have confirmed that miRNAs regulate the expression of target genes through target mRNA degradation or translation inhibition [1][2][3]. As an important mechanism of post-transcriptional regulation, miRNAs could regulate genes involved in many developmental processes, such as flowering time, leaf development, auxin signaling and organ polarity [4][5][6][7][8].…”