Identification and functional analysis of flowering related microRNAs in common wild rice (Oryza rufipogon Griff.)

• Published in: PloS one Vol. 8; no. 12; p. e82844
• Main Authors: Chen, Zongxiang, Li, Fuli, Yang, Songnan, Dong, Yibo, Yuan, Qianhua, Wang, Feng, Li, Weimin, Jiang, Ying, Jia, Shirong, Pei, Xinwu
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 30.12.2013; Public Library of Science (PLoS)
• Subjects: Agriculture; Analysis; Annotations; Arabidopsis; Base Sequence; Biology; Biotechnology; Cloning; Cloning, Molecular; DNA methylation; Domestication; Flowering; Flowers & plants; Flowers - genetics; Flowers - growth & development; Functional analysis; Gene expression; Gene Library; Genes; Genetic aspects; Genomics; MicroRNA; MicroRNAs; MicroRNAs - chemistry; MicroRNAs - genetics; MicroRNAs - physiology; miRNA; Molecular Sequence Data; Next-generation sequencing; Nucleic Acid Conformation; Oryza; Oryza - genetics; Oryza - growth & development; Oryza rufipogon; Phase transitions; Plant Development - genetics; Proteins; Ribonucleic acid; Rice; RNA; RNA polymerase; RNA, Plant - chemistry; RNA, Plant - genetics; RNA, Plant - physiology; Transcription; Transcription (Genetics); Transcription factors; Beijing China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0082844

MicroRNAs (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. Three 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. This 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.