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| Status |
Public on Oct 22, 2014 |
| Title |
Identification of miRNAs and their target genes in developing maize ears by deep sequencing |
| Organism |
Zea mays |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
In plants, MicroRNAs (miRNAs) are a new class of endogenous small RNAs that play essential regulatory roles in plant growth, development and stress response. Extensive studies of miRNAs have been performed in model plants such as rice, Arabidopsis thaliana and other plants. However, the number of miRNAs discovered in maize is relatively low and little is known about miRNAs involved in the four stages during maize ear development. Here, we use deep-sequencing, miRNA microarray assays and computational methods to identify, profile, and describe conserved and non-conserved miRNAs at four developmental stages. A total of 27 conserved miRNA families were identified in all four stages, In addition to known miRNAs, we also found 23 new maize-specific miRNAs together with their star strands. We have also shown that almost all of them originated from single genes. We have found that many known and new miRNAs showed temporally expression. Finally, a total of 251 transcripts (140 genes) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs.This study led to the confirmation of the authenticity of 27 conserved miRNA families and the discovery of 23 novel miRNAs in maize. In addition, we have identified 130 targets of known and new miRNAs and ta-siRNA using recently developed tools for the global identification of miRNA targets. Identification and characterization of this important class of regulatory genes in maize may improve our understanding of molecular mechanism controlling flower development.
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| Overall design |
The seeds of maize inbred line B73 were first sterilized and germinated in an incubator, then grown in a controlled environment with 28°C/21°C (day/night) under a 16-h day/8-h night photoperiod with a relative humidity of 70%. Ear development can be divided into four stages: the growth point elongation phase, spikelet differentiation phase, the floret primordium differentiation phase and floret organ differentiation phase. Plant materials (ears) were collected as described previously. In brief, ears were manually collected at the four developmental stages according to the plant features (number of visible leaves, leaf age index, and number of unfolded and folded leaves) combined with microscopic observation.
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| Contributor(s) |
Liu H, Qin C, Chen Z, Zhou H, Xu M, Shen Y, Liu H, He X, Zhang Y, Li L, Ding H, Lubberstedt T, Zhang Z, Pan G |
| Citation(s) |
24422852 |
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| Submission date |
Jun 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
hongjun liu |
| E-mail(s) |
lhj20305@163.com
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| Organization name |
Sichuan Agricultural University
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| Street address |
211 Huimin Road
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| City |
Wenjiang,Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
611130 |
| Country |
China |
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| Platforms (1) |
| GPL9361 |
Illumina Genome Analyzer II (Zea mays) |
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| Samples (5)
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| Relations |
| BioProject |
PRJNA208063 |
| SRA |
SRP025172 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE47837_RAW.tar |
96.4 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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