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| Status |
Public on Sep 23, 2016 |
| Title |
A Widespread Impact on Small RNAs and Gene Networks in Rice msp1/ostdl1a Mutants, Partners with Key Roles in Anther Development |
| Organism |
Oryza sativa |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Dissection of the genetic pathways and mechanisms by which anther development occurs in grasses is crucial for both a basic understanding of plant development and for traits of agronomic importance like male sterility. In rice, MULTIPLE SPOROCYTES1 (MSP1), a leucine-rich-repeat receptor kinase, play an important role in anther development by limiting the number of sporocytes. OsTDL1a (a TPD1-like gene in rice) encodes a small protein which acts as a cofactor of MSP1 in the same regulatory pathway. In this study, we analyzed small RNA and mRNA changes in different stages of spikelets from wildtype rice, and from msp1 and ostdl1a mutants. Analysis across different stages of rice spikelets of the small RNA data identified miRNAs demonstrating differential abundances. miR2275 was depleted in the two rice mutants; this miRNA is specifically enriched in anthers and functions to trigger the production of 24-nt phased secondary siRNAs (phasiRNAs) from PHAS loci. We observed that the 24-nt phasiRNAs as well as their precursor PHAS mRNAs were also depleted in the two mutants. Based on comparisons of transcript levels across the spikelet stages and mutants, we identified 22 transcription factors as candidates to have roles specific to anther development, potentially acting downstream of the OsTDL1a-MSP1 pathway. An analysis of co-expression identified three Argonaute-encoding genes (OsAGO1d, OsAGO2b, and OsAGO18) that accumulate transcripts coordinately with phasiRNAs, suggesting a functional relationship. By mRNA in situ analysis, we demonstrated a strong correlation between the spatiotemporal pattern of accumulation of these OsAGO transcripts with previously-published phasiRNA accumulation patterns from maize.
Raw files for smallRNA-Seq were not provided by submitter.
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| Overall design |
Genome-wide small RNA and mRNA profiling was done by Illumina TruSeq sample preparation followed by high-throughput sequencing with the Illumina HiSeq 2000 platform.
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| Contributor(s) |
Meyers BC, Fei Q, Yang L, Liang W, Zhang D |
| Citation(s) |
27702997 |
| |
| Submission date |
Jan 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Blake C. Meyers |
| E-mail(s) |
bmeyers@danforthcenter.org
|
| Phone |
314-587-1422
|
| Organization name |
Donald Danforth Plant Science Center
|
| Lab |
Meyers lab
|
| Street address |
975 N Warson Road
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL13160 |
Illumina HiSeq 2000 (Oryza sativa) |
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| Samples (54)
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| Relations |
| BioProject |
PRJNA309991 |
| SRA |
SRP068966 |
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