 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 18, 2016 |
| Title |
miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species |
| Organisms |
Oryza glaberrima; Oryza barthii |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Rice was domesticated independently in Asia and Africa, leading to two distinct but closely related crop species, Oryza sativa and Oryza glaberrima, respectively. The two domestications lead to morphological changes, in which a higher branching complexity of the panicles, influencing seed production and crop yield. Although much emphasis was placed on changes in transcriptional regulation during rice domestication and improvement, no large-scale study of small RNA regulation changes during domestication has been reported so far. To analyze whether rice domestication has altered the expression of small RNAs, we performed deep sequencing of small RNA transcriptomes from early developmental stages of panicles from 10 genotypes of the cultivated African species and 10 genotypes of its wild-relative O. barthii. Our study shows a drastic expression change of the 21-nucleotide smallRNA population. A total of 29% of these smallRNAs are overexpressed in panicles of O. barthii vs. O. glaberrima, corresponding mainly to 21-nucleotide phased siRNAs (or phasiRNAs). We also show that these changes are associated with a differential expression of a known regulator of phased siRNAs, miR2118 during early panicle development. Finally, these changes are associated to a heterochronic alteration of phasiRNAs and miR2118 expression pattern, during panicle development with a delayed expression in the domesticated species. Our study suggests a major reshaping of the regulation network from a specific class of small RNA during African rice domestication.
|
| |
|
| Overall design |
Examination of panicle-associated smallRNA populations from Oryza glaberrima and Oryza barthii
|
| |
|
| Contributor(s) |
Jouannic S, Adam H, Vigouroux Y, Ta K, de Mita S, Ghesquière A, Sabot F |
| Citation(s) |
26969003 |
| |
| Submission date |
Jun 26, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephane Jouannic |
| E-mail(s) |
stephane.jouannic@ird.fr
|
| Organization name |
IRD
|
| Department |
UMR DIADE
|
| Street address |
911 Avenue Agropolis BP 64501
|
| City |
Montpellier Cedex 5 |
| ZIP/Postal code |
34394 |
| Country |
France |
| |
|
| Platforms (2) |
| GPL17362 |
Illumina HiSeq 2000 (Oryza glaberrima) |
| GPL17363 |
Illumina HiSeq 2000 (Oryza barthii) |
|
| Samples (2) |
|
| Relations |
| BioProject |
PRJNA209731 |
| SRA |
SRP026352 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE48346_African_rices_smallRNA_21nt.txt.gz |
146.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
