|
| Status |
Public on Mar 08, 2018 |
| Title |
A Domestication-Selected Retrotransposon for Quenching Genomic Immunity in Rice [small RNA-Seq] |
| Organism |
Oryza sativa |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Transposable elements (TEs) are genomic parasites that constitute the most abundant portions of higher plant genomes. However, whether TE selection occurred during crop domestication remains unknown. HUO is active under normal growth conditions, present at low copy numbers, inserts preferentially into regions capable of transcription, but absent in almost all modern varieties, indicating its removal during rice domestication and modern rice breeding. HUO triggers genomic immunity and dramatically alters genome-wide methylation levels and small RNA biogenesis, as well as global gene expression. Its presence specifically affects agronomic traits by decreasing yield performance and disease resistance but enhancing salt tolerance, which mechanistically explains its domestication removal. Thus, our study reveals a unique retrotransposon as a negative target for maintaining genetic and epigenetic stability during crop domestication and selection.
|
| |
|
| Overall design |
The small RNA profiles of two-weeks seedling of WT line 308D and the HUO restrotransposon insertion lines 307T1 (1 copy) and 307T3 (3 copy) were generated by deep sequence dependent on illumina Hiseq2000.
|
| |
|
| Contributor(s) |
Deng Y, Zhang Y, Peng Y, Li Q, He Z |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Mar 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
yiwen Deng |
| E-mail(s) |
ywdeng@sibs.ac.cn
|
| Phone |
86-21-54924128
|
| Organization name |
Shanghai Institute for Biological Sciences, Chinese Academy of Sciences
|
| Department |
Institute of Plant Physiology and Ecology
|
| Lab |
zuhua He
|
| Street address |
300 Fenglin Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platforms (1) |
| GPL13160 |
Illumina HiSeq 2000 (Oryza sativa) |
|
| Samples (3) |
| GSM2080684 |
two-weeks seedling plants_308D_smallRNAseq |
| GSM2080685 |
two-weeks seedling plants_307T1_smallRNAseq |
| GSM2080686 |
two-weeks seedling plants_307T3_smallRNAseq |
|
| This SubSeries is part of SuperSeries: |
| GSE78903 |
A Domestication-Selected Retrotransposon for Quenching Genomic Immunity in Rice |
|
| Relations |
| BioProject |
PRJNA314332 |
| SRA |
SRP071147 |
