|
| Status |
Public on May 02, 2022 |
| Title |
Rice root response atlas |
| Organism |
Oryza sativa Japonica Group |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Rice has evolved regulatory programs and specialized cell types that allow the plant to withstand different environments. To understand how rice root systems cope with water stresses, we profiled translatomes (ribosome-associated mRNAs) and accessible chromatin of developmentally-defined root cell populations from well-watered and drained control (aerobic control), water deficit, waterlogged, fully submerged plants and recovery conditions. Whereas, the waterlogging responses are limited to specific root domains, water deficit and submergence signatures are extensive, and mostly reversible after 1 day of recovery, relative to control roots. Root systems were also evaluated in rice cultivated in a paddy field. Specific responses include a halt in the cell-cycle and DNA synthesis-related genes translation in meristematic tissue under submergence and exo/endodermis suberin-related pathways bolstering under water deficit. Chromatin accessibility and translatome data integration was used to generate inferred regulatory networks that are dynamically regulated by changing water availability. The data collection is further enriched by translatome and chromatin accessibility data for the root systems of plate-grown seedlings (7 day old) and those cultivated in a paddy field (49 day old). An atlas of eight cell population translatomes for field-grown plants exhibited robust cell type expression. Collectively, these data for specific cell populations at multiple developmental ages and in multiple environments including growth two limiting water stresses will serve as a community resource.
|
| |
|
| Overall design |
Evaluation of root domains TRAP seq and ATAC-seq profiles in rice roots in different environments and water stresses. Greenhouse pot-based translating ribosome affinity purification and chromatin experiments were conducted in five independent replicates of each line, with T1 or T2 seed stocks and whole root tissue was quickly dissected and frozen in liquid nitrogen. All tissue collection and TRAP and INTACT-ATAC library processing was performed with three biological replicates. Complete root systems were harvested. Nine conditions were assessed. Plate: plants grown from seed on petri dishes with 1X MS, 1 % [w/v] Sucrose, pH 5.8. Plate-based TRAP experiments were conducted with three or four independent replicates. Greenhouse grown plants were cultivated in GreenGrades Profile with seven treatments. (1) Control: controlled well-watered and drained irrigation growth. (2) Water Deficit: 5-6 days of no watering, with a fall to 72% (v/v) relative water content. (3) Waterlogging: 5 days of standing water covering root systems. (4) Submergence: 5 days of complete plant submergence. (5) Water Deficit Recovery: water deficit followed by a 1 day irrigation. (6) Waterlogging Recovery: pots allowed to fully drain for 1 day. (7) Submergence Recovery: plants returned to the bench and pots allowed to drain for 1 day. Field: Seedlings grown in the greenhouse transplanted to a paddy field at age 14 days; tissue collected after 35 days. This was performed with six randomized independent replicates of each line. For greenhouse and field sampling, 3 bioreplicates of up to 2 RNA pools (total mRNA, TRAP-RNA for different root domains) and ATAC-seq.
|
| |
|
| Contributor(s) |
Pauluzzi GC, Reynoso MA, Bailey-Serres J |
| Citation(s) |
35504287 |
| Submission date |
Jul 14, 2021 |
| Last update date |
Aug 06, 2022 |
| Contact name |
Mauricio A Reynoso |
| Phone |
951-827-6376
|
| Organization name |
University of California Riverside
|
| Department |
Botany and Plant Sciences
|
| Lab |
Bailey-Serres
|
| Street address |
4126 Genomics Bldg
|
| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL22250 |
Illumina HiSeq 3000 (Oryza sativa Japonica Group) |
| GPL26083 |
Illumina NextSeq 500 (Oryza sativa Japonica Group) |
|
| Samples (238)
|
|
| Relations |
| BioProject |
PRJNA746561 |
| SRA |
SRP328354 |
Less...
More...