|
| Status |
Public on Aug 05, 2005 |
| Title |
Grape (Vitis riparia) buds long day (paradormant) verses short day (endodormancy induced) on Arabidopsis 9.2K (B) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Long day axillary buds
|
| Organism |
Vitis riparia |
| Characteristics |
Axillary buds harvested from shoot basal nodes 2 to 12. Buds were harvested from plants that were grown for 8 weeks under long photoperiods (LD-14h).
|
| Biomaterial provider |
Anne Fennell, South Dakota State University, Brookings, SD
|
| Treatment protocol |
Axillary buds were collected from intact plants after 8 weeks of LD. Buds were excised, frozen in liquid nitrogen, and stored at -80C until RNA extractions were preformed.
|
| Growth protocol |
Five to seven-year-old clonally propagated Vitis riparia vines were used for these studies. In mid-March, two hundred forty ecodormant spur pruned vines with three or four spurs were placed in 15-L containers with media consisting of a 1:2:2 (v/v) mixture of soil, peat, and perlite. Three or four shoots (one on each spur) were trained vertically on each plant and all flower clusters were removed . Plants were grown under a long photoperiod (LD, 14 h) at 25/20 + 3 oC day/night temperatures (D/N) with 600 to 1400 µmol·m-2·s-1 photosynthetic photon flux (PPF) in a climate-controlled unshaded glass greenhouse (En Tech Control Systems Inc., Montrose, Minn.) from March through May in Brookings, S. Dak. (42oN). High pressure sodium lamps (400 W) were used to extend daylength to 15 h (March through May) and to increase PPF when the natural PPF was below 600 µmol·m-2·s-1. All plants were watered daily and fertilized weekly with a complete nutrient solution. After 6 weeks of growth two hundred uniform plants (having 3 shoots with 12 or more nodes) were selected and randomly assigned to the long photoperiod (endodormancy inhibiting) or short photoperiod (endodormancy inducing) during May and June. White covered black cloth was used daily to impose SD starting at 1700 h. Temperatures were maintained at 25/20 + 3 oC D/N in both photoperiod treatments. Thirty plants were randomly assigned to each of the 2, 4, and 6 treatment weeks in the LD and SD conditions. For this study, buds were harvested between 8:00 and 12:00 AM after 8 weeks of LD , frozen in liquid nitrogen, and stored at -80C until RNA extractions were performed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from ground axillary buds using the Pine tree extraction method (Chang et al. 1993).
|
| Label |
Cy5
|
| Label protocol |
Schaffer R., J. Landgraf, M. Accerbi, V. V. Simon, M. Larson and El Wisman. 2001. Microarray analysis of diurnal and circadian regulated genes in Arabidopsis. Plant Cell 13:113-123.
|
| |
|
| Channel 2 |
| Source name |
Short day axillary buds
|
| Organism |
Vitis riparia |
| Characteristics |
Axillary buds harvested from shoot basal nodes 2 to 12. Buds were harvested from plants that were grown for 6 weeks under long photoperiods (LD-14h) and then 2 weeks under short photoperiod (SD-8h).
|
| Biomaterial provider |
Anne Fennell, South Dakota State University, Brookings, SD
|
| Treatment protocol |
Axillary buds were collected from intact plants after 6 weeks of LD + 2 weeks of SD. Buds were excised, frozen in liquid nitrogen, and stored at -80C until RNA extractions were performed.
|
| Growth protocol |
Five to seven-year-old clonally propagated Vitis riparia vines were used for these studies. In mid-March, two hundred forty ecodormant spur pruned vines with three or four spurs were placed in 15-L containers with media consisting of a 1:2:2 (v/v) mixture of soil, peat, and perlite. Three or four shoots (one on each spur) were trained vertically on each plant and all flower clusters were removed . Plants were grown under a long photoperiod (LD, 14 h) at 25/20 + 3 oC day/night temperatures (D/N) with 600 to 1400 µmol·m-2·s-1 photosynthetic photon flux (PPF) in a climate-controlled unshaded glass greenhouse (En Tech Control Systems Inc., Montrose, Minn.) from March through May in Brookings, S. Dak. (42oN). High pressure sodium lamps (400 W) were used to extend daylength to 15 h (March through May) and to increase PPF when the natural PPF was below 600 µmol·m-2·s-1. All plants were watered daily and fertilized weekly with a complete nutrient solution. After 6 weeks of growth two hundred uniform plants (having 3 shoots with 12 or more nodes) were selected and randomly assigned to the long photoperiod (endodormancy inhibiting) or short photoperiod (endodormancy inducing) during May and June. White covered black cloth was used daily to impose SD starting at 1700 h. Temperatures were maintained at 25/20 + 3 oC D/N in both photoperiod treatments. Thirty plants were randomly assigned to each of the 2, 4, and 6 treatment weeks in the LD and SD conditions. For this study, buds were harvested between 8:00 and 12:00 AM after 6 weeks of LD + 2 weeks of SD treatment, frozen in liquid nitrogen, and stored at -80C until RNA extractions were performed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from ground axillary buds using the Pine tree extraction method (Chang et al. 1993).
|
| Label |
Cy3
|
| Label protocol |
Schaffer R., J. Landgraf, M. Accerbi, V. V. Simon, M. Larson and El Wisman. 2001. Microarray analysis of diurnal and circadian regulated genes in Arabidopsis. Plant Cell 13:113-123.
|
| |
|
| |
| Hybridization protocol |
Schaffer R., J. Landgraf, M. Accerbi, V. V. Simon, M. Larson and El Wisman. 2001. Microarray analysis of diurnal and circadian regulated genes in Arabidopsis. Plant Cell 13:113-123.
|
| Scan protocol |
Hybridization was visualized using an Affy428scanner. Spots were identified and signal intensities calculated using Jaguar software provided with the scanner.
|
| Description |
This experiment compares the differences in expression of grape buds following 6 weeks growth under long photoperiods (LD-14h paradormancy maintenance) followed by either 2 weeks LD or 2 weeks SD (8h - endodormancy induction).
|
| Data processing |
The N_LOG_VALUE is the log base 2 of the ratio of long day over short day spot intensities following removal of poorly hybridizing or high background (>1.5X CH/CH_BG) in both channels followed by log normalization.
|
| |
|
| Submission date |
Jun 09, 2005 |
| Last update date |
Aug 04, 2005 |
| Contact name |
Anne Y Fennell |
| E-mail(s) |
anne.fennell@sdstate.edu
|
| Phone |
605-688-6373
|
| Fax |
605-688-4452
|
| Organization name |
South Dakota State University
|
| Department |
Plant Science
|
| Lab |
Fruit Crops Research
|
| Street address |
201 N. Campus Dr
|
| City |
Brookings |
| State/province |
SD |
| ZIP/Postal code |
57007 |
| Country |
USA |
| |
|
| Platform ID |
GPL2526 |
| Series (1) |
| GSE3052 |
Photoperiod induction of endodormancy in Vitis riparia axillary buds. |
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