Rice is a crop sensitive to salinity stress. Nearly 7 million ha of cultivated area is affected by salinity across the globe. In the near future, more areas in the Southern hemisphere are expected to turn saline with increase in the ocean temperatures, esp., in the Pacific and the Indian Ocean. This database is an attempt to consolidate the various salinity specific experiments undertaken in rice to help the molecular biologists and breeders alike. Search options specific to genotypes, tissues, growth stages as well as genes commonly identified as responsive across experiments are possible.
Our database has salt responsive genes (SRGs) in rice identified from different experiments. SRGs identified from the raw data available in the public domain and analyzed employing uniform parameters in R are given here. Search for SRGs has been enabled from genotypes (varieties), growth stages and specific tissues used in the microarray experiment. Common SRGs across varieties (up to 3) can also be searched by the user. Search for a particular rice locus would fetch information whether it is a SRG and if yes, the different experiments which identified it. External link to genome browser is also available under Locus search. For the benefit of breeders, the search for microsatellites markers in SRG loci is also enabled.
Data Details
| S.No | GEO Accession ID | No. of Samples | Rice Genotype | Growth Stage | Tissue | Response to Drought Stress |
|---|---|---|---|---|---|---|
| 1 | GSE4438 | 24 | Agami | Vegatative Stage | Root | Tolerant |
| M103 | Vegatative Stage | Root | Susceptible | |||
| 2 | GSE13735 | 11 | FL478 | Vegatative Stage | Root | Tolerant |
| IR29 | Vegatative Stage | Root | Susceptible | |||
| 3 | GSE14403 | 23 | IR63731 | Vegatative Stage | Root | Tolerant |
| Pokkali | Vegatative Stage | Root | Tolerant | |||
| 4 | GSE16108 | 16 | CSR27 | Seedling Stage | Seedling | Tolerant |
| MI48 | Seedling Stage | Seedling | Susceptible | |||
| 5 | GSE58603 | 36 | IR64 | Seedling Stage | Leaf | Susceptible |
| IR64 | Seedling Stage | Root | Susceptible |
How do I use DB?
For SRGs in a variety:Click on drop down list to choose a variety. This will give you 1000 SRGs in a variety with their fold change expression values and annotation. This entire information can be copied to any text document for further use.
For SRGs in a tissue or growth stage:First, click on the appropriate option (tissue/growth stage) and further click on the drop down menu to choose the tissue or growth stage of your choice. This will give the list of SRGs in the item chosen across varieties. The list of varieties in which the SRGs were identified is also mentioned for the user's reference.
For common SRGs in more than one variety:It is possible to search for differentially expressed SRGs common to two or three genotypes. The user may select any two or three genotypes of his interest and the output would consist of common SRGs with their LOC and RAP IDs and annotation. Further information on the nature of expression in the individual genotypes could be gathererd by selecting the particular locus ID.
For SRG locus search:Here any locus ID can be given as input. The format should be LOC_Os06g01590. This will give complete information on the tissue, stage and variety from which the gene was identified as SRG.
For SSR locus search:The input format is as same as above. If the input gene is a SRG then the microsatellite motifs in the gene and appropriate primers for its amplification will be displayed.