Table 12.
Candidate genes in genomic regions associated to salinity tolerance. Details are given for RAP locus IDs and their putative functions from where the respective SNP was selected. Last column shows the tissue in which the given gene has highest transcription at normal condition based on Unigene database (supplementary Table S8)
| Chromosome | Related traits | Position of associated SNP (bp) | Gene RAP ID | Gene function | Tissue with highest transcription |
|---|---|---|---|---|---|
| 1 | RWC | 7,086,172 | Os01g0228300 | Mpv17/PMP22 family protein | Leaf |
| RFW | 11,259,217 | Os01g0304100 | Cation chloride cotransporter | Seed | |
| RFW | 24,946,338 | Os01g0624700 | WRKY transcription factor 12 | – | |
| RDW | 32,358,779 | Os01g0767700 | DEIH-box RNA/DNA helicase | Panicle | |
| TW | 34,510,717 | Os01g0812000 | Transcriptional activator of gibberellin-dependent alpha-amylase expression (GAMyb) | Seed | |
| RFW | 40,794,206 | Os01g0929500 | Carbonyl reductase-like protein | Panicle | |
| RFW | 41,101,759 | Os01g0936200 | Lipase class 3 family protein | Stem | |
| RDW | 41,534,764 | Os01g0944700 | Beta-1-glucanase precursor | Stem | |
| RDW, RFW | 42,254,208 | Os01g0958500 | RNA binding protein-like | Leaf | |
| RDW, RFW | 42,267,480 | Os01g0958800 | Protein of unknown function DUF2305 domain containing protein | Flower | |
| RDW, RFW | 42,339,521 | Os01g0960400 | Protein kinase core domain containing protein | Stem | |
| RDW, RFW | 42,351,049 | Os01g0960500 | Zinc finger RING/FYVE/PHD-type domain containing protein | Seed | |
| RDW, RFW | 42,442,204 | Os01g0963000 | Peroxidase BP 1 precursor | Leaf | |
| RDW, RFW | 42,575,260 | Os01g0965600 | Growth inhibition and differentiation-related protein 88 | Root | |
| RDW, RFW | 42,591,390 | Os01g0966000 | Plasma membrane H+-ATPase (EC 3.6.1.3) | Stem/leaf | |
| RDW, RFW | 42,622,164 | Os01g0966500 | Vacuolar protein sorting protein 55 | Vegetative meristem | |
| RDW, RFW | 42,627,050 | Os01g0966700 | Beta-fructofuranosidase (EC 3.2.1.26) | Leaf | |
| RDW, RFW | 42,649,896 | Os01g0967100 | Ascorbate peroxidase 2 | Seed | |
| RDW, RFW | 42,723,932 | Os01g0968700 | tRNA isopentenyltransferase family protein | Vegetative meristem | |
| RDW, RFW | 42,976,353 | Os01g0973300 | Armadillo-like helical domain containing protein, Adaptin | Flower | |
| 2 | SL-R, RDW-R | 30,423,080 | Os02g0730300 | High-affinity Potassium(K+) Transporter 25, OsHAK25 | Stem |
| 5 | RFW | 28,534,662 | Os05g0572900 | Pentatricopeptide repeat domain containing protein | Flower |
| 6 | RFW | 4,612,802 | Os06g0191200 | Zinc ion binding | Flower |
| RFW | 20,037,449 | Os06g0535300 | DnaJ domain protein C55 | Leaf | |
| RFW, RL | 29,757,694 | Os06g0704600 | Delta-aminolevulinic acid dehydratase | Leaf | |
| RFW | 30,484,421 | Os06g0717400 | Pseudouridine synthase domain containing protein | Stem | |
| RFW | 31,018,842 | Os06g0728600 | EPS15 homology (EH) domain containing protein | Vegetative meristem | |
| RFW | 31,144,213 | Os06g0730600 | Peptidase S9A prolyl oligopeptidase family protein | Seed | |
| 8 | RL | 63,899 | Os08g0101000 | ABI3/VP1 transcription factor family protein | Flower |
| RL | 125,422 | Os08g0102250 | H0913C04.5 protein | – | |
| RFW | 26,726,527 | Os08g0535200 | MtN3-like protein; OsXa13 | Panicle | |
| RFW | 26,752,345 | Os08g0535700 | Glycerophosphodiester phosphodiesterase | Seed | |
| RFW | 26,906,046 | Os08g0538200 | Protein of unknown function DUF247 plant family protein | – | |
| RFW | 26,926,958 | Os08g0538700 | Retinoblastoma-related protein | Callus | |
| 11 | RWC | 6,061,643 | Os11g0216000 | Pyruvate kinase family protein | Flower |
| RFW | 21,681,513 | Os11g0575600 | Lipoxygenase 10 | Callus | |
| RFW | 21,851,184 | Os11g0578700 | F-box domain containing protein | Callus |