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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)

From: Genome-Wide Association Study (GWAS) to Identify Salt-Tolerance QTLs Carrying Novel Candidate Genes in Rice During Early Vegetative Stage

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