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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