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Table 7 Annotation of genes harbouring the homolog trait-associated SNPs across all chromosomes in rice under normal conditions

From: Genome-Wide Association Study (GWAS) and genome prediction of seedling salt tolerance in bread wheat (Triticum aestivum L.)

Marker

Sequence

Trait

Ch.

Position (bp)

p-value

FDR

R2 (%)

Homolog gene ID in rice

Description

rs23576

TGCAGCCCCCTCAAAGTCCAACAAAGGAAGCCTGTGTTCAAACATATCATCAGTCTTCACCCGAA

ELI

4

3,555,377-3,562,902

0.000102795

0.934867761

5.42

OsAGO4b Os04g0151800

Argonaute and Dicer protein, PAZ domain containing protein

rs57411

TGCAGTATCTTCGAGGGCTATGTACCTCAAGGTATCATGCAGATGGTGTCCTCTTGGAGCATCT

SPAD

1

26,923,017-26,924,486

0.00017542

0.997601354

10.88

Os_F0640 Os01g0660700

Protein of unknown function DUF295 family protein

rs38145

TGCAGCTCTTCAGTACTACGCACGAAGACATCTGGAAGGTGCTTTTCAAGTCCAACGAGACGTG

SFW

3

11,449,370-11,450,605

0.000138462

0.934754317

8.86

Os03g0317900

Similar to Eukaryotic aspartyl protease family protein

rs12892

TGCAGCAATCATATTATCCAAAGGGCTCGAAAAGTGACCCGATGGTGTTGGCACATATTGCGGC

SDW

1

2,713,300-2,717,425

0.000144389

0.991476107

10.81

Os01g0150100

Similar to Geranylgeranyltransferase type I beta subunit

rs19020

TGCAGCATATGTTACGACTTACGACTACAGCTATGGCGGCTTCTCAGCCTCCACCTCGCGCGAC

RWC

3

31,048,351-31,055,017

0.000167852

0.897008387

8.89

PAP2 Os03g0753100

MADS-box transcription factor, Inflorescence and spikelet developmen

rs2460

TGCAGAATACAAGAAAACTTGGGTTGGACAGAATGCCCTTCCAACACCTCCAGGTCGAAGTTCC

RFW

8

9,921,522-9,923,218

0.000174577

0.999283649

19.32

OsCYP96B8 Os08g0262500

Cytochrome P450 family protein

rs43005

TGCAGGAATGCTTAGGAGTCCTGGATTACGGGGTTCTCGGGGAGCTGCCCTATGTGTCATGGGC

RDW

2

5,131,380-5,132,629

0.000323829

0.999773413

12.93

Os02g0192300

Zinc finger, RING/FYVE/PHD-type domain containing protein

rs14133

TGCAGCACCAGGTTTAGTAATGGCGCGTGAAGCGCCGATTAAGCACTGCCGAGATCGGAAGAGC

RV

2

25,329,183-25,341,924

0.000155995

0.660997839

10.17

Os02g0632500

Arf GTPase activating protein family protein

rs20420

TGCAGCATTTTGCCACCGCGAGGGTCATAAAAGGACGATATGCCCAGAAAGAGGTGATGCACCG

SH

4

18,458,075-18,458,875

0.000100427

0.5998512

22.73

Os04g0377932

Similar to Gonidia forming protein GlsA

rs5991

TGCAGAGCCCACCGCTGTGGAGGCGCAACCCGAAGGCACTAGCTTGTTTGACGAGAGTGCCCGA

RH

1

3,924,401-3,926,323

0.000118389

0.410072448

8.12

Os01g0176200

UDP-glucuronosyl/UDP-glucosyltransferase family protein

rs27832

TGCAGCGAAACCATACGATGGATGAAAATAGTACATGATGTATCAAATGGAAACTATGCCACGA

Chl a

3

3,260,107-3,270,386

0.00012644

0.922732948

6.15

Os03g0161100

Similar to Viral A-type inclusion protein repeat containing protein, expressed

rs24738

TGCAGCCGACCGATAGAATTGATCCAGCCATCACTCTAGGCAGCAAGGTTCTACATCTGTGTGC

Chl b

2

35,091,247-35,099,291

0.000103314

0.945323776

6.03

CYP97A4 Os02g0817900

Cytochrome P450 family protein

rs7710

TGCAGATAGAACCTTGTATTTTGCTCACAAAAAAGAAGAAGATAGAACCTGGATTCTCCTTCTT

Total Chl

1

2,226,409-2,229,526

0.000111059

0.969036099

6.32

Os01g0141300

Similar to vacuolar sorting protein 4b

rs53598

TGCAGGTCTGGTGAGTTTGTGCTGGTCATCAGTCATCGCTCGTGCAGACGATACGAGGCTCCTA

Car

2

30,011,066-30,015,609

0.000127541

0.863340516

7.23

Os02g0722700

Similar to Nucleic acid binding protein

rs59088

TGCAGTCGGAGCATCCGATGAAAATCAAATAAATTTGTTTTAGCTTCATACATACTCCAAGCAA

protein

3

23,989,148-23,997,520

0.000168358

0.999760957

5.22

Os03g0628800

Similar to H1flk (Fragment)

rs14676

TGCAGCACCTTCCGCCCAATCGCCACCGACTGCTCCTTCCGCCGCCGATTCCGCCGAGATCGGA

proline

3

11,613,231-11,614,737

0.000173086

0.999106429

32.56

OsFbox137 Os03g0321300

Cyclin-like F-box domain containing protein

rs3861

TGCAGACCCCTTTCCAGAACAGCCTCCGCGAGGTGCTGGAGGATGAGGAGGGGGTGCCGAGATC

CAT

8

23,648,009-23,651,073

0.000369888

0.995744042

6.33

CycD4 Os08g0479300

Cyclin, A/B/D/E domain containing protein

rs9866

TGCAGATTACATCAAGGAGGACACCCCCGCCGACGGGCTCGGTGATCTGCCCGCCCAGCCACCG

GPX

10

94,937-97,746

0.000141706

0.999955014

5.85

Os10g0101000

Serine/threonine protein kinase domain containing protein

rs9047

TGCAGATGAGGCGGTGGACGATGCGGTCGATGCAGTCCTGGGCGTCGTGCACCAGGCCAAGCAT

MDA

5

27,441,786-27,445,901

0.000315678

0.999277164

6.37

Os05g0551900

Similar to EMB1865 (embryo defective 1865); RNA binding

rs63113

TGCAGTTCCAAATTGCCCATAACAACGCATACACTCCTACACGAATATGTCTAGCTGTATCGGA

Na-s

6

16,400,699-16,432,426

0.000170855

0.999948041

5.37

OsOSC6 Os06g0483200

Similar to cycloartenol synthase

rs58688

TGCAGTCCGTTTTTAATTTCTGGCCTGGATCAGTTTCTTCCTCTGGATGGCCACGCTTATTTGT

Na-r

12

21,230,590-21,232,506

0.000146445

0.999834851

10.13

DHQDT/SDH Os12g0534000

Similar to Dehydroquinate dehydratase/shikimate:NADP oxidoreductase

rs46450

TGCAGGCAGTCATGTACCAGTACTACAACTCTCGCGGCCGTGGCATCTGAGCATTGGATCACGT

K-s

6

28,699,601-28,706,417

0.000270262

0.999928028

7.98

Os06g0688100

Hypothetical conserved gene

rs46450

TGCAGGCAGTCATGTACCAGTACTACAACTCTCGCGGCCGTGGCATCTGAGCATTGGATCACGT

K-r

6

28,699,601-28,706,417

0.000270262

0.999928028

7.98

Os06g0688100

Hypothetical conserved gene

rs37461

TGCAGCTCGGCCAGCTCCGCGAGCAGCGCCGCGTCGGCCGACGACTTGGACATGTCGCCGAGAT

K/Na-s

10

22,294,896-22,297,645

0.000142161

0.566933932

5.62

SAPK3 Os10g0564500

Serine/threonine protein kinase, Hyperosmotic stress respons

rs774

TGCAGAAATAAATATCTTTGCCGCCCCGCATCATTGGAACCTAGTCTCAACCCGAGATCGGAAG

K/Na-r

3

34,257,858-34,263,571

0.000149427

0.999795877

7.93

OsSCAR3 Os03g0816900

Conserved hypothetical protein