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Rice

Table 1 Significantly associated loci for sheath blight resistance in rice based on a genome-wide association study

From: Genome-Wide Association Analysis of the Genetic Basis for Sheath Blight Resistance in Rice

SAL ID

Chr.

LD block interval (bp)

LD block size (kb)

No. of suggestive SNPs in LD block

Panel

Lead SNP position (bp)

Lead SNP P value

MSU ID of genes harboring lead SNP

QTL/Marker/Gene previously reported

L1

1

23,999,888–23,999,975

0.1

1

Whole

23,999,975

1.3E-08

LOC_Os01g42294-LOC_Os01g42310

 

L2

1

25,337,514–25,449,724

112.2

1

Whole

25,350,468

6.8E-08

LOC_Os01g44200-LOC_Os01g44210

 

L3

2

17,849,943–17,960,809

110.9

1

Whole

17,889,517

4.8E-14

LOC_Os02g30114

 

L4

2

35,718,082–35,816,634

98.6

17

Aus

35,752,298

8.9E-07

LOC_Os02g58470

QDs2b and QRh2b (Li et al. 2009)

L5

3

16,203,266–16,251,439

48.2

1

Xian

16,214,232

9.5E-07

LOC_Os03g28170

 

L6

3

21,967,065–22,099,455

132.4

1

Whole

22,062,214

4.2E-09

LOC_Os03g39660-LOC_Os03g39670

 

L7

3

33,180,575–33,294,172

113.6

1

Geng

33,211,402

9.3E-07

LOC_Os03g58290-LOC_Os03g58300

qSBR-3 (Kunihiro et al. 2002); qSBPL-3-2 (Wen et al. 2015); qHNLH3 (Zeng et al. 2015); OsWRKY4 (Wang et al. 2015)

L8

4

9,578,771–9,768,308

189.5

1

Geng

9,676,399

4.5E-06

LOC_Os04g17660-LOC_Os04g17669

 

L9

4

17,248,318–17,355,392

107.1

 

Whole

17,255,541

5.8E-07

LOC_Os04g29080-LOC_Os04g29090

 

L10

5

28,879,416–28,948,601

69.2

1

Aus

28,939,653

4.4E-06

LOC_Os05g50480

RM5784 and RM3286 (Taguchi-Shiobara et al. 2013)

L11

6

1,826,635–1,964,451

137.8

1

Geng

1,913,825

1.3E-06

LOC_Os06g04460

 

L12

6

22,541,170–22,604,225

63.1

1

Whole

22,546,226

2.0E-06

LOC_Os06g38100-LOC_Os06g38110

 

L13

6

28,352,324–28,363,626

11.3

1

Whole

28,362,652

2.1E-06

LOC_Os06g46680-LOC_Os06g46690

QRlh6 (Xie et al. 2008); qshb6.1 (Yadav et al. 2015); OsCHI11 (Karmakar et al. 2017)

L14

7

8,485,551–8,669,352

183.8

1

Aus

8,569,372

4.2E-06

LOC_Os07g14940-LOC_Os07g14950

 

L15

7

15,236,665–15,247,698

11.0

1

Whole

15,244,300

4.4E-10

LOC_Os07g26490-LOC_Os07g26500

qSBR7–1 (Channamallikarjuna et al. 2010)

L16

9

6,313,772–6,328,962

15.2

1

Whole

6,317,362

2.3E-07

LOC_Os09g11360-LOC_Os09g11370

qHZaDR9 (Zeng et al. 2015)

L17

9

10,897,450–10,929,683

32.2

1

Whole

10,915,359

8.2E-07

LOC_Os09g17830-LOC_Os09g17840

 

L18

9

18,082,609–18,092,891

10.3

1

Geng

18,092,604

3.9E-06

LOC_Os09g29760-LOC_Os09g29780

qSB-9 (Han et al. 2002); qSBR9–1 (Channamallikarjuna et al. 2010); qshb9.1 (Yadav et al. 2015); RM6251 and RM3533 (Taguchi-Shiobara et al. 2013); bc15/OsCTL1 (Wu et al. 2012)

L19

10

3,996,721–4,021,580

24.9

1

Whole

4,011,130

2.5E-09

LOC_Os10g07520-LOC_Os10g07530

QRlh10b (Xie et al. 2008)

L20

10

9,226,748–9,327,350

100.6

1

Geng

9,326,435

8.1E-07

LOC_Os10g18360

 

L21

10

11,281,341–11,387,999

106.7

1

Whole

11,381,173

1.2E-08

LOC_Os10g22030

 

L22

10

11,610,905–11,623,071

12.2

1

Whole

11,620,213

2.1E-08

LOC_Os10g22440-LOC_Os10g22450

 

L23

10

14,423,809–14,585,826

162.0

1

Geng

14,523,517

5.3E-12

LOC_Os10g28009-LOC_Os10g28020

qDs10 (Li et al. 2009)

L24

10

16,612,339–16,716,107

103.8

1

Whole

16,616,152

6.1E-08

LOC_Os10g31680-LOC_Os10g31700

 

L25

11

5,702,715–5,767,077

64.4

1

Geng

5,708,512

1.8E-07

LOC_Os11g10460-LOC_Os11g10470

qSB-11LE (Zuo et al. 2013); qSBPL-11-2 (Wen et al. 2015)

L26

11

25,530,571–25,595,331

64.8

33

Aus

25,580,510

6.9E-07

LOC_Os11g42450-LOC_Os11g42470

QDs11b and QRh11 (Li et al. 2009); qSBR11–1 (Channamallikarjuna et al. 2010)

L27

12

21,483,436–21,483,932

0.5

1

Whole

21,483,904

8.4E-08

LOC_Os12g35340-LOC_Os12g35350

qSBPL-12 (Wen et al. 2015)

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