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Table 2 Heading date QTLs confirmed in BC4F3 populations

From: Genetic architecture of variation in heading date among Asian rice accessions

Population

Chromosome

Physical position ofQTL (Mbp)

Marker interval

LOD a

Additive effect b

Dominance effect c

PVE (%) d

Corresponding gene e

Located near gene f

QZZ

1

0.2–10.8

RM6887–RM1287

5.3

1.7

0.2

20.0

  
 

3

0.5–5.5

RM4108–RM5442

12.1

-1.7

0.2

52.1

 

Ehd4, DTH3

 

3

30.4–35.6

RM3199–RM3329

36.2

-8.1

4.0

77.5

Hd6

Hd16

 

7

7.1–13.4

RM21251–RM7273

32.1

10.9

8.6

89.9

Ghd7

 
 

7

26.8–29.4

RM1364–RM22164

2.4

3.3

-0.1

5.7

 

OsPRR37

TUP

2

1.9

RM7562

8.3

1.6

0.0

37.6

  
 

2

6.7–11.3

RM5897–RM1234

6.8

-1.4

-0.2

26.4

  
 

2

27.1–30.6

RM1367–RM3316

4.1

-0.5

-0.8

13.2

 

DTH2

 

3

0.5

RM4108

19.0

-2.4

-0.6

54.6

 

Ehd4, DTH3

 

4

2.0–11.6

RM5414–RM16606

2.8

0.7

-0.8

20.9

  
 

5

23.9–29.5

RM3476–RM3286

14.6

-1.3

0.4

35.0

  
 

6

24.5–26.0

RM5957–RM6395

5.0

-0.8

-0.1

22.5

  
 

10

11.7–17.4

RM4455–RM5620

2.5

-0.5

-0.9

18.3

 

Ehd1

 

12

20.0–24.4

RM28305–RM5479

8.5

-0.9

-0.4

19.7

  

MUH

3

0.5–1.5

RM4108–RM3372

12.6

-2.0

0.3

47.6

 

Ehd4, DTH3

 

5

23.9–27.9

RM3476–RM5784

9.5

-1.9

0.4

16.1

  
 

6

8.1–8.8

RM19725–RM5963

26.1

4.2

-1.1

67.3

Hd1

 
 

6

15.8–20.3

RM20023–RM7193

20.8

4.6

-0.4

66.1

  
 

8

6.8–10.3

RM22617–RM3395

25.0

-4.0

0.5

74.0

DTH8

 
 

11

3.8–8.1

RM5599–RM3701

2.2

0.5

-0.9

3.9

  

BAS

2

11.3–13.5

RM1234–RM13106

4.4

-0.6

0.0

9.8

  
 

2

33.0–35.4

RM7286–RM3850

3.6

-1.1

0.7

8.5

 

DTH2

 

3

6.9–10.1

RM3872–RM14778

7.0

-1.1

0.2

17.4

 

Ehd4, DTH3

 

3

10.1–14.5

RM14778–RM6959

4.3

-1.1

0.7

9.8

  
 

3

17.4–21.4

RM1334–RM5488

7.9

-0.9

-0.4

16.7

  
 

7

29.4

RM22164

21.0

-3.7

-0.1

69.7

 

OsPRR37

DPZ

2

13.4–18.4

RM13101–RM1211

2.5

-1.0

0.0

5.4

  
 

2

29.3–35.4

RM6933–RM3850

9.2

-1.1

0.3

38.3

 

DTH2

 

6

0.2

RM6467

39.5

-3.6

-3.3

85.2

  
 

7

13.2–16.2

RM21433–RM5481

10.6

-4.0

-0.9

42.5

Ghd7

 
 

7

28.1–29.4

RM22105–RM22164

31.6

-5.0

0.0

53.4

 

OsPRR37

 

10

17.5–20.7

RM5620–RM25771

5.3

0.5

0.1

18.2

 

Ehd1

 

12

7.1–10.1

RM27792–RM6973

5.7

-0.6

-0.1

20.1

  

KMK

2

4.3–9.5

RM4355–RM12921

2.2

0.5

-0.3

7.8

  
 

2

20.1–24.0

RM1379–RM3515

2.1

0.5

0.2

7.3

  
 

6

8.1

RM19725

34.4

4.0

-0.8

81.0

Hd1

 
 

8

3.0–3.7

RM4955–RM1148

9.5

-1.3

0.2

45.4

  

NAB

2

27.1–34.7

RM1367–RM3789

2.2

-0.6

0.1

5.5

 

DTH2

 

3

9.9–15.0

RM1371–RM3204

13.4

-1.6

0.2

43.6

 

Ehd4, DTH3

 

5

27.9–29.7

RM5784–RM19218

7.0

-1.0

0.2

18.7

  
 

6

0.2–2.2

RM6467–RM8112

10.7

1.3

0.1

29.1

 

Hd17

 

6

8.8–13.0

RM5963–RM19951

30.2

5.9

0.6

79.2

Hd1

 
 

8

5.9

RM6838

5.5

-1.8

0.3

7.9

DTH8

 
 

9

14.4–16.7

RM5657–RM6235

2.9

0.5

-0.1

4.5

  

BKH

3

0.5–5.5

RM4108–RM5442

13.9

-3.8

-0.5

46.2

 

Ehd4, DTH3

 

5

22.3–27.9

RM3295–RM5784

7.1

-1.3

-0.2

13.3

  
 

6

0.2–5.2

RM6467–RM5754

18.3

-2.5

0.1

59.6

RFT1, Hd3a

Hd17

 

7

13.4–18.4

RM7273–RM6394

16.9

-2.2

0.3

60.8

Ghd7

 
 

8

10.3–14.7

RM3395–RM22896

9.4

3.4

0.6

36.6

DTH8

 

KNJ

5

23.9–27.9

RM3476–RM5784

5.7

-1.8

-0.2

25.7

  
 

6

16.1–29.8

RM3615–RM20045

15.5

-4.6

1.1

31.3

  
 

7

26.8–29.4

RM1364–RM22164

18.3

-2.0

0.5

63.3

 

OsPRR37

 

9

3.4–9.2

RM23736–RM1328

2.7

-1.0

0.3

4.4

  

BLE

3

0.5

RM4108

20.1

-2.8

-0.5

65.9

 

Ehd4, DTH3

 

3

30.4–35.6

RM3199–RM3329

32.1

-5.2

3.4

81.2

Hd6

Hd16

 

6

26.0–28.5

RM6395–RM1370

3.4

-1.4

-0.3

6.9

  
  1. aLog-likelihood value. LOD threshold to detect QTLs was determined in each BC4F3 population.
  2. bAdditive effect of KSH allele on days to heading.
  3. cDominance effect of KSH allele on days to heading.
  4. dPercentage of phenotypic variance explained by QTL.
  5. ePreviously identified heading date genes corresponding to the QTLs detected in this study based on their physical positions on IRGSP 1.0.
  6. fPreviously identified heading date genes located near the QTLs detected in this study based on their physical positions on IRGSP 1.0.
  7. The BC4F3 populations were derived from crosses between Koshihikari (KSH) and 11 diverse accessions of Asian rice. Abbreviations of rice accessions are described in Table 1.