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Table 3 Genes and QTLs located on the chromosomic segments bearing the independent loci under selection

From: Genome Scan of Rice Landrace Populations Collected Across Time Revealed Climate Changes’ Selective Footprints in the Genes Network Regulating Flowering Time

Independent loci under selection

Genetic group involved

DTHD QTLs (2)

DTHD genes (3)

N°

Type

Nb of SNP (1)

Chr

Start

End

Nb

Known name

MSU Identity

Name

GRP

Reference

1

M2

2

chr01

3,930,523

4,504,261

Og and Osj

1

 

LOC_Os01g08700

OsGI

1

Izawa et al. (2011)

2

M2

1

chr01

5,540,432

6,040,432

Og

14

dth1.1, QHd1a, QHd1a

LOC_Os01g10590

OsFTL8

1

Zhang et al. (2020)

3

M2

9

chr01

18,423,679

19,143,461

Og

2

     

4

M1

2

chr02

6,762,905

7,267,332

Osj

4

     

5

M2

1

chr02

24,604,636

25,104,636

Og

12

qHD-2, QHd2a

LOC_Os02g41550

OsCRY2

1

Hirose et al. (2006)

6

M2

1

chr03

5,079,703

5,579,703

Og

15

dth3.1, QHd3b

    

7

M2

3

chr03

10,132,774

12,145,360

Og

6

Hd8, dth3.1

LOC_Os03g19480

OsSWN; SDG718

2

Liu et al. (2014)

7

M2

3

chr03

10,132,774

12,145,360

Og

6

Hd8, dth3.1

LOC_Os03g19590

OsPHYB

2

Ishikawa et al. (2011)

8

M1

4

chr04

0

827,020

Og and Osj

1

qDTH-4

    

9

M1

9

chr04

1,085,381

3,005,652

Osj

12

qDTH-4, QHd4

    

10

M2

4

chr04

3,993,589

4,670,203

Og and Osj

0

 

LOC_Os04g08034

OsEMF2

3

Luo et al. (2009)

11

M2

1

chr04

32,129,645

32,629,645

Og

2

dth4.2

    

12

M2

6

chr05

8,974,371

9,788,465

Og

2

     

13

M2

15

chr05

14,743,007

16,632,418

Osj

2

qHD-5

    

14

M2

8

chr06

9,422,923

10,942,740

Osj

3

Hd1

LOC_Os06g16370

Hd1

1

 

14

M2

8

chr06

9,422,923

10,942,740

Osj

3

 

LOC_Os06g16390

OsCLF; SDG711

2

Liu et al. (2014)

15

M2

1

chr06

11,153,613

11,653,613

Osj

0

     

16

M2

45

chr06

13,095,417

18,074,177

Og and Osj

5

Hd6b, dth6.1

LOC_Os06g30370

OsMFT1

1

Gao et al. (2014)

17

M2

1

chr07

17,212,559

17,712,559

Og

5

     

18

M2

1

chr07

29,373,622

29,873,622

Og

6

Hd2, QTL7c

LOC_Os07g49460

OsPRR37

1

Hu et al. (2021)

19

M2

2

chr08

4,860,945

5,579,786

Osj

3

Hd-5, dth8

    

20

M2

14

chr08

17,288,523

18,502,122

Osj

21

QHd8, aQHd8, qDTH-8

    

21

M1

2

chr08

19,800,834

20,305,131

Og

2

qDTH-8

    

22

M2

1

chr08

23,308,242

23,808,242

Og

2

qDTH-8

LOC_Os08g37490

OsGF14a

3

Liu et al. (2019)

23

M2

1

chr09

14,585,036

15,085,036

Og

3

QHd9, FLTQ3

    

24

M1

2

chr09

19,597,853

21,078,706

Og and Osj

18

qHDD9-1, qDTH-9

LOC_Os09g33850

OsFTL4

3

Fang et al. (2019)

24

M1

2

chr09

19,597,853

21,078,706

Og and Osj

18

qHDD9-1, qDTH-9

LOC_Os09g34070

OsFPA

2

Mouradov et al. (2002)

24

M1

2

chr09

19,597,853

21,078,706

Og and Osj

18

qHDD9-1, qDTH-9

LOC_Os09g36220

OsPRR95

1

Murakami et al. (2005)

25

M2

2

chr09

22,453,022

22,953,023

Og

1

qDTH-9

    

26

M1

3

chr11

3,400,294

3,922,487

Osj

1

dth11.1

    

27

M2

1

chr11

23,361,713

23,861,713

Osj

2

QHd11

    

28

M2

14

chr11

25,384,918

26,543,152

Og and Osj

1

hd11

    

29

M2

4

chr11

26,942,125

27,922,719

Og

0

     

30

M1

14

chr12

16,142,460

17,897,080

Og

12

dth12.1, QHd12

    

31

M2

1

chr12

20,923,730

21,423,730

Og

4

 

LOC_Os12g34850.1

OsVRN5; OsVIL2

2

Wang et al. (2013)

  1. RP heading time regulation pathway. (1) Photoperiod and circadian clock pathway, (2) chromatin-related pathway, and (3) hormones pathway. Type: M1 = Independent loci under selection detected under one detection method; M2 = Independent loci under selection including at least one locus detected to be under selection by the two detection methods implemented. Og: O. glaberrima; Osj: O. sativa japonica (1) Number of SNP loci under selection composing the independent loci; chr Chromosome; DTHD day to heading; (2) source http://www.gramene.org/; (3) see detailed data and references in S Table 7