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Table 3 Statistics summary for core haplotypes with P <0.01 after the relative extended haplotype homozygosity (REHH) test

From: A genome-wide scan of selective sweeps in two broiler chicken lines divergently selected for abdominal fat content

Lean line

Chr

Core position

Hap Freq

EHH

REHH1

REHH P-value1

Genes

1

39360501-39455853

0.46

0.98

3.99

0.0027

/

1

49926970-49964278

0.30

0.97

4.18

0.0021

C12orf69, WBP11, H2A4, H2B1, H4, H32, H2B8

1

173098805-173190831

0.37

0.99

4.25

0.0027

RB1, LPAR6, O57531, RCBTB2

1

198071099-198113519

0.55

0.80

3.03

0.0031

GDPD4, MYO7A

2

3631683-3739002

0.32

0.70

4.88

0.0004

Q5ZK34

2

19934135-20028093

0.30

0.97

3.88

0.0035

RSU1

2

26912546-26974875

0.28

1.00

3.65

0.0050

/

2

99818321-100051643

0.41

1.00

3.00

0.0047

GNAL, NRGN

2

131104507-131150076

0.48

0.98

3.24

0.0029

Q6V0P0, INTS8, F1P3N8

2

143016981-143059231

0.36

0.97

3.46

0.0034

/

2

145836411-145908271

0.30

1.00

3.72

0.0045

/

2

150489129-150540434

0.34

1.00

3.51

0.0044

/

3

3794973-3861882

0.30

0.79

4.72

0.0005

C20orf26, CRNKL1

3

3794973-3861882

0.30

0.82

3.85

0.0020

C20orf26, CRNKL1

3

10257926-10454969

0.55

0.49

2.49

0.0019

F1NRN6

3

14895290-14957057

0.44

0.72

3.16

0.0048

PLCB4

3

26957549-26996618

0.46

0.80

3.69

0.0009

/

3

26957549-26996618

0.46

0.83

3.47

0.0013

/

3

27303800-27335510

0.52

0.92

3.78

0.0009

SRBD1

3

27382993-27430067

0.54

0.84

3.77

0.0009

SRBD1

3

35555718-35610466

0.47

0.66

3.02

0.0031

E1C4G2

3

68936320-69076223

0.27

0.98

3.79

0.0041

RPF2, GTF3C6, Q5F484, CDK19

4

3522359-3551494

0.59

0.54

3.10

0.0023

MBNL3

4

9568761-9604871

0.55

1.00

2.95

0.0040

/

4

17765695-17819334

0.41

1.00

3.56

0.0037

F1NEF4, HMGB3

4

46149116-46190279

0.36

0.99

3.35

0.0044

EREG, Q645M5

4

55424480-55472209

0.66

0.9

2.60

0.0005

TRPC3, BBS7

4

83051637-83117974

0.39

0.87

3.72

0.0022

/

5

9740941-9828144

0.49

1.00

3.42

0.0014

IF4G2, CTR9, MRVI1

5

23825115-23872187

0.41

0.78

3.19

0.0030

O93582

5

42592517-42679460

0.30

1.00

3.70

0.0044

/

6

6546601-6626145

0.39

1.00

4.42

0.0011

/

6

35354459-35390346

0.38

0.99

3.72

0.0030

PTPRE

7

28869664-28906344

0.31

1.00

4.88

0.0015

MYLK

7

35674098-35715122

0.67

0.48

2.09

0.0027

 

8

6107407-6172105

0.36

0.63

3.72

0.0020

IER5, KIAA1614, XPR1

9

16264832-16366749

0.45

0.97

4.04

0.0024

PSMD1, ARMC9, B3GNT7

10

5831963-5856349

0.59

0.97

1.83

0.0034

/

10

19717086-19745274

0.48

1.00

2.90

0.0011

CHSY1

11

17094961-17160195

0.30

0.63

3.35

0.0001

BCDO1, GAN

13

2628777-2664596

0.35

1.00

3.94

0.0048

Q5ZHQ9

13

2726706-2746894

0.39

0.79

4.06

0.0041

/

13

16758621-16783127

0.26

0.69

3.26

0.0050

FSTL4

15

7345639-7377799

0.26

0.54

2.38

0.0004

SEZ6L, ASPHD2, HPS4

18

9949736-10015444

0.39

1.00

2.34

0.0031

SPAG9

18

10117401-10135964

0.39

1.00

2.64

0.0013

F1NM51

19

8727596-8786448

0.60

0.55

1.77

0.0038

MSI1

20

9090808-9113453

0.29

0.95

6.18

0.0036

MYT1

20

9246245-9278998

0.32

0.80

5.39

0.0040

E1C8M0

20

9879361-9899719

0.27

0.96

6.40

0.0030

CSK21

22

2952274-3002268

0.29

0.29

3.93

0.0039

/

Fat line

1

51248496-51279543

0.33

0.81

4.45

0.0018

TCF20

1

58120009-58215364

0.55

0.99

3.15

0.0016

Q8UVD4

1

60171076-60254771

0.46

1.00

4.12

0.0049

/

1

67763862-67830818

0.26

0.96

4.06

0.0026

/

1

68213617-68257241

0.61

0.94

4.21

0.0016

SOX5

1

69634186-69686357

0.66

0.99

2.89

0.0003

/

1

101535615-101635667

0.29

1.00

5.24

0.0005

SAMSN1

1

114789487-114875623

0.29

0.99

3.66

0.0048

MAOB, MAOA

1

125909995-126011984

0.35

1.00

3.77

0.0036

E1BTB5

1

154665510-154752965

0.72

0.89

2.09

0.0034

/

1

181800227-181883545

0.33

0.99

4.00

0.0033

A1XGV6

1

181800227-181883545

0.33

1.00

3.81

0.0043

A1XGV6

2

76768841-76854523

0.31

1.00

4.30

0.0041

/

2

151203953-151251059

0.62

0.82

2.32

0.0033

TRAPPC9

2

153117092-153143883

0.71

0.77

1.68

0.0038

/

3

9177907-9222825

0.38

0.95

4.00

0.0024

EHBP1

3

9177907-9222825

0.38

0.90

3.66

0.0039

EHBP1

3

16143474-16194865

0.30

0.98

4.98

0.0016

/

3

24945839-24986772

0.61

0.70

2.15

0.0014

/

3

44265116-44311493

0.40

0.99

3.50

0.0050

UNC93A

3

69863850-69906698

0.34

1.00

4.29

0.0038

/

3

85874137-85931473

0.41

1.00

3.97

0.0031

LMBRD1

3

97227680-97337906

0.28

0.99

3.81

0.0042

/

4

11582141-11642538

0.27

0.96

4.53

0.0029

/

4

40653593-40713404

0.32

0.93

4.40

0.0010

C4orf20, LRP2BP, SNX25

4

55950677-55991394

0.28

0.99

4.55

0.0028

/

4

55950677-55991394

0.28

1.00

4.36

0.0036

/

4

86719441-86754976

0.57

0.75

2.88

0.0048

/

5

556571-628531

0.25

0.67

4.37

0.0026

F1NYX6, PLCB2, BUB1B, PAK6

5

40239840-40261525

0.29

0.97

4.48

0.0038

VSX2, F1N9P5

5

47240577-47282933

0.40

0.95

2.91

0.0029

RIN3, LGMN

5

59811459-59880511

0.39

0.66

3.36

0.0041

/

6

26756202-26793956

0.34

0.98

3.94

0.0049

/

6

29341938-29401207

0.32

0.97

5.50

0.0007

ABLIM1

7

30090927-30155133

0.30

0.88

3.77

0.0033

F1NF72

7

31374271-31418061

0.42

1.00

2.88

0.0049

LYPD1, NCKAP5

7

33795201-33904515

0.47

1.00

2.20

0.0025

LRP1B

7

36818722-36875768

0.26

0.99

3.95

0.0024

Q9DEH4

7

37031922-37124566

0.56

1.00

2.92

0.0047

STAM2, FMNL2

8

5597-492518

0.56

0.99

1.94

0.0036

F1NF53

8

2178258-2252969

0.47

0.92

4.20

0.0004

NEK7

9

2952291-3007034

0.41

0.71

3.85

0.0044

/

10

763998-831991

0.50

0.78

5.04

0.0004

MYO9A, F1P0M4

11

9804894-9826761

0.47

0.52

3.11

0.0014

/

11

16253047-16303345

0.58

0.35

1.80

0.0040

/

12

1157199-1170169

0.37

0.63

4.57

0.0030

/

13

1533552-1640154

0.40

1.00

3.41

0.0049

SRA1, APBB3, F1NH59

14

8048059-8173629

0.42

0.86

3.09

0.0015

/

15

8495796-8543001

0.29

1.00

4.86

0.0003

TBX6, CRKL, KLHL22

15

8495796-8543001

0.29

0.99

4.43

0.0006

TBX6, CRKL, KLHL22

17

3250605-3271593

0.27

0.97

3.91

0.0033

/

17

4062173-4087131

0.26

0.94

3.77

0.0040

C4PCF3

18

4433126-4445816

0.26

0.79

5.99

0.0037

PRPSAP1

18

8365846-8400245

0.47

0.80

3.53

0.0038

/

23

935267-970086

0.31

0.91

5.40

0.0040

EDN2

24

5613517-5633477

0.28

0.86

4.38

0.0024

ZW10, F1NC10

24

6145308-6158962

0.31

0.80

5.30

0.0047

/

  1. 1REHH and P-values are presented for upstream and downstream sides from each core haplotype, respectively.