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Table 2 Summary of major candidate genes related to meat quality characteristics and feed intake in Sanga cattle population detected by XP-EHH and XP-CLR statistics (see Additional file 1: Table S1 and Additional file 2: Table S2)

From: Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef

Candidate genes

Chr.

Window (Mbp)

XP-CLR

Max XP-EHH

XP-EHH P-value

Tajima’s D

Weighted FST

Species, trait and reference

PIK3CB

1

131.50–131.55

121.48

2.21

1.69.E-03

−1.06

0.27

RFI [79]a

MRAS

1

131.73–131.78

112.25

-

-

−1.87

0.16

FCE [79]a

PLA2G2A

2

133.28–133.33

117.48

-

-

0.70

0.27

IMF [58]b, [59]c

CAPZB

2

133.78–133.83

142.50

-

-

−0.47

0.22

Tenderness [32]c

COL9A2

3

106.38–106.43

107.14

1.93

5.95.E-03

−1.30

0.15

Tenderness [46]b

LIMA

5

29.78–29.83

117.18

-

-

−0.33

0.39

Tenderness [45]b

SLC48A1

5

32.63–32.68

101.45

1.80

6.96.E-03

−0.35

0.26

Meat color [68]d

MB

5

74.18–74.23

129.86

1.96

5.00.E-03

−0.98

0.20

Meat color [41, 67]d

APOL6

5

74.20–74.25

-

2.00

5.00.E-03

−0.91

0.13

IMF [65]d

ATP8A1

6

62.90–62.95

264.27

2.02

4.00.E-03

−1.39

0.36

FCE [76]c

PDGFRA

6

71.35–71.40

408.60

2.61

3.00.E-04

−2.29

0.45

Tenderness [53]b

MAP3K5

9

75.55–75.60

147.37

2.09

3.00.E-03

−0.23

0.15

RFI [75]b

PARK2

9

99.13–99.18

132.40

2.34

2.36.E-03

−0.27

0.30

IMF [62]a

PKM2

10

18.95–19.00

-

1.97

2.00.E-03

−1.18

0.25

Tenderness [32]d, [52]a; IMF [64]b; Drip loss [70, 71]b

ZNF410

10

85.68–85.73

165.86

2.18

1.94.E-03

−0.67

0.28

Tenderness [32]c, [35]b

AHSA1

10

89.70–89.75

-

2.23

2.00.E-03

−1.47

0.31

IMF [66]c

MAP4K4

11

6.65–6.70

-

1.85

9.00.E-03

0.72

0.08

Drip loss [70, 71]b

NFATC2

13

80.00–80.05

-

2.01

4.24.E-03

2.53

0.25

Tenderness [55]d

WWP1

14

78.63–78.68

133.90

-

-

1.03

0.18

Tenderness [50]d

OR2D2, OR10A4, OR2D3

15

46.40–46.45

-

2.07

3.45.E-03

2.61

0.18

Feed intake [78]d; [77]b

MAP2K3

19

35.85–35.90

-

1.93

4.00.E-03

−0.20

0.16

IMF [49]b

PLCD3

19

45.40–45.45

-

1.89

5.00.E-03

−0.18

0.03

IMF [56]d

TIMP2

19

54.10–54.15

-

1.88

7.46.E-03

−0.73

0.18

RFI [73]c

PLCD1

22

11.45–11.50

195.30

2.12

3.00.E-03

−1.43

0.14

IMF [56]d

ROCK1

24

35.48–35.53

130.40

2.22

1.61.E-03

0.93

0.29

Tenderness [48]a; IMF [61]b

PRKG1

26

7.43–7.48

166.61

-

-

−1.27

0.13

Tenderness [54]d; IMF [36]b; RFI [72]c

  1. Note: Chr. Chromosome, Window: start and end positions of the gene region; RFI residual feed intake, FCE feed conversion efficiency, IMF intramuscular fat; Superscripts in the Species, Trait and Reference column indicate the species that the trait has been previously reported for as achicken, bpork, cbeef, dgeneral (not for a specific species)
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BMC Genomic Data

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