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Table 2 Selective sweeps and candidate genes related to acclimation and economically important traits found in genomes of Russian sheep breeds

From: High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia

OAR

Start (Mbp)

End (Mbp)

q-value

Breed/Group

Method

No. genes

Candidate genes (rank)

Trait

1

119.12

119.49

1.90E-09

Karachaev

DCMS

6

KCNE2 (1)

growth

1

119.09

119.49

7.67E-05

Karakul

DCMS

6

KCNE2 (1)

growth

1

119.23

119.45

0.001775722

Tuva

DCMS

5

KCNE2 (1)

growth

1

127.64

127.75

0.000366751

Altai Mountain

DCMS

1

ADAMTS5 (1)

acclimation

1

127.63

127.74

0.000199884

Baikal

DCMS

1

ADAMTS5 (1)

acclimation

1

127.63

127.69

0.007036415

Kulundin

DCMS

1

ADAMTS5 (1)

acclimation

2

35.41

36.06

0.000153169

GROUP1

hapFLK

6

UBQLN1 (5)

reproduction

2

35.87

35.92

0.004399798

Salsk

DCMS

1

UBQLN1 (1)

reproduction

2

58.59

58.75

0.000834252

Edillbai

DCMS

1

GNAQ (1)

reproduction

2

58.62

58.74

0.002702535

Lezgin

DCMS

1

GNAQ (1)

reproduction

2

58.64

58.71

0.008858869

Karakul

DCMS

1

GNAQ (1)

reproduction

2

142.19

142.30

2.19E-05

Buubei

DCMS

1

SCN9A (1)

temperature sensation

2

232.36

232.41

0.00631797

Romanov

DCMS

1

NMUR1 (1)

acclimation

3

124.57

124.69

0.000275686

Edillbai

DCMS

1

KITLG (1)

coat colour/domestication

3

124.55

124.68

8.86E-05

Buubei

DCMS

1

KITLG (1)

coat colour/domestication

3

132.24

132.94

9.65E-05

GROUP1

hapFLK

16

HOXC@ (1–7, 9)

growth

3

132.26

132.53

6.51E-07

Lezgin

DCMS

9

HOXC@ (1–6, 8,9)

growth

3

132.31

132.51

0.000416517

Karakul

DCMS

9

HOXC@ (1–6,8,9)

growth

3

132.31

132.42

0.008497984

Edillbai

DCMS

7

HOXC@ (1–6)

growth

3

133.58

133.77

9.72E-13

Salsk

DCMS

8

KRT@ (1–8)

wool

3

133.59

133.76

1.36E-07

Krasnoyarsk

DCMS

7

KRT@ (1–7)

wool

3

133.60

133.75

3.73E-07

Groznensk

DCMS

6

KRT@ (1–6)

wool

3

133.56

133.75

3.24E-10

Baikal

DCMS

6

KRT@ (1–6)

wool

3

133.57

133.72

1.35E-08

Kulundin

DCMS

5

KRT@ (1–5)

wool

3

133.61

133.66

0.005739761

Volgograd

DCMS

1

KRT72 (1)

wool

3

211.49

211.62

0.000569719

Salsk

DCMS

1

WNK1 (1)

temperature sensation

4

68.29

69.18

4.31E-08

GROUP1

hapFLK

12

HOXA@ (1–9)

growth

4

68.81

69.17

6.70E-06

Karakul

DCMS

8

HOXA@ (1–8)

growth

4

68.75

69.13

3.56E-08

Buubei

DCMS

10

HOXA@ (1–9)

growth

4

68.64

68.99

1.25E-06

Russian Longhaired

DCMS

10

HOXA@ (2–9)

growth

4

68.62

68.97

9.34E-14

Karachaev

DCMS

10

HOXA@ (1,3–10)

growth

4

68.62

68.92

5.18E-05

Kulundin

DCMS

4

HOXA@ (2–4)

growth

4

85.61

85.75

3.38E-07

Karachaev

DCMS

1

CPED1 (1)

growth

4

85.66

85.71

0.000339136

Krasnoyarsk

DCMS

1

CPED1 (1)

growth

4

85.67

85.71

0.002455069

Edillbai

DCMS

1

CPED1 (1)

growth

4

85.67

85.70

0.002368717

Altai Mountain

DCMS

1

CPED1 (1)

growth

5

49.07

49.38

0.000134196

Karakul

DCMS

12

HARS (1)

temperature sensation

5

49.19

49.27

0.001308813

Kulundin

DCMS

4

HARS (1)

temperature sensation

6

24.71

25.01

1.33E-08

Kulundin

DCMS

3

DNAJB14 (3)

reproduction

6

24.71

25.01

4.37E-09

Baikal

DCMS

3

DNAJB14 (1)

reproduction

6

24.69

24.98

0.000102818

Salsk

DCMS

3

DNAJB14 (1)

reproduction

6

24.71

24.97

6.53E-09

Krasnoyarsk

DCMS

3

DNAJB14 (1)

reproduction

6

24.74

24.95

0.000157066

Altai Mountain

DCMS

3

DNAJB14 (1)

reproduction

6

24.74

24.94

8.54E-05

Lezgin

DCMS

3

DNAJB14 (1)

reproduction

6

24.75

24.90

0.005804894

Edillbai

DCMS

1

DNAJB14 (1)

reproduction

6

24.71

24.89

0.000171107

Tuva

DCMS

2

DNAJB14 (1)

reproduction

6

24.65

24.88

6.15E-06

Buubei

DCMS

1

DNAJB14 (1)

reproduction

6

24.71

24.88

0.000392132

Karakul

DCMS

1

DNAJB14 (1)

reproduction

6

24.71

24.86

0.000596432

Karachaev

DCMS

1

DNAJB14 (1)

reproduction

6

34.63

40.33

0

GROUP2

hapFLK

25

MEPE (1) IBSP (2) SPP1 (3) PKD2 (4) ABCG2 (5) LAP3 (6) MED28 FAM184B (8) NCAPG (11) HERC6 (12) LCORL (13) FAM13A (19) SNCA (22)

growth, milk

6

35.67

39.19

8.04E-10

Volgograd

DCMS

19

HERC6 (1) ABCG2 (8) PKD2 (10) SPP1 (11) MEPE (12) IBSP (13) LAP3 (14) FAM184B (16) NCAPG (18) LCORL (19)

growth, milk

6

34.85

38.82

0

All

hapFLK

21

LCORL (1) NCAPG (2) FAM184B (4) LAP3 (6) IBSP (7) MEPE (8) SPP1 (9) PKD2 (10) ABCG2 (11) HERC6 (13) FAM13A (19)

growth, milk

6

36.40

38.62

3.50E-08

Kulundin

DCMS

11

LAP3 (2) FAM184B (3) NCAPG (5) LCORL (6) IBSP (7) MEPE (8) SPP1 (9) PKD2 (10) ABCG2 (11)

growth, milk

6

36.87

38.28

3.13E-11

Baikal

DCMS

6

LAP3 (1) FAM184B (2) NCAPG (4) LCORL (5)

growth

6

36.52

38.24

3.68E-08

Salsk

DCMS

10

LAP3 (2) FAM184B (3) NCAPG (5) LCORL (6) IBSP (7) MEPE (8) SPP1 (9) PKD2 (10) ABCG2 (11)

growth, milk

6

36.45

37.87

5.07E-07

Krasnoyarsk

DCMS

11

PKD2 (1) SPP1 (2) ABCG2 (3) MEPE (4) IBSP (5) LAP3 (6) FAM184B (7) NCAPG (9) LCORL (10)

growth, milk

6

37.23

37.63

3.10E-06

Lezgin

DCMS

4

LCORL (1) NCAPG (2) FAM184B (4)

growth

6

37.36

37.60

0.000701655

Edillbai

DCMS

1

LCORL (1)

growth

6

37.25

37.45

0.008575203

GROUP1

hapFLK

3

NCAPG (1) FAM184B (3)

growth

6

37.35

37.44

0.007856497

Buubei

DCMS

1

LCORL (1)

growth

6

37.09

37.14

0.009452078

Altai Mountain

DCMS

2

LAP3 (1)

growth

6

36.52

36.80

7.87E-05

Baikal

DCMS

3

SPP1 (1) PKD2 (2) ABCG2 (3)

milk

6

36.09

36.51

5.45E-05

Karakul

DCMS

5

HERC6 (1)

growth

6

36.09

36.45

4.06E-07

Lezgin

DCMS

6

HERC6 (2)

growth

6

36.11

36.40

0.000168675

Kulundin

DCMS

4

HERC6 (4)

growth

6

36.05

36.33

0.000432111

Krasnoyarsk

DCMS

5

HERC6 (4)

growth

6

36.23

36.30

0.003706257

Altai Mountain

DCMS

1

HERC6 (1)

growth

6

36.16

36.30

0.000321255

Salsk

DCMS

4

HERC6 (4)

growth

6

34.87

35.07

1.56E-05

Kulundin

DCMS

1

SNCA (1)

milk

6

34.87

35.03

0.000133556

Volgograd

DCMS

1

SNCA (1)

milk

6

34.89

35.02

0.000295081

Krasnoyarsk

DCMS

1

SNCA (1)

milk

6

34.90

35.02

0.000209331

Baikal

DCMS

1

SNCA (1)

milk

6

34.29

34.84

0.003646083

All

hapFLK

1

MMRN1 (1)

acclimation

6

34.72

34.80

0.003960894

Krasnoyarsk

DCMS

1

MMRN1 (1)

acclimation

6

34.50

34.75

6.39E-06

Volgograd

DCMS

1

MMRN1 (1)

acclimation

6

33.28

34.60

0.001085822

GROUP2

hapFLK

1

CCSER1 (1)

feed intake

6

34.22

34.47

8.89E-05

Volgograd

DCMS

1

CCSER1 (1)

feed intake

6

33.33

34.26

0.000135783

All

hapFLK

1

CCSER1 (1)

feed intake

6

59.32

59.45

3.41E-09

Altai Mountain

DCMS

1

RBM47 (1)

growth

6

59.34

59.45

3.26E-06

Groznensk

DCMS

1

RBM47 (1)

growth

6

59.35

59.42

0.004758624

Kulundin

DCMS

1

RBM47 (1)

growth

6

59.36

59.41

0.001116515

Krasnoyarsk

DCMS

1

RBM47 (1)

growth

6

69.84

70.85

5.07E-08

All

hapFLK

4

KIT (1)

coat colour/domestication

6

69.66

70.59

0

GROUP1

hapFLK

3

PDGFRA (1) KIT (2)

acclimation, coat colour/domestication

6

115.08

115.56

0.003511895

GROUP2

hapFLK

5

ADD1 (1)

acclimation

7

20.98

21.22

2.53E-08

Karachaev

DCMS

11

ZFHX2 (1)

temperature sensation

7

20.96

21.11

8.00E-05

Buubei

DCMS

6

ZFHX2 (4)

temperature sensation

7

21.01

21.08

0.005941688

Lezgin

DCMS

1

ZFHX2 (1)

temperature sensation

7

21.00

21.04

5.71E-05

Krasnoyarsk

DCMS

1

ZFHX2 (1)

temperature sensation

7

21.01

21.04

0.000126518

Salsk

DCMS

1

ZFHX2 (1)

temperature sensation

7

21.01

21.04

0.006713729

Altai Mountain

DCMS

1

ZFHX2 (1)

temperature sensation

7

89.24

89.81

2.26E-05

GROUP1

hapFLK

4

TSHR (1)

acclimation

7

89.35

89.55

9.23E-08

Lezgin

DCMS

2

TSHR (2)

acclimation

7

89.39

89.48

0.004845986

Karakul

DCMS

1

TSHR (1)

acclimation

9

77.25

77.91

1.34E-07

Edillbai

DCMS

2

VPS13B (2)

milk

9

77.24

77.87

0.000648121

GROUP1

hapFLK

2

VPS13B (1)

milk

9

77.07

77.17

0.001546422

Karakul

DCMS

1

VPS13B (1)

milk

9

77.09

77.13

0.006246497

Salsk

DCMS

1

VPS13B (1)

milk

10

23.77

24.44

0.000617495

GROUP2

hapFLK

2

UFM1 (1)

Domestication

10

23.60

24.42

9.64E-05

All

hapFLK

3

UFM1 (1)

Domestication

10

23.90

24.31

0.007350694

GROUP1

hapFLK

1

UFM1 (1)

Domestication

10

25.16

30.13

0

All

hapFLK

18

RXFP2 (1) HSPH1 (4)

wool, horns, acclimation

10

28.03

30.10

0

GROUP2

hapFLK

11

RXFP2 (1) HSPH1 (4)

horns, acclimation

10

30.06

30.10

0.005654316

Baikal

DCMS

1

HSPH1 (1)

acclimation

10

28.16

30.00

0

GROUP1

hapFLK

10

RXFP2 (1)

horns

10

29.39

29.75

3.78E-12

Edillbai

DCMS

1

RXFP2 (1)

horns

10

29.36

29.64

2.56E-06

Russian Longhaired

DCMS

1

RXFP2 (1)

horns

10

29.32

29.63

1.23E-06

Romanov

DCMS

1

RXFP2 (1)

horns

10

29.47

29.63

1.14E-05

Karachaev

DCMS

1

RXFP2 (1)

horns

10

29.47

29.55

0.002108118

Groznensk

DCMS

1

RXFP2 (1)

horns

10

29.44

29.49

0.000484163

Altai Mountain

DCMS

1

RXFP2 (1)

horns

10

25.19

28.02

1.42E-07

GROUP2

hapFLK

7

NBEA (1)

wool

10

26.17

26.93

0.000427859

GROUP1

hapFLK

1

NBEA (1)

wool

10

26.55

26.66

0.001229851

Kulundin

DCMS

1

NBEA (1)

wool

10

26.30

26.56

0.000110212

Edillbai

DCMS

1

NBEA (1)

wool

10

26.33

26.41

0.000152487

Groznensk

DCMS

1

NBEA (1)

wool

10

26.15

26.17

0.001280272

Kulundin

DCMS

1

NBEA (1)

wool

10

26.15

26.17

0.009743166

Baikal

DCMS

1

NBEA (1)

wool

10

35.95

36.35

0.000164969

Tuva

DCMS

8

IFT88 (6)

reproduction

10

36.05

36.25

3.80E-05

Edillbai

DCMS

2

IFT88 (2)

reproduction

10

35.99

36.12

0.003724073

Romanov

DCMS

3

IFT88 (1)

reproduction

10

53.47

53.76

0.005873975

GROUP1

hapFLK

1

EDNRB (1)

acclimation

11

36.89

37.00

0.00235957

Volgograd

DCMS

1

B4GALNT2 (1)

reproduction

11

36.92

36.95

0.00700516

Groznensk

DCMS

1

B4GALNT2 (1)

reproduction

11

36.92

36.95

0.002079112

Karachaev

DCMS

1

B4GALNT2 (1)

reproduction

11

36.89

36.94

0.008582697

Karakul

DCMS

1

B4GALNT2 (1)

reproduction

13

41.71

41.86

1.37E-05

Groznensk

DCMS

4

ACSS1 (1)

milk

13

41.70

41.84

5.56E-07

Volgograd

DCMS

4

ACSS1 (1)

milk

13

41.72

41.83

7.68E-06

Altai Mountain

DCMS

3

ACSS1 (1)

milk

13

47.98

49.75

7.29E-11

All

hapFLK

3

PPP1CC (1) BMP2 (2)

body size, reproduction

13

48.34

49.40

1.74E-11

Karachaev

DCMS

3

PPP1CC (1) BMP2 (3)

body size, reproduction

13

48.43

49.30

9.62E-07

GROUP1

hapFLK

3

PPP1CC (1) BMP2 (3)

body size, reproduction

13

48.52

49.30

7.96E-09

Tuva

DCMS

2

PPP1CC (1)

reproduction

13

48.83

49.17

8.51E-11

Kulundin

DCMS

1

PPP1CC (1)

reproduction

13

48.80

49.15

3.36E-08

Salsk

DCMS

1

PPP1CC (1)

reproduction

13

48.84

49.15

5.59E-05

Volgograd

DCMS

1

PPP1CC (1)

reproduction

13

48.83

49.12

4.19E-05

Russian Longhaired

DCMS

1

PPP1CC (1)

reproduction

13

48.83

49.08

0.003588777

Groznensk

DCMS

1

PPP1CC (1)

reproduction

13

48.29

48.66

0.005674193

GROUP2

hapFLK

1

BMP2 (1)

body size

13

63.47

63.91

3.91E-06

Romanov

DCMS

10

ACSS2 (1)

milk

14

7.30

7.48

0.000183645

Karachaev

DCMS

2

GAN (1)

temperature sensation

14

13.59

15.49

0

GROUP1

hapFLK

30

MC1R (1)

coat colour/acclimation

14

13.75

14.80

0

All

hapFLK

22

MC1R (2)

coat colour/acclimation

14

14.15

14.43

2.15E-06

Karachaev

DCMS

8

MC1R (3)

coat colour/acclimation

14

14.14

14.27

1.18E-05

Karakul

DCMS

6

MC1R (3)

coat colour/acclimation

14

14.20

14.26

0.003770506

Lezgin

DCMS

5

MC1R (3)

coat colour/acclimation

14

14.14

14.25

8.10E-05

Tuva

DCMS

5

MC1R (4)

coat colour/acclimation

14

14.20

14.23

0.002109007

Baikal

DCMS

3

MC1R (2)

coat colour/acclimation

14

14.21

14.23

0.005865778

Altai Mountain

DCMS

2

MC1R (1)

coat colour/acclimation

14

54.32

54.41

7.27E-07

Volgograd

DCMS

3

MAMSTR (1)

lipid metabolosm

14

54.33

54.40

2.20E-05

Karachaev

DCMS

1

MAMSTR (1)

lipid metabolosm

14

54.34

54.40

5.36E-05

Baikal

DCMS

2

MAMSTR (1)

lipid metabolosm

14

54.31

54.39

0.000163454

Salsk

DCMS

4

MAMSTR (4)

lipid metabolosm

14

54.35

54.39

0.003248022

Groznensk

DCMS

1

MAMSTR (4)

lipid metabolosm

14

54.31

54.39

0.001065341

Kulundin

DCMS

4

MAMSTR (4)

lipid metabolosm

14

54.34

54.39

0.00166944

Altai Mountain

DCMS

1

MAMSTR (1)

lipid metabolosm

14

54.36

54.39

0.001659425

Romanov

DCMS

1

MAMSTR (1)

lipid metabolosm

15

17.37

17.43

0.001101253

Groznensk

DCMS

1

ATM (1)

milk

15

17.37

17.42

0.003777078

Baikal

DCMS

1

ATM (1)

milk

15

17.37

17.41

0.002123085

Salsk

DCMS

1

ATM (1)

milk

18

65.86

66.20

0.000807705

Tuva

DCMS

3

TECPR2 (1)

temperature sensation

18

65.89

66.04

0.003657536

Lezgin

DCMS

2

TECPR2 (2)

temperature sensation

19

0.85

0.89

0.006060865

Altai Mountain

DCMS

1

EGFR (1)

acclimation

19

6.84

6.88

0.002683568

Edillbai

DCMS

1

CMTM6 (1)

reproduction

19

6.83

6.85

0.006206755

Karakul

DCMS

1

CMTM6 (1)

reproduction

19

31.51

31.87

1.06E-06

GROUP1

hapFLK

1

MITF (1)

coat colour/domestication

19

31.51

31.86

0.000136197

All

hapFLK

1

MITF (1)

coat colour/domestication

19

31.60

31.65

0.002412391

Karakul

DCMS

1

MITF (1)

coat colour/domestication

20

34.19

34.23

0.003574509

Volgograd

DCMS

1

PRL (1)

acclimation

22

41.25

41.33

0.003671941

Buubei

DCMS

1

HTRA1 (1)

reproduction

22

41.23

41.31

0.00040073

Karakul

DCMS

1

HTRA1 (1)

reproduction

22

41.25

41.31

0.006635799

Tuva

DCMS

1

HTRA1 (1)

reproduction

23

25.42

26.46

0

GROUP1

hapFLK

12

DSG@ (1–4), DSC@ (7–9)

wool

23

26.20

26.36

1.05E-05

Russian Longhaired

DCMS

2

DSC@ (1–2)

wool

23

25.90

26.34

5.97E-05

All

hapFLK

5

DSG@ (1–2), DCG@ (3–5)

wool

23

25.90

26.33

8.02E-10

Altai Mountain

DCMS

6

DSG@ (1–3,5), DSC@ (4,6)

wool

23

25.98

26.11

0.002876356

Russian Longhaired

DCMS

3

DSG@ (−3)

wool

23

43.81

44.51

9.44E-06

Salsk

DCMS

3

MC5R (1) MC2R (3)

acclimation

23

43.75

44.06

0.000654721

Baikal

DCMS

3

MC2R (1) MC5R (2)

acclimation

25

18.69

18.88

0.001140569

GROUP1

hapFLK

2

EGR2 (1)

temperature sensation