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Table 3 List of SNPs associated with clinical mastitis occurrence and three mastitis indicator traits in Chios sheep

From: The genomic architecture of mastitis resistance in dairy sheep

Trait

Lactation stage

SNP

aChr(position)

GAS

a

d

PVA

PVP

p

q

    

P-value

(P-value)

(P-value)

    

SCC

early (weeks 1–7)

oar3_OAR19_27,830,713

19(27830713)

5.54E-04

−0.39(0.00)

−0.09(0.42)

0.36

0.04

0.62

0.38

  

oar3_OAR19_27,397,476

19(27397476)

7.74E-04

−0.41(0.03)

0.32(0.15)

0.38

0.04

0.34

0.66

  

OAR19_29193780

19(27558690)

8.00E-04

0.46(0.00)

0.30(0.04)

0.4

0.04

0.75

0.25

  

OAR19_29776311

19(28134366)

1.28E-03

0.33(0.09)

0.09(0.26)

0.12

0.01

0.87

0.13

 

late (weeks 18–23)

oar3_OAR2_208,650,955

2(208650955)

2.31E-05

−0.24(0.07)

−0.52(0.00)

0.19

0.01

0.71

0.29

  

oar3_OAR2_206,805,418

2(206805418)

8.25E-05

−0.27(0.00)

0.45(0.13)

0.07

0

0.99

0.01

  

OAR2_219641896

2(207420807)

1.65E-04

−0.14(0.46)

0.22(0.25)

0.01

0

0.83

0.17

  

OAR2_216496832

2(204569747)

1.89E-04

−0.22(0.04)

0.01(0.91)

0.11

0.01

0.38

0.62

  

oar3_OAR2_208,711,940

2(208711940)

6.73E-04

0.11(0.41)

−0.68(0.00)

0.18

0

0.19

0.81

  

oar3_OAR2_207,141,059

2(207141059)

9.52E-04

−0.14(0.00)

−0.84(0.00)

0.14

0

0.96

0.04

  

oar3_OAR2_205,201,880

2(205201880)

1.44E-03

−0.28(0.01)

0.03(0.79)

0.08

0.01

0.64

0.36

  

oar3_OAR2_204,683,757

2(204683757)

1.51E-03

−0.20(0.04)

0.09(0.42)

0.04

0.01

0.49

0.51

  

oar3_OAR19_27,100,147

19(27100147)

2.75E-05

0.52(0.02)

0.63(0.00)

0.39

0.03

0.85

0.15

 

overall (weeks 1–23)

OAR16_38842323

16(35633299)

1.69E-03

−0.18(0.01)

0.12(0.13)

0.04

0

0.8

0.2

  

oar3_OAR19_27,830,713

19(27830713)

1.45E-03

−0.21(0.01)

0.15(0.16)

0.09

0.01

0.62

0.38

CMT

early (weeks 1–7)

oar3_OAR19_27,397,476

19(27397476)

3.67E-04

−0.36(0.00)

0.07(0.50)

0.28

0.03

0.34

0.66

  

oar3_OAR19_27,100,147

19(27100147)

3.93E-04

0.57(0.06)

0.33(0.31)

0.39

0.05

0.85

0.15

  

OAR19_29776311

19(28134366)

4.78E-04

0.37(0.05)

0.10(0.60)

0.15

0.02

0.87

0.13

  

OAR19_29193780

19(27558690)

9.22E-04

0.42(0.00)

0.21(0.12)

0.31

0.04

0.75

0.25

  

oar3_OAR19_27,723,161

19(27723161)

1.18E-03

0.34(0.04)

0.11(0.54)

0.14

0.02

0.85

0.15

 

mid (weeks 8–17)

oar3_OAR19_27,830,713

19(27830713)

4.31E-04

−0.20(0.01)

0.09(0.35)

0.11

0.01

0.62

0.38

  

OAR19_27896777

19(26442150)

6.20E-04

0.61(0.01)

0.15(0.56)

0.19

0.04

0.91

0.09

  

oar3_OAR19_27,264,253

19(27264253)

9.35E-04

0.20(0.01)

−0.02(0.79)

0.11

0.01

0.59

0.41

 

late (weeks 18–23)

oar3_OAR2_206,805,418

2(206805418)

9.71E-04

−0.19(0.00)

0.29(0.28)

0.03

0

0.99

0.01

  

oar3_OAR3_130,101,204

3(130101204)

1.18E-03

0.12(0.00)

0.14(0.15)

0.01

0

0.9

0.1

  

OAR3_130,096,528.3SR

3(130096528)

1.32E-03

0.93(0.17)

0.98(0.16)

0.43

0.07

0.9

0.1

  

oar3_OAR16_35,319,166

16(35319166)

4.60E-04

−0.22(0.12)

0.26(0.16)

0.04

0.01

0.81

0.19

  

OAR16_37125504

16(34187287)

1.21E-03

−0.69(0.02)

−0.38(0.23)

0.24

0.04

0.89

0.11

  

oar3_OAR19_27,100,147

19(27100147)

1.79E-05

0.63(0.00)

0.79(0.00)

0.27

0.05

0.85

0.15

  

oar3_OAR19_26,711,220

19(26711220)

7.13E-04

0.08(0.00)

−0.03(0.74)

0.01

0

0.93

0.07

  

oar3_OAR19_27,830,713

19(27830713)

1.16E-03

−0.20(0.01)

0.09(0.35)

0.05

0.01

0.62

0.38

  

OAR16_37125504

16(34187287)

1.21E-03

−0.69(0.02)

−0.38(0.23)

0.24

0.04

0.89

0.11

 

overall (weeks 1–23)

OAR16_37125504

16(34187287)

1.08E-03

−0.22(0.26)

0.12(0.56)

0.04

0.01

0.89

0.11

  

oar3_OAR19_27,100,147

19(27100147)

1.09E-03

0.36(0.03)

0.42(0.01)

0.51

0.02

0.85

0.15

  

oar3_OAR19_27,830,713

19(27830713)

1.16E-03

−0.18(0.00)

0.09(0.21)

0.07

0.01

0.62

0.38

  

oar3_OAR19_27,830,713

19(27830713)

8.81E-04

−0.27(0.00)

0.08(0.37)

0.2

0.04

0.62

0.38

TVC

early (weeks 1–7)

OAR2_219801849

2(207575434)

5.81E-09

0.27(0.00)

−0.23(0.03)

0.33

0.02

0.25

0.75

 

late (weeks 18–23)

OAR2_219838408_X

2(207609417)

1.49E-08

0.22(0.03)

−0.17(0.11)

0.22

0.02

0.26

0.74

  

OAR2_219641896

2(207420807)

1.26E-06

−0.15(0.27)

−0.08(0.59)

0.07

0.01

0.83

0.17

  

oar3_OAR2_209,240,636

2(209240636)

2.85E-06

−0.19(0.51)

−0.32(0.09)

0.05

0

0.93

0.07

  

oar3_OAR2_208,650,955

2(208650955)

2.26E-05

−0.12(0.18)

−0.32(0.00)

0.07

0

0.71

0.29

  

oar3_OAR2_206,805,418

2(206805418)

4.11E-04

−0.15(0.00)

0.28(0.19)

0.03

0

0.99

0.01

  

OAR2_220844191

2(208597501)

4.81E-04

−0.10(0.22)

−0.16(0.10)

0.05

0

0.69

0.31

  

oar3_OAR2_206,036,682

2(206036682)

1.24E-03

−0.49(0.00)

−0.50(0.00)

0.12

0.01

0.84

0.16

 

overall (weeks 1–23)

OAR16_38842323

16(35633299)

1.27E-03

0.05(0.00)

−0.01(0.84)

0.06

0

0.8

0.2

  

OAR16_37125504

16(34187287)

1.32E-03

−0.30(0.01)

−0.13(0.29)

0.15

0.01

0.89

0.11

  

OAR19_27896777

19(26442150)

9.83E-04

0.16(0.16)

−0.03(0.79)

0.07

0

0.91

0.09

CM

 

OAR16_39143709

16(35930429)

6.98E-06

−1.72(0.36)

0.41(0.52)

0.25

0.05

0.54

0.46

 

early (weeks 1–7)

OAR16_37226202

16(34279856)

4.16E-04

2.04(0.02)

−0.80(0.39)

0.28

0.05

0.51

0.49

  

s74559

16(35801129)

4.41E-04

3.50(0.53)

2.81(0.61)

0.33

0.02

0.58

0.42

  

OAR16_37419505

16(34392335)

1.21E-03

−3.27(0.06)

1.74(0.16)

0.19

0.05

0.62

0.38

  

OAR16_37539041

16(34550197)

1.76E-03

1.60(0.01)

−1.17(0.13)

0.26

0.05

0.39

0.61

  

oar3_OAR19_28,110,151

19(28110151)

6.23E-06

0.98(0.04)

0.74(0.12)

0.25

0.05

0.86

0.14

  

OAR19_29776311

19(28134366)

5.92E-05

1.02(0.05)

0.88(0.13)

0.25

0.04

0.87

0.13

  

OAR19_29193780

19(27558690)

4.95E-04

3.02(0.76)

2.66(0.79)

0.21

0.04

0.75

0.25

  

oar3_OAR19_27,018,360

19(27018360)

8.26E-04

−1.11(0.05)

0.95(0.12)

0.26

0.05

0.46

0.54

  

OAR5_104431404

5(95881956)

1.18E-06

0.82(0.00)

0.29(0.39)

0.35

0.06

0.6

0.4

 

mid (weeks 8–17)

oar3_OAR5_96,114,753

5(96114753)

8.66E-06

0.87(0.00)

0.41(0.25)

0.39

0.07

0.59

0.41

  

OAR5_104389335_X

5(95841910)

2.28E-05

1.02(0.02)

−1.01(0.06)

0.27

0.09

0.64

0.36

  

oar3_OAR5_96,077,046

5(96077046)

1.08E-04

0.59(0.03)

0.89(0.05)

0.12

0.03

0.41

0.59

  

oar3_OAR5_96,062,963

5(96062963)

1.07E-03

0.44(0.07)

−0.22(0.14)

0.12

0.02

0.43

0.57

  

OAR16_37226202

16(34279856)

1.26E-03

2.02(0.02)

1.27(0.03)

0.21

0.04

0.51

0.49

  

OAR16_37539041

16(34550197)

1.94E-03

1.60(0.01)

−1.17(0.13)

0.26

0.05

0.39

0.61

  

oar3_OAR19_26,565,985

19(26565985)

5.65E-04

−0.70(0.04)

0.32(0.48)

0.25

0.05

0.52

0.48

  

oar3_OAR19_26808003

19(268,080,030

6.95E-04

−0.58(0.05)

−0.07(0.97)

0.14

0.02

0.74

0.26

  

OAR19_29482474

19(27864985)

1.30E-03

−3.49(0.86)

−3.33(0.87)

0.23

0.04

0.1

0.9

 

late (weeks 18–23)

oar3_OAR5_96,114,753

5(96114753)

1.81E-03

1.00(0.03)

0.81(0.10)

0.42

0.08

0.59

0.41

  

OAR5_104431404

5(95881956)

2.89E-04

0.98(0.03)

0.71(0.15)

0.4

0.07

0.6

0.4

  

OAR5_104389335_X

5(95841910)

9.99E-04

0.47(0.04)

0.66(0.17)

0.21

0.02

0.64

0.36

  

oar3_OAR5_96,114,753

5(96114753)

1.14E-03

0.62(0.01)

0.32(0.25)

0.24

0.04

0.59

0.41

  

OAR19_29776311

19(28134366)

1.08E-03

1.08(0.00)

1.07(0.01)

0.28

0.05

0.87

0.13

  

oar3_OAR19_27,264,253

19(27264253)

1.31E-03

1.00(0.03)

0.23(0.64)

0.42

0.08

0.59

0.41

  

oar3_OAR19_28,110,151

19(28110151)

1.53E-04

0.98(0.05)

0.74(0.21)

0.25

0.05

0.86

0.14

  

oar3_OAR19_26,565,985

19(26565985)

5.21E-04

−0.42(0.06)

−0.06(0.82)

0.1

0.02

0.52

0.48

  

OAR19_29193780

19(27558690)

1.35E-03

0.56(0.10)

0.08(0.82)

0.15

0.02

0.75

0.25

 

overall (weeks 1–23)

oar3_OAR2_207,141,059

2(207141059)

1.25E-03

−0.24(0.00)

−1.95(0.01)

0.1

0

0.96

0.04

  

oar3_OAR19_27,264,253

19(2726253)

1.35E-03

0.88(0.00)

0.11(0.71)

0.36

0.07

0.59

0.41

  1. SCC log-transformed milk somatic cell counts; CMT California mastitis Test; TVC total viable bacterial count in milk; CM occurrence of clinical mastitis
  2. aChr(position) is based on the Oar v3.1 assembly; GAS P–value: P-value from genomic association study (genome-wide significant in bold, suggestive significance otherwise); a: additive allele substitution effect; d: dominance effect; PVA: proportion of the genetic variance explained by the SNP; PVP: proportion of the phenotypic variance explained by the SNP; p and q allelic frequencies. No significant associations were identified for TVC and SCC in mid lactation