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Table 4 Contributions of five missense mutations and genomic regions to eggshell quality traits at different wk of age

From: Genome-wide association study revealed a promising region and candidate genes for eggshell quality in an F2 resource population

SNP

rs312347405

rs14837998

rs316793137

rs14840004

rs316607577

Region 1

Chromosome

GGA1

GGA1

GGA1

GGA1

GGA1

GGA1

Position (bp)

64,287,542

65,472,759

67,081,703

67,315,919

67,961,420

57.3–71.4 Mb

Gene symbol

PIK3C2G

RECQL

ABCC9

CASC1

ITPR2

-

EA/AAa

C/G

A/G

A/G

T/G

C/T

-

MAF

0.485

0.353

0.414

0.386

0.413

-

Amino acid change

Leu/ Val

Cys/ Arg

Asn/ Asp

Thr/ Pro

Ger/ Gly

-

ESW32

beta (SE)b

−0.253 (0.048)

0.276 (0.051)

0.269 (0.049)

−0.151 (0.051)

0.246(0.052)

-

CPV (%)

5.25

3.36

3.12

0.82

4.90

8.55

ESW40

beta (SE)

−0.361 (0.050)

0.320 (0.050)

0.349 (0.049)

−0.264 (0.050)

0.347(0.051)

-

CPV (%)

7.21

4.79

5.67

3.08

4.78

12.5

ESW44

beta (SE)

−0.285 (0.046)

0.280 (0.052)

0.302 (0.049)

−0.265 (0.051)

0.291(0.051)

-

CPV (%)

8.06

3.37

3.97

2.92

6.08

11.17

ESW48

beta (SE)

−0.286 (0.051)

0.228 (0.056)

0.297 (0.053)

−0.195 (0.055)

0.285(0.056)

-

CPV (%)

7.31

2.33

4.26

1.71

4.93

8.45

ESW52

beta (SE)

−0.321 (0.051)

0.220(0.056)

0.292 (0.053)

−0.179 (0.055)

0.298(0.055)

-

CPV (%)

7.51

2.21

3.86

1.31

7.77

18.54

ESW56

beta (SE)

−0.333 (0.050)

0.251 (0.053)

0.297 (0.021)

−0.124 (0.053)

0.269(0.053)

-

CPV (%)

6.8

2.81

4.13

0.52

7.44

15.25

ESW60

beta (SE)

−0.368 (0.054)

0.276 (0.052)

0.295 (0.049)

−0.215 (0.051)

0.291(0.052)

-

CPV (%)

6.64

3.53

4.11

2.01

5.74

13.77

ESW66

beta (SE)

−0.388 (0.046)

0.252 (0.055)

0.316 (0.052)

−0.234 (0.053)

0.316(0.054)

-

CPV (%)

8.73

2.86

4.82

2.37

5.86

10.15

ESW72

beta (SE)

−0.382 (0.047)

0.252 (0.056)

−0.332 (0.053)

−0.211 (0.055)

0.292(0.056)

-

CPV (%)

8.12

2.92

5.19

1.94

6.90

15.14

EST40

beta (SE)

−0.361(0.054)

0.245(0.052)

0.236(0.05)

−0.158(0.051)

0.198(0.053)

-

CPV (%)

5.33

2.78

2.67

1.07

3.98

5.56

EST44

beta (SE)

−0.313(0.049)

0.211(0.051)

0.225(0.048)

−0.236(0.049)

0.222(0.049)

-

CPV (%)

4.87

2.01

2.27

2.48

3.42

6.15

EST48

beta (SE)

−0.291(0.053)

0.19(0.054)

0.2(0.052)

−0.141(0.053)

0.199(0.053)

-

CPV (%)

4.22

1.62

1.86

0.86

4.55

5.44

EST52

beta (SE)

−0.308(0.051)

0.2(0.054)

0.196(0.05)

−0.141(0.052)

0.168(0.052)

-

CPV (%)

4.63

1.75

1.77

0.81

4.18

5.51

EST56

beta (SE)

−0.312(0.047)

0.222(0.05)

0.234(0.048)

−0.19(0.049)

0.181(0.05)

-

CPV (%)

4.81

2.21

2.68

1.65

5.33

5.61

EST60

beta (SE)

−0.387(0.051)

0.245(0.053)

0.267(0.05)

−0.25(0.051)

0.212(0.052)

-

CPV (%)

7.01

2.72

3.42

2.84

4.21

6.92

EST66

beta (SE)

−0.269(0.047)

0.203(0.052)

0.201(0.048)

−0.178(0.049)

0.171(0.05)

-

CPV (%)

3.49

1.74

1.87

1.33

4.63

4.12

EST72

beta (SE)

−0.339(0.05)

0.165(0.054)

0.237(0.05)

−0.25(0.051)

0.217(0.052)

-

CPV (%)

5.86

1.21

2.77

3.04

4.02

5.35

ESS32

beta (SE)

−0.253(0.048)

0.172(0.049)

0.129(0.047)

−0.128(0.047)

0.126(0.048)

-

CPV (%)

3.18

1.28

0.74

0.73

2.65

2.95

ESS40

beta (SE)

−0.361(0.05)

0.245(0.05)

0.264(0.048)

−0.193(0.049)

0.267(0.05)

-

CPV (%)

6.56

2.80

3.55

1.73

4.82

6.59

ESS44

beta (SE)

−0.285(0.046)

0.189(0.049)

0.185(0.047)

−0.165(0.048)

0.187(0.048)

-

CPV (%)

4.04

1.57

1.63

1.21

2.43

4.11

ESS48

beta (SE)

−0.286(0.051)

0.152(0.054)

0.149(0.051)

−0.129(0.052)

0.183(0.052)

-

CPV (%)

4.16

0.96

1.04

0.78

3.56

4.22

ESS52

beta (SE)

−0.321(0.051)

0.169(0.054)

0.241(0.05)

−0.17(0.052)

0.224(0.052)

-

CPV (%)

5.30

1.20

2.97

1.39

5.62

5.26

ESS56

beta (SE)

−0.333(0.05)

0.217(0.052)

0.207(0.05)

−0.142(0.051)

0.21(0.052)

-

CPV (%)

5.64

2.18

2.13

0.92

6.10

5.56

ESS60

beta (SE)

−0.368(0.054)

0.303(0.06)

0.318(0.055)

−0.233(0.058)

0.227(0.058)

-

CPV (%)

6.70

4.09

4.68

2.29

11.52

16.12

ESS66

beta (SE)

−0.388(0.046)

0.226(0.052)

0.25(0.048)

−0.229(0.049)

0.304(0.049)

-

CPV (%)

7.59

2.31

3.15

2.43

5.86

6.06

ESS72

beta (SE)

−0.382(0.047)

0.26(0.053)

0.271(0.049)

−0.239(0.051)

0.235(0.051)

-

CPV (%)

7.35

3.06

3.62

2.70

5.16

6.75

  1. EA effect allele (minor allele), AA alternative allele (major allele), MAF minor allele frequency, CPV contribution to phenotypic variance (%), ESW32, ESW40, ESW44, ESW48, ESW52, ESW56, ESW60 eggshell weights of 32, 40, 44, 48, 52, 56, 60, 66, 72 weeks of age
  2. aEstimated allelic substitution effect per copy of the effect allele (EA); SE standard error of the beta bBeta means the effect size of minor alleles. Positive/negative effect size value means that the substitution of major allele to minor allele can lead to heavier/lighter yolk or ovary weight