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Table 3 Significant SNPs identified for traits in Horro chickens

From: Genome-wide association studies of immune, disease and production traits in indigenous chicken ecotypes

Trait

SNP

Location

Chr (bp)

GWAS

P-value

Additive

effect

(P-value)

Dominance

effect

(P-value)

Phenotypic

variance

(%)

p

q

IBDV

Affx-5Affx-51526157* ,a

5 (15315358)

2.55E−08

0.033 (0.05)

0.035 (0.09)

2

0.03*

0.97

 

AfAffx-51242536* ,a

3 (3148207)

1.96E−07

0.033 (0.01)

−0.014 (0.14)

10

0.12*

0.88

 

Affx-50862142 a,b

2 (139341263)

5.47E−07

0.065 (8E−05)

−0.041 (0.02)

21

0.07*

0.93

 

Affx-51878048 a,b

9 (866678)

1.68E−06

0.0270.04)

0.034 (0.05)

2

0.07*

0.93

 

Affx-51183095 a,b

28 (581149)

8.47E−07

−0.025 (0.04)

0.117 (0.01)

2

0.03

0.97*

 

Affx-50756295 b

18 (5404597)

1.25E−06

−0.003 (0.37)

0.032 (0.00)

7

0.13

0.87*

 

Affx-51884018 a

Z (15058127)

2.31E−06

0.043 (6E−0.4)

−0.025 (0.07)

12

0.08*

0.92

 

Affx-51084536a,b

23 (1467133)

2.72E−06

0.072 (0.002)

−0.048 (0.05)

18

0.04*

0.96

 

Affx-50584797a,b

12 (19824359)

3.88E−06

0.025 (0.027)

0.000 (0.39)

4

0.09*

0.91

MDV

Affx-51262165 a

3 (42096244)

1.05E−06

−0.180 (8E−04)

−0.020 (0.37)

5

0.27

0.63*

 

Affx-50589622a

12 (3932659)

3.34E−06

−0.144 (5E−05)

0.059 (0.22)

5

0.35

0.65*

 

Affx-50758514a

18 (6099330)

7.22E−06

0.383 (5E−05)

NA

10

0.10

0.90*

SG

Affx-50376191 b

1 (51661206)

4.35E−07

–0.041 (0.39)

0.380 (0.03)

2

0.05

0.95*

 

Affx-51254552

3 (38112387)

1.33E−06

−0.032 (0.06)

0.025 (0.09)

2

0.31

0.69*

 

Affx-50583084

Affx-50712674a

12 (19159478)

16 (78709)

3.55E−06

1.20E−04

0.100 (0.08)

0.197 (0.02)

−0.080 (0.14)

−0.000 (0.39)

4

5

0.12*

0.10*

0.88

0.90

PM

Affx-51540438 a

5 (22760016)

2.31E−06

0.081 (9E−04)

0.025 (0.29)

4

0.42*

0.58

 

Affx-50463812a

10 (10377622)

2.76E−06

0.095 (0.01)

0.012 (0.39)

10

0.20*

0.80

 

Affx-50463814a

10 (10378046)

3.19E−06

0.08 (0.03)

0.017 (0.38)

9

0.22*

0.78

 

Affx-50463818a

10 (10379061)

3.19E−06

0.08 (0.03)

0.017 (0.38)

9

0.22*

0.78

Cestodes

Affx-51266852* ,a,b

3 (44583022)

4.03E−08

0.289 (7E−06)

−0.146 (0.03)

11

0.15

0.85*

 

Affx-50313244 a,b

1 (193416334)

6.93E−07

0.131 (1E−06)

−0.051 (0.15)

7

0.30

0.70*

 

Affx-50311899 a,b

1 (18927296)

1.12E−06

0.165 (9E−07)

−0.096 (0.02)

10

0.23

0.77*

 

Affx-51085176 a

23 (1631142)

6.27E−06

0.339 (2E−04)

−0.180 (0.12)

4

0.07*

0.93

Body weight

Affx-51856375 a

9 (22119113)

6.87E−07

−0.044 (0.04)

−0.016 (0.32)

5

0.07

0.93*

 

Affx-50919051 a

2 (40447782)

7.96E−07

−0.041 (1E−06)

0.016 (0.11)

16

0.27

0.73*

 

Affx-51500100a

4 (86100031)

6.26E−06

−0.027 (1E−04)

9E−05 (0.24)

7

0.62

0.38*

 

Affx-50595206a

12 (6188503)

8.96E−06

0.040 (0.03)

−0.008 (0.32)

10

0.19*

0.81

BCS

AfAf fx-51794123* ,a,

8(23157421)

6.28E−08

−0.224 (2E−07)

0.011 (0.39)

7

0.57

0.43*

 

Affx-51794141* ,a

8 (23164238)

6.28E−08

−0.224 (2E−07)

0.011 (0.39)

7

0.57

0.43*

 

Affx-51794116 a

8 (23154277)

2.08E−06

−0.193 (2E−05)

0.050 (0.24)

5

0.38

0.62*

 

Affx-50709156a

15 (8941550)

8.85E−06

0.286 (7E−03)

0.057 (0.39)

5

0.13*

0.87

  1. SNPs with an asterisk * and highlighted in italics exceed the genome-wide threshold. SNPs in italics exceed the suggestive genome-wide threshold. SNPs not highlighted exceed the chromosome-wide threshold
  2. Phenotypic variance:  % proportion of phenotypic variance explained by SNPs; p and q allelic frequencies, with an * mark the frequencies of the alleles corresponding to high antibody titres for IBDV, MDV, SG, PM, low egg counts for cestodes, high body weight and high BCS; NA: not applicable
  3. IBDV infectious bursal disease virus antibody titre, MDV Mareks’ disease virus antibody titre, SG Salmonella enterica serovan Gallinarum antibody titre, PM Pasteurella multocida antibody titre, Cestodes resistance to cestodes parasitism, BCS body condition score, Add additive effects, Dom dominance effects
  4. aSNPs that had significant additive effects
  5. bSNPs that had significant dominance effects