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Table 3 Description of SNPs significantly associated with meat quality traits in Erhualian and DLY pigs

From: Genome-wide association analyses for meat quality traits in Chinese Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) commercial population

Traits 2

Peak SNP

No. 3

Chr

Pos (bp) 4

PPL 5

Nearest genes 6

Freq 7

Effects 8

P -value 9

EHL 1

         

LM_pH24h

ss131409440

1

9

144 399 17

 

INTS7

0.67

0.088

9.78E-06

SM_pH24h

ss131225834

1

3

15 271 92

 

WBSCR17

0.33

0.185

3.13E-06

LM_pHdrop_45min-24 h

ss107857062

1

16

79 490 30

c

SEMA5A

0.53

0.158

8.05E-06

LM_DripEZ_24h

ss131261254

1

4

44 336 60

 

ENSSSCG00000019169

0.15

0.686

7.97E-09

LM_DripEZ_24h

ss478940762

2

4

35 761 053

 

RIMS2

0.12

0.618

2.62E-06

LM_DripEZ_24h

ss131270350

1

4

85 151 430

 

ST18

0.14

1.092

6.26E-06

SM_DripEZ_24h

ss131134976

1

1

181 797 733

 

MEGF11

0.50

0.247

2.31E-06

LM_ColorM_a24h

ss131341943

1

7

31 500 144

 

KLHL31

0.60

0.505

9.1E-06

LM_ColorM_a24h

ss478937995

3

12

58 130 567

b

MYH3

0.18

0.945

1.04E-05

LM_ColorM_a24h

ss131565824

1

5

2 588 817

 

EFCAB6

0.65

0.545

1.18E-05

LM_ColorM_b24h

ss120027962

1

14

11 463 494

 

BNIP3L

0.02

1.628

3.64E-06

LM_ColorM_b24h

ss478937995

2

12

58 130 567

b

MYH3

0.18

0.976

1.65E-05

LM_ColorScore_24h

ss131352394

1

7

5 406 955

a

EEF1E1

0.74

0.234

5.49E-06

LM_ColorScore_24h

ss131461879

1

12

36 158 023

 

SUPT4H1

0.63

0.208

2.29E-05

SM_ColorM_b24h

ss107878019

1

12

9 939 154

 

ENSSSCG00000025361

0.95

1.435

1.88E-05

SM_ColorScore_24h

ss478943784

1

17

56 358 556

 

SULF2

0.33

0.235

7.70E-06

LM_MoistureContent

ss131186989

1

2

43 911 957

 

LDHA

0.01

1.010

5.18E-06

LM_MoistureContent

ss131458048

1

12

24 427 829

 

NFE2L1

0.01

0.860

5.31E-06

LM_MoistureContent

ss131054125

1

8

14 014 229

 

ENSSSCG00000029791

0.51

0.653

8.07E-06

LM_MoistureContent

ss131538960

2

16

74 982 852

c

MFAP3

0.86

1.112

1.67E-05

LM_Firmness

ss131096544

2

12

57 123 997

b

WDR16

0.72

0.232

4.10E-06

LM_Firmness

ss478937524

1

7

7 764 396

a

TMEM14C

0.64

0.225

1.81E-05

DLY 1

         

LM_DripEZ_36h

ss131494523

1

13

141 530 003

 

FAM43A

0.36

0.435

1.53E-05

LM_DripEZ_36h

ss131400253

1

9

95 957 104

d

SNX13

0.88

0.740

1.57E-05

LM_ColorM_a36h

ss107833468

1

15

134 397 712

e

RESP18

0.37

0.245

1.78E-05

LM_ColorM_b36h

ss107856037

1

15

92 671 886

 

AGPS

0.32

0.569

9.17E-06

LM_ColorScore_36h

ss131398982

1

9

84 832 035

d

ASNS

0.62

0.122

4.78E-06

LM_ColorScore_36h

ss131528409

1

15

127 419 860

e

IKZF2

0.56

0.153

7.27E-06

LM_ColorScore_36h

ss107897208

1

9

45 577 347

 

NCAM1

0.44

0.148

9.96E-06

LM_ColorScore_36h

ss107799219

1

0

0

  

0.98

0.543

1.46E-05

LM_Firmness

ss131184920

1

2

34 977 540

 

KIF18A

0.37

0.172

1.47E-05

  1. 1Chinese Erhualian indigenous population and Western Duroc × (Landrace × Yorkshire) commercial population; 2description of the traits is in Table 1; 3number of SNPs that surpassed the suggestive significance level within the QTL regions; 4positions of the most significant SNP according to the Sus Scrofa Build 10.2 assembly; 5possible pleiotropic loci (PPL) were indicated by common letters on different rows; 6annotated genes nearest to the most significant SNP; gene names starting with ENSSSCG follow the Ensembl nomenclature while other gene symbols follow the HUGO nomenclature; 7,8frequencies and effects of the allele that increases phenotype value in the two populations; 9genome-wide significant associations are underlined.
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Genetics Selection Evolution

ISSN: 1297-9686