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Table 4 Top genome-wide significant SNPs associated with growth, body measurements, carcass measurements and fat area

From: SNP- and haplotype-based genome-wide association studies for growth, carcass, and meat quality traits in a Duroc multigenerational population

  

Most significant SNP

Haplotype-based

Nearby genesg

Traita

SSCb

Positionc (bp)

refSNP variation ID

EAd

EAFd

β (SE)

Proportione

P-value

P-valuef

 

Growth

 

DG

1

304,667,314

rs81352956

A

0.454

−34.75 (6.035)

0.06

1.22 × 10−8

6.71 × 10−6 h

PRDM12_EXOSC2

 

BF

1

304,694,455

rs81352969

A

0.495

0.18 (0.029)

0.07

6.30 × 10−10

2.26 × 10−5 h

ABL1

  

10

27,636,391

rs81422289

G

0.227

0.17 (0.034)

0.04

7.04 × 10−7

3.63 × 10−2

KIF14

Body measurements

 

CW

1

304,694,455

rs81352969

A

0.495

0.45 (0.084)

0.05

1.17 × 10−7

1.45 × 10−4

ABL1

 

CC

1

304,694,455

rs81352969

A

0.495

0.87 (0.148)

0.06

6.82 × 10−9

3.36 × 10−5 h

ABL1

 

CCB at F105

7

39,512,713

rs80892802

G

0.171

0.29 (0.045)

0.07

3.14 × 10−10

1.75 × 10−3

DNAH8

 

CCB at R105

7

39,089,506

rs196955082

G

0.249

0.21 (0.039)

0.05

4.38 × 10−8

1.19 × 10−3

BTBD9

Carcass measurements

 

CL

7

103,457,401

VRTN

C

0.368

1.13 (0.187)

0.14

3.64 × 10−9

3.36 × 10−6 h

VRTN

 

CL1

7

103,457,401

VRTN

C

0.368

1.13 (0.162)

0.18

1.56 × 10−11

4.87 × 10−8 H

VRTN

 

CL2

7

103,457,401

VRTN

C

0.368

1.37 (0.172)

0.22

2.96 × 10−14

2.22 × 10−9 H

VRTN

  

7

107,279,922

rs80977788

G

0.267

−0.97 (0.196)

0.09

1.20 × 10−6

1.25 × 10−5 h

NRXN3

 

CL3

7

103,457,401

VRTN

C

0.368

1.48 (0.159)

0.27

3.10 × 10−18

1.94 × 10−11 H

VRTN

  

7

106,308,596

rs80813652

G

0.311

1.02 (0.177)

0.12

2.14 × 10−8

1.55 × 10−5 h

LOC102158165

  

11

53,204,914

rs330963199

G

0.253

−1.00 (0.191)

0.10

3.32 × 10−7

1.31 × 10−2

LOC102167198

 

TVN

7

101,863,838

rs80966250

G

0.349

−0.35 (0.059)

0.13

9.93 × 10−9

4.44 × 10−16 H

LOC102164420_LOC102164550

  

7

103,457,401

VRTN

C

0.368

0.67 (0.046)

0.50

9.42 × 10−37

4.44 × 10−16 H

VRTN

  

7

106,308,596

rs80813652

G

0.311

0.44 (0.056)

0.20

5.17 × 10−14

2.67 × 10−9 H

LOC102158165

 

BSFT

18

7,107,781

rs81345146

A

0.361

−0.19 (0.037)

0.10

4.37 × 10−7

7.80 × 10−4

ZYX

 

LSFT

9

46,466,374

rs81257576

A

0.017

0.65 (0.129)

0.07

7.36 × 10−7

4.41 × 10−1

ZBTB16_NNMT

 

LEA at 45r

9

124,098,143

rs81415869

G

0.023

3.98 (0.746)

0.10

1.94 × 10−7

8.35 × 10−1

LOC102162561_LOC100524389

Fat area of carcass cross section at 4–5 rib

 

IFAat 45r

8

25,653,506

rs81398418

A

0.279

7.15 (1.380)

0.09

4.18 × 10−7

1.14 × 10−4

LOC100624133_LOC102162593

Fat area of carcass cross section at the middle

 

SFA at HBL

7

41,720,015

rs80928067

G

0.030

−16.52 (3.219)

0.11

5.35 × 10−7

5.11 × 10−1

LOC100737927

 

ALLFA at HBL

7

41,720,015

rs80928067

G

0.030

−30.43 (5.433)

0.13

5.09 × 10−8

5.41 × 10−1

LOC100737927

  1. aAbbreviations of trait are shown in Table 2
  2. b SSC Sus Scrofa chromosome
  3. cPosition for genome build 10.2
  4. d EA effect allele, EAF effect allele frequency
  5. eThe proportion of phenotypic variance explained by the SNP effects
  6. fThe results of haplotype-based association study are indicated by h = suggestive, H = significant difference
  7. gNearby genes are bolded if SNP is within the reference gene