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Table 4 Expression QTL significantly associated with phenotypic traits

From: Genetic control of longissimus dorsi muscle gene expression variation and joint analysis with phenotypic quantitative trait loci in pigs

Gene

SSC Gene

h2

SSC eQTL

Interval eQTL

Regulatorb

Peak eQTL SNP

Position

Ec

valued

Phenotypee

TEX9

1

3.76e-01

15

27.666–122.219

Distant

H 3GA 0052416

121.806

+

6.09e-04

M eat Quality, Protein Percent

FRM D8

2

4.00e01

2

6.383–12.242

Local

ASGA0098756

12.242

–

7.25e-04

WBS, SP Tenderness, SP

Overall Tenderness

PK P2

5

2.91e-01

15

121.806–121.873

Distant

H 3GA 0052416

121.806

–

9.47e-03

M eat Quality, Protein Percent

NQO1

6

3.28e-01

15

121.806–122.219

Distant

H 3GA 0052416

121.806

+

1.74e-04

M eat Quality, Protein Percent

H PN

6

3.62e-01

6

43.809–72.625

Local

ALGA0113420

68.085

+

1.20e-03

Loin MuscleArea16-wk Last-Rib Backf at 10, 13, 22

M ETTL4

6

1.70e-01

6

99.932–136.022

Local

MA RC0107785

101.29

–

9.55e-04

wk, Carcass 10th- Ri b Backf at, Loin Weight

SSX 21 P

6

4.60e-01

6

120.497–143.338

Local

ALGA0104761

141.317

+

5.27e-03

Carcass 10th- Rib Backf at, Loin Weight

CEP128

7

4.47e-01

15

121.562–122.219

Distant

H 3GA 0052416

121.806

+

1.39e-04

M eat Quality, Protein Percent

CH RNA 9

8

4.21 e-01

15

120.031–122.219

Distant

D I A S0000678

121.562

–

7.96e-05

M eat Quality, Protein Percent

PFKFB3

10

7.44e-03

15

121.806–121.873

Distant

M A RC0027291

121.873

–

5.03e-03

M eat Quality, Protein Percent

SSC11:2.19a

11

5.23e-01

11

0.215–5.406

Local

ALGA0060277

2.798

 

1.05e-04

Loin Weight

SUCLG2

13

2.34e-01

15

120.031–121.873

Distant

M A RC0027291

121.873

–

1.06e-03

M eat Quality, Protein Percent

CI T

14

1.90e-01

15

121.562–122.219

Distant

H 3GA 0052416

121.806

+

9.14e-06

M eat Quality, Protein Percent

CCDC60

14

3.90e-01

15

121.806–122.767

Distant

H 3GA 0052416

121.806

+

1.67e-03

M eat Quality, Protein Percent

M RLN

14

4.00e-01

15

121.562–122.219

Distant

M A RC0027291

121.873

–

1.54e-04

M eat Quality, Protein Percent

SSC15:48.94a

15

1.75e-01

15

121.562–121.873

Distant SC

H 3GA 0052416

121.806

+

4.67e-03

M eat Quality, Protein Percent

  1. aNovel gene transcripts: Sus scrofa chromosome and start position
  2. bRegulator type for eQTL
  3. cEffect the peak eQTL marker has on the gene’s expression: positive indicates B allele increases and negative indicates B allele decreases expression
  4. dqvalue of peak eQTL marker (FDR < 0.01)
  5. ePhenotypes significantly associated with the gene’s expression. Meat Quality includes the phenotypes for sensory panel juiciness, tenderness and overall tenderness, Warner Bratzler Shear Force, Cook Yield, Drip Loss and 24-h pH
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BMC Genomics

ISSN: 1471-2164

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