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Table 2 QTL regions with at least one SNP with a P -value less than 5.10 -5

From: A genome-wide association study of production traits in a commercial population of Large White pigs: evidence of haplotypes affecting meat quality

 

QTL1

Thresholds2

Positions of flanking markers (kb)

Traits3

Effects in STD4(min-max)

  

5.10-4

5.10-5

5.10-6

   

Growth rate, feed intake, feed efficiency

3a

2

1

0

100 098–100 119

FCR

0.29 – 0.33

6a

4

3

0

27 650–28 138

RFI

0.41 – 0.46

11

1

1

0

48 555

FCR

0.36

18b

4

1

0

17 724–17 817

FCR

0.29 – 0.33

Carcass traits

1c

4

4

0

45 536–45 998

BELLY

0.57 – 0.59

3b

5

3

0

109 719–110 511

BELLY

0.43 – 0.55

6b

7

1

0

134 691–135 078

BACKFAT- ELMC- HAM

0.25 – 0.32

7

10

2

1

100 145–105 315

CL

0.28 – 0.40

9b

2

1

0

116 328–116 390

LOIN

0.33 – 0.42

10

3

1

1

2 015 – 2 080

BELLY

0.28 – 0.35

14

5

1

0

139 323–140 810

BACKFAT- ELMC - CBF - CL

0.29 – 0.39

15

3

1

0

137 725–139 857

DP

0.30 – 0.52

16a

6

2

0

34 003–35 190

HAM

0.30 – 0.39

16b

17

5

1

82 092–82 664

BACKFAT- ELMC

0.30 – 0.45

17

4

3

3

16 788–17 549

CL

0.28 – 0.42

18a

9

1

1

7 813 – 11 122

HAM- ELMC - CBF - BELLY

0.27 – 0.40

Meat quality traits

1a

14

3

1

8 715–12 869

a*GS - b*GS - L*GS

0.27 – 0.35

1b

7

2

0

30 337–32 684

pH24 SM - b*GS - MQI

0.28 – 0.32

1d

16

8

4

80 701–80 884

b*GS - L*GS - MQI

0.30 – 0.49

4

5

2

0

80 963–82 252

a*GS

0.27 – 0.38

8

6

2

2

124 786–129 300

pH24 SM - b*GS - MQI

0.29 – 0.45

9a

7

3

2

11 043–11 445

L*GS - MQI

0.27 – 0.37

13

3

1

1

24 391–29 002

L*GS - MQI

0.29 – 0.75

  1. Lines in bold are regions where at least one SNP had a P-value < 5.10-6; 1QTL region as defined by the chromosome number and location (letters are ordered by positions on chromosomes, see Figure 2); 2For each QTL region, the number of SNP × trait combinations with a P-value lower than the corresponding threshold; 3see Table 1 for trait abbreviations; 4STD = phenotypic standard deviation estimated on phenotypes adjusted for systematic environmental effects.