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Table 3 Top GWAS SNPs for RG level and for six other meat quality traits within the PRKAG3 locus in the DLY pigs

From: Muscle glycogen level and occurrence of acid meat in commercial hybrid pigs are regulated by two low-frequency causal variants with large effects and multiple common variants with small effects

Traits

Peak SNP

Na

Chr

Pos (bp)b

Nearest or candidate genec

MAFd

Effectse

P-valuef

RG

rs339643601

1

3

123,067,585

LRATD1

0.09

0.77

1.08 × 10−5

RG

rs319599168

1

4

84,976,996

TMCO1

0.06

3.00

2.31 × 10−5

RG

rs326377357

8

15

117,255,752

PRKAG3

0.21

10.55

2.54 × 10−11$

pH 36 h

rs81454395

1

15

114,816,163

PRKAG3

0.41

0.06

3.99 × 10−5

Color score

rs80853255

1

15

115,312,329

PRKAG3

0.44

0.15

1.84 × 10−5

Color L*

rs80853255

1

15

115,312,329

PRKAG3

0.44

0.82

3.64 × 10−4

Color a*

rs80925998

1

15

121,364,252

PRKAG3

0.37

0.25

1.44 × 10−5

Color b*

rs80925998

1

15

121,364,252

PRKAG3

0.37

0.32

4.11 × 10−5

Drip loss

rs80925998

2

15

121,364,252

PRKAG3

0.37

0.42

9.92 × 10−6

  1. aNumber of SNPs that surpassed the suggestive significance level within the QTL regions
  2. bPositions of the most significant SNP according to the Sus Scrofa Build 11.1 assembly
  3. cAnnotated gene nearest to the most significant SNP or involved in energy homeostasis (candidate gene shown in italics); gene names starting with ENSSSCG follow the Ensembl nomenclature while other gene symbols follow the HUGO nomenclature
  4. dMinor allele frequency
  5. eAdditive effects
  6. fGenome-wide significant association is indicated with a $ symbol
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Genetics Selection Evolution

ISSN: 1297-9686