Skip to main content

Table 4 A summary of top lead SNPs of each chromosome in significant association with carcass merit traits based on imputed 7.8 M WGS variant GWAS with a threshold value of P-value < 10−5 in a beef cattle multibreed population

From: Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: II: carcass merit traits

Traita

Lead SNP

Numb

Chr

Pos (bp)

Nearest Genec

Distance (bp)d

Annotatione

P-value

FDRf

b ± SEg

Var_Phe (%)h

HCW

rs467949024

3

2

94,243,607

ENSBTAG00000046783

41,253

intergenic_region

8.45E-06

4.95E-02

11.17 ± 2.51

0.62

HCW

Chr6:39111019

128

6

39,111,019

LCORL

118,907

intergenic_region

1.37E-22

1.74E-16

20.73 ± 2.12

4.79

HCW

rs109658371

185

6

39,213,566

LCORL

221,454

intergenic_region

2.98E-23

1.74E-16

20.2 ± 2.03

4.65

HCW

rs210782610

68

7

93,205,703

ARRDC3

34,716

intergenic_region

5.15E-08

7.80E-04

9.73 ± 1.79

1.10

HCW

rs380715719

27

8

18,612,164

TUSC1

42,366

intergenic_region

8.67E-06

5.03E-02

−7.54 ± 1.69

0.56

HCW

rs385024196

12

9

93,866,211

ENSBTAG00000035623

196,060

intergenic_region

9.20E-06

5.19E-02

11.06 ± 2.49

0.58

HCW

rs109815800

48

14

25,015,640

PLAG1

6344

intergenic_region

1.26E-21

5.82E-16

−21.9 ± 2.29

3.41

HCW

rs384702880

30

16

38,967,953

GORAB

43,016

intergenic_region

7.45E-06

4.53E-02

−8.73 ± 1.95

0.60

HCW

rs472775501

1

17

63,413,884

RASAL1

Within

intron_variant

1.59E-06

1.45E-02

18.73 ± 3.9

0.57

HCW

rs379088920

7

18

2,001,155

GLG1

Within

intron_variant

9.83E-06

5.49E-02

−12.84 ± 2.9

0.52

HCW

rs41934045

123

20

4,563,925

ERGIC1

Within

intron_variant

3.66E-11

1.23E-06

13.22 ± 2

1.47

HCW

Chr21:20514810

27

21

20,514,810

ENSBTAG00000001526

11,408

intergenic_region

4.92E-06

3.39E-02

−18.69 ± 4.09

0.60

HCW

rs110918739

26

26

19,498,886

HPS1

112,317

intergenic_region

3.91E-06

2.88E-02

−8.42 ± 1.83

0.65

HCW

rs452209056

0

28

29,895,281

CAMK2G

Within

intron_variant

8.09E-06

4.78E-02

20.57 ± 4.61

0.53

AFAT

rs42820451

14

3

77,060,742

DEPDC1

32,480

intergenic_region

9.75E-06

2.97E-01

−0.42 ± 0.09

0.72

AFAT

rs41594006

69

4

28,702,952

MACC1

133,040

intergenic_region

2.46E-07

1.77E-02

0.73 ± 0.14

1.07

AFAT

rs110995268

61

6

38,914,196

LCORL

Within

intron_variant

1.64E-12

9.39E-07

− 0.85 ± 0.12

2.87

AFAT

rs384948399

114

7

50,565,278

KLHL3

100,732

intergenic_region

5.70E-06

2.00E-01

0.67 ± 0.15

0.70

AFAT

rs380092738

12

8

45,378,038

PIP5K1B

23,538

intergenic_region

2.18E-06

9.46E-02

−0.6 ± 0.13

0.83

AFAT

rs209683528

96

8

45,076,648

FAM122A

100,581

intergenic_region

8.62E-06

2.75E-01

−0.72 ± 0.16

0.78

AFAT

rs470535700

0

11

102,954,409

SPACA9

Within

intron_variant

2.81E-06

1.15E-01

−0.62 ± 0.13

0.84

AFAT

rs209930593

84

13

63,970,531

RALY

Within

intron_variant

1.87E-06

8.29E-02

−0.64 ± 0.13

0.81

AFAT

rs134958846

142

14

24,894,463

LYN

Within

intron_variant

5.63E-06

2.00E-01

0.69 ± 0.15

0.82

AFAT

Chr15:50136986

11

15

50,136,986

ENSBTAG00000039298

3061

upstream_gene_variant

2.64E-06

1.09E-01

−1.15 ± 0.25

0.73

AFAT

rs381910687

26

16

24,333,881

RAB3GAP2

Within

downstream_gene_variant

5.89E-07

3.10E-02

−0.63 ± 0.13

0.98

AFAT

rs133531965

26

17

62,789,778

RBM19

96,955

intergenic_region

9.61E-06

2.95E-01

−0.44 ± 0.1

0.79

AFAT

rs464417711

8

28

5,603,922

U6

11,263

intergenic_region

3.43E-06

1.31E-01

1.96 ± 0.42

0.66

AFAT

rs714693579

62

29

32,805,714

KCNJ1

18,117

intergenic_region

4.63E-06

1.68E-01

−0.9 ± 0.2

0.70

REA

rs110874471

101

2

6,210,115

MSTN

3451

upstream_gene_variant

6.05E-07

5.04E-03

1.33 ± 0.27

0.80

REA

rs109890976

184

4

80,815,147

SUGCT

51,830

intergenic_region

3.95E-06

2.87E-02

1.63 ± 0.35

0.66

REA

rs109658371

164

6

39,213,566

LCORL

221,454

intergenic_region

3.05E-17

2.39E-10

2.37 ± 0.28

3.32

REA

rs109901274

78

7

93,244,933

ARRDC3

Within

missense_variant

5.28E-08

9.39E-04

1.36 ± 0.25

1.11

REA

rs109777279

33

9

57,219,389

ENSBTAG00000003743

296,654

intergenic_region

1.42E-06

1.09E-02

1.98 ± 0.41

0.74

REA

rs381345179

54

13

69,321,377

ENSBTAG00000045562

285,750

intergenic_region

6.28E-06

4.40E-02

1.72 ± 0.38

0.59

REA

rs135551190

24

14

24,977,053

MOS

105

upstream_gene_variant

4.40E-07

3.98E-03

−1.76 ± 0.35

0.83

REA

rs208370128

6

23

49,370,473

LYRM4

Within

intron_variant

2.30E-07

2.60E-03

2.3 ± 0.44

0.83

REA

Chr29:47488685

5

29

47,488,685

CCND1

55,695

intergenic_region

5.66E-07

4.84E-03

1.62 ± 0.32

0.70

LMY

rs383507504

64

1

58,167,076

GTPBP8

492

downstream_gene_variant

2.91E-06

1.27E-01

0.49 ± 0.1

0.79

LMY

rs136199724

22

2

123,199,149

PUM1

2620

downstream_gene_variant

6.29E-06

2.00E-01

0.72 ± 0.16

0.67

LMY

Chr3:46944817

50

3

46,944,817

PTBP2

34,161

intergenic_region

1.56E-06

7.69E-02

−0.5 ± 0.1

0.97

LMY

rs41594006

82

4

28,702,952

MACC1

133,040

intergenic_region

1.48E-06

7.37E-02

−0.67 ± 0.14

0.94

LMY

rs380838173

65

6

39,120,384

LCORL

128,272

intergenic_region

3.25E-11

2.92E-05

0.79 ± 0.12

2.59

LMY

rs110302982

339

6

38,760,889

NCAPG

5080

intergenic_region

4.71E-11

2.92E-05

0.78 ± 0.12

2.53

LMY

rs109722048

26

7

94,363,721

7SK

163,407

intergenic_region

4.27E-06

1.56E-01

0.47 ± 0.1

0.75

LMY

rs380092738

0

8

45,378,038

PIP5K1B

23,538

intergenic_region

1.90E-06

9.01E-02

0.6 ± 0.12

0.84

LMY

rs381625716

32

10

4,416,146

TMED7

Within

intron_variant

6.03E-06

1.98E-01

0.75 ± 0.17

0.68

LMY

rs41704822

21

13

64,131,777

EIF2S2

62,477

intergenic_region

7.72E-06

2.22E-01

−0.44 ± 0.1

0.90

LMY

rs379496842

24

14

25,350,856

PENK

127,865

intergenic_region

9.22E-06

2.40E-01

−0.6 ± 0.14

0.63

LMY

rs381910687

24

16

24,333,881

RAB3GAP2

Within

downstream_gene_variant

1.38E-06

7.08E-02

0.6 ± 0.12

0.92

LMY

rs446854454

0

17

71,415,918

LIF

Within

intron_variant

9.66E-07

5.38E-02

1.58 ± 0.32

0.68

LMY

rs209255508

3

20

36,664,583

GDNF

8055

intergenic_region

5.03E-06

1.75E-01

−0.82 ± 0.18

0.77

LMY

rs207913354

32

24

61,430,674

TNFRSF11A

155,480

intergenic_region

8.01E-06

2.22E-01

−0.43 ± 0.1

0.68

LMY

rs714693579

70

29

32,805,714

KCNJ1

18,117

intergenic_region

6.22E-08

6.03E-03

1.03 ± 0.19

0.96

CMAR

rs211292205

32

1

618,934

MRPS6

50,986

intergenic_region

4.40E-10

3.22E-03

10.63 ± 1.7

1.20

CMAR

rs441393071

62

1

724,086

MRPS6

Within

intron_variant

4.89E-09

5.12E-03

17.04 ± 2.9

1.04

CMAR

rs439430086

23

2

47,341,262

KIF5C

Within

intron_variant

2.35E-07

3.93E-02

−15.87 ± 3.07

0.96

CMAR

rs378618208

146

5

93,931,571

MGST1

Within

intron_variant

5.17E-06

2.17E-01

9.84 ± 2.16

0.74

CMAR

rs440019287

5

7

76,590,855

5S_rRNA

561,482

intergenic_region

2.04E-06

1.32E-01

−16.96 ± 3.57

0.65

CMAR

rs137214938

50

7

93,217,990

ARRDC3

21,912

intergenic_region

7.56E-06

2.79E-01

8.09 ± 1.81

0.57

CMAR

rs483021344

0

10

95,272,095

ENSBTAG00000018039

158,321

intergenic_region

3.90E-06

1.89E-01

−16.78 ± 3.63

0.60

CMAR

rs472692192

30

11

40,899,992

FANCL

155,573

intergenic_region

8.25E-07

9.54E-02

18.32 ± 3.72

0.73

CMAR

rs207650107

59

13

79,174,479

PTPN1

89,039

intergenic_region

7.17E-07

8.79E-02

10.1 ± 2.04

0.78

CMAR

rs382677800

119

15

37,550,837

ENSBTAG00000048131

40,352

intergenic_region

4.38E-06

2.06E-01

−8.9 ± 1.94

0.67

CMAR

rs454770498

45

17

22,076,614

SNORA25

8202

intergenic_region

9.92E-06

3.05E-01

9.33 ± 2.11

0.61

CMAR

rs137224539

35

18

29,266,132

ENSBTAG00000045255

Within

splice_region_variant&non_coding_exon_variant

5.05E-06

2.15E-01

15.06 ± 3.3

0.62

CMAR

rs43729456

10

19

42,229,279

KRT34

Within

intron_variant

9.66E-06

3.04E-01

11.88 ± 2.68

0.57

CMAR

rs379945647

6

20

20,934,339

U6

33,805

intergenic_region

5.04E-06

2.15E-01

−10.96 ± 2.4

0.72

CMAR

rs719382346

175

22

59,998,321

GATA2

18,664

intergenic_region

3.15E-06

1.73E-01

17.76 ± 3.81

0.74

CMAR

rs42610694

34

26

11,625,615

KIF20B

157,906

intergenic_region

6.04E-06

2.38E-01

14.7 ± 3.25

0.62

  1. aHCW hot carcass weight in kg, AFAT average backfat thickness in mm, REA rib eye area in cm2, LMY lean meat yield in %, CMAR carcass marbling score from 100 (trace marbling) to 499 (more marbling). bThe number of significant support SNPs associated with a lead SNP within 70 k bps. cThe nearest annotated gene to the significant SNP. The annotated gene database was downloaded from https://www.ensembl.org/index.html. dSNP designated as in a gene or distance (bp) from a gene region in the UMD3.1 bovine genome assembly. eFunctional annotation for the SNP. fFDR = genome-wise false discovery rate (FDR) calculated from the Benjamini-Hochberg procedure [27]. g,hThe estimated allelic substitution effect (b) ± standard error (SE) and phenotypic variance explained by the significant SNP, respectively
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us