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Table 4 Location of the most significant QTL, limited to the top 5 per breed, which were associated with thigh width, and the genes located within these QTL within each breed

From: Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds

Breed

Chr

Start

End

Number of suggestive and significant SNPs

Most significant SNP

P-value

Allele frequency of + allele

Candidate genes within this QTL

AA

CH

HE

LM

SI

AA

11

53741952

54849531

2

54349531a

2.65 × 10−6

0.017

0.047

0.000

0.997

0.994

CTNNA2

 

13

78082912

79223584

10

78722523b

2.99 × 10−7

0.191

0.232

0.866

0.157

0.108

ZNFX1, B4GALT5, SLC9A8f, UBE2V1

 

14

22612620

23619374

3

23116129a

1.99 × 10−6

0.026

0.994

0.074

0.962

0.971

OPRK1, ATP6V1H, RGS20

 

16

1654734

2669694

4

2169248a

5.14 × 10−6

0.986

0.980

0.985

0.056

0.979

ETNK2, GOLT1A, PPP1RI5B, PIK3C2B, NFASC

 

16

63066185

64073838

2

63066185d

4.07 × 10−6

0.027

0.948

0.991

0.072

0.000

ACBD6, STX6, MR1

CH

2

7850

10186234

1860

6808074a

4.09 × 10−25

0.000

0.079

0.000

0.028

0.004

WDR75g, ASNSD1g, NAB1g, MFSD6g, MSTNg, PMS1g, ORMDL1, COL3A1g, COL5A2g, ANKARg, SLC40A1g

 

9

12470065

13731582

11

12970065e

8.65 × 10−9

0.000

0.013

0.000

0.003

0.000

KHDC3Lg, EEF1A1

 

20

61727533

63246384

5

62296495b

7.78 × 10−9

0.997

0.010

0.000

0.000

0.000

CTNND2f, DAP, FAM173B

 

28

9234253

24087892

1025

16275379a

4.17 × 10−9

0.581

0.829

0.476

0.430

0.523

ANK3f, CDK1, RHOBTB1, EGR2

 

28

24331178

40249741

1322

26134688a

3.87 × 10−9

0.388

0.810

0.424

0.591

0.486

SIRT1, MYPNf, DNA2f, SLC25A16, SRGNf, COL13A1f, AIFM2, ADAMTS14f, SGLP1, PCBD1, SPOCK2f, ANAPC16f, DDIT4, MYOZ1

HE

5

17326996

18595093

3

18095093a

1.75 × 10−6

0.000

0.996

0.003

0.985

0.000

C5H12orf50, C5H12orf29, CEP290

 

7

75039465

75039465

2

75539465d

4.24 × 10−6

0.990

0.000

0.997

0.000

0.000

GABRA6f

 

10

87480123

88487031

3

87980123b

1.72 × 10−6

0.959

0.034

0.020

0.981

0.033

TTLL5f, TGFB3

 

20

35840468

37412173

5

36340468a

1.30 × 10−6

0.342

0.589

0.421

0.230

0.328

LIFR, EGFLAM, GDNF

 

20

39512041

41162914

10

40272197b

1.01 × 10−6

0.015

0.985

0.985

0.994

0.003

C1QTNF3, ADAMTS12f

LM

2

4973607

10670961

1526

7772897a

2.88 × 10−15

0.617

0.571

0.000

0.116

0.642

WDR75f, ASNSD1g, NAB1f, MFSD6f, MSTNf, PMS1f, ORMDL1, COL3A1, COL5A2, ANKARg, SLC40A1g

 

2

11570479

12640428

43

12083258a

1.01 × 10−7

0.561

0.205

0.057

0.097

0.809

ZNF804A

 

2

13916060

14952210

55

14450953b

1.92 × 10−6

0.434

0.565

0.374

0.394

0.477

PDE1Af, PPP1R1C

 

9

36716988

37719425

4

37216988a

6.31 × 10−7

0.245

0.649

0.547

0.247

0.286

HS3ST5

 

27

35767035

36785436

7

36267035c

8.03 × 10−6

0.057

0.000

0.998

0.997

0.000

SFRP1, GOLGA7, GPAT4, ANK1

SI

9

32996000

34105290

5

33604527b

4.82 × 10−7

0.969

0.980

0.981

0.985

0.019

NEPN, GOPC

 

14

76746937

78193017

13

77271966a

1.65 × 10−7

0.712

0.107

0.052

0.916

0.085

MMP16f, SLC2A5

 

24

17511696

18515510

3

18015356a

8.99 × 10−7

0.461

0.449

0.299

0.506

0.378

ENSBTAG00000045320, ENSBTAG00000011094

 

26

35041033

36071133

3

35541033a

1.97 × 10−6

0.000

0.006

0.004

0.994

0.995

AFAP1L2, ABLIM1, ATRNL1

 

29

47398869

48688066

30

47898869a

5.42 × 10−7

0.790

0.197

0.886

0.850

0.108

CCND1, FGF19, FGF4

  1. SNP classification: aintergenic, bintron, cupstream gene variant, ddownstream gene variant, esynonymous gene variant
  2. Significance of SNPs within genes: fgene contains at least one suggestive SNP, ggene contains at least one significant SNP