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Table 3 Location of the most significant QTL, limited to the top 5 per breed, which were associated with development of inner thigh, 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

1

146687440

147685998

7

147187440b

9.55 × 10−7

0.988

0.712

0.073

0.179

0.631

TRAPPC10, COL18A1, SLC19A1, PCBP3e, COL6A1, COL6A2

 

4

69229353

70999401

38

70373241a

4.19 × 10−7

0.991

0.015

0.990

0.014

0.900

HOXA1, HOXA2, HOXA3, HOXA4, HOXA5, HOXA6, HOXA7, HOXA9, HOXA10, HOXA11, HOXA13

 

24

36998437

38030390

4

37530390bd

2.24 × 10−7

0.977

0.000

0.014

0.036

0.983

NDC80, EMILIN2e, MYOM1, MYL12A, MYL12B

 

25

35042698

36122096

6

35542698a

3.50 × 10−7

0.998

0.000

0.000

0.000

0.002

POLR2J, MYL10, ALKBH4, COL26A1

 

29

23787949

24826548

7

24290699a

1.82 × 10−7

0.048

0.043

0.937

0.939

0.919

SLC6A5, PRMT3

CH

2

7850

10711228

5075

6808074a

9.07 × 10−49

0.000

0.079

0.000

0.028

0.005

WDR75f, ASNSD1f, NAB1f, MFSD6f, MSTNf, PMS1f, ORMDLe COL3A1, COL5A2f, ANKARf, SLC40A1f

 

14

33353270

34360874

4

33855595a

2.20 × 10−7

0.013

0.026

0.054

0.054

0.018

ARFGEF1, CPA6, PREX2

 

14

67849241

68850085

4

6834924a

2.69 × 10−6

0.000

0.062

0.000

0.000

0.000

STK3, KCNS2, POP1, RPL30, MATN2

 

16

60443313

62320499

4

60943313a

6.72 × 10−6

0.904

0.230

0.063

0.853

0.821

RASAL2, ANGPTL1, TOR3A, ABL2, SOAT1

 

29

21313583

22460213

38

21917306a

3.58 × 10−6

0.000

0.989

0.000

0.978

0.000

GAS2, FANCF

HE

4

3924012

5000928

3

4424012a

4.05 × 10−7

0.755

0.032

0.082

0.000

0.939

ENSBTAG00000023806

 

7

72100887

73679002

67

72608186b

9.09 × 10−7

0.000

0.998

0.046

0.000

0.995

EBF1e, ADRA1B

 

13

6038290

8341939

9

7003978a

1.84 × 10−7

0.000

0.000

0.002

0.004

0.000

ESF1, NDUFAF5, FLRT3

 

14

57257740

58269158

3

57757740a

7.98 × 10−7

0.262

0.122

0.758

0.104

0.000

TRHR

 

25

37995664

39005834

3

38505834c

2.68 × 10−7

0.160

0.928

0.097

0.056

0.071

LMTK2, PMS2, EIF2AK1, USP42

LM

2

313343

3758925

102

3226165a

5.94 × 10−10

0.907

0.032

0.997

0.066

0.057

NIPA1, NIPA2e, ARHGEF4

 

2

4973733

11101064

2441

6747317a

2.20 × 10−28

0.802

0.409

0.617

0.074

0.490

WDR75, ASNSD1f, NAB1f, MFSD6e, MSTNf, PMS1f, ORMDL1e, COL3A1e, COL5A2f, ANKARf, SLC40A1f

 

2

11556240

12618550

36

12116324a

1.36 × 10−8

0.308

0.402

0.231

0.195

0.556

ZNF804A

 

2

13935604

14957932

55

14447892bc

1.67 × 10−6

0.433

0.562

0.374

0.394

0.524

PDE1Ae, PPP1R1C, NEUROD1

 

4

23124509

24137261

59

23630609b

2.52 × 10−7

0.096

0.027

0.996

0.994

0.010

AGMOe, MEOX2

SI

1

22558133

23622641

49

23117106a

5.21 × 10−6

0.949

0.043

0.866

0.060

0.870

ENSBTAG00000046369

 

14

79492849

80610485

17

80090294b

2.33 × 10−7

0.104

0.052

0.980

0.886

0.072

E2F5

 

17

21615210

22651417

8

22115210a

1.47 × 10−6

0.474

0.619

0.639

0.359

0.297

ENSBTAG00000044703

 

21

17057917

18336523

18

17836523a

5.30 × 10−8

0.003

0.010

0.000

0.000

0.997

ENSBTAG00000045960

 

22

33706576

34737653

10

34236342b

2.08 × 10−6

0.000

0.995

0.000

0.987

0.002

SUCLG2e, KBTBD8

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