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Table 5 Genome-wide significant SNPs for rump and the component traits

From: Genome wide association studies for body conformation traits in the Chinese Holstein cattle population

Trait

SNP name

Chr.

Position (bp)

Nearest gene

Distance (bp)

Heritability/-log10(P)b

Threshold

Rump

BTB-01660659

1

145986598

KRTAP10-12

688

0.01280

0.00916

ARS-BFGL-NGS-12856

4

8155616

CDK14

within

0.01100

0.00916

BTB-00323505

7

82338362

ODZ2

within

0.00966

0.00916

Rump width

BTB-00168895

4

20788689

LOC781728

166,306

0.01260

0.00917

Hapmap40061-BTA-28737

9

1775187

LOC616304

826,933

0.00924

0.00917

BTB-02035532a

7

58436123

LOC100138639

348,605

6.07b

6.02c

ARS-BFGL-NGS-14128a

10

36665562

ACYP2

within

7.21b

6.02c

ARS-BFGL-NGS-86147a

10

49856100

ACYP2

44,441

6.89b

6.02c

ARS-BFGL-NGS-53281a

15

66603229

SLC1A2

within

8.35b

6.02c

BTB-00611649a

15

67429625

LDLRAD3

within

6.05b

6.02c

ARS-BFGL-NGS-97658a

15

68069900

C15H11orf74

158,748

7.27b

6.02c

BTA-30189-no-rsa

X

60101130

MAGED2

42,513

6.34b

6.02c

ARS-BFGL-NGS-80859a

X

61237718

NXF3

338,723

7.01b

6.02c

Rump angle

BTA-94299-no-rs

5

93940507

MGST1

within

0.01500

0.00906

Hapmap48553-BTA-10000

7

59019641

LOC788619

36,977

0.01610

0.00906

BTB-01219012

7

65799159

LOC100296765

48,625

0.01020

0.00906

ARS-BFGL-NGS-31810

11

105631144

LOC536255

within

0.00960

0.00906

ARS-BFGL-NGS-54462

25

13405791

MIR365

61,471

0.01190

0.00906

 

ARS-BFGL-NGS-102900

27

4720968

AGPAT5

within

0.01300

0.00906

  1. Note: Heritability and threshold were obtained using the LASSO method; -log10(P) was calculated using SMMA. aSNP detected by SMMA only; b-log10(P) obtained from SMMA; cthreshold of SMMA. Nearest gene are symbols of gene full name in the NCBI database (http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/).