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Table 3 Copy number variants (CNVs) associated with each of the carcass traits in Charolais (CH), Holstein-Friesian (HF), and Limousin (LM) with no obvious underlying pedigree relationship. When a CNV was present as both duplications and deletions in the population the CNV type was reported as mixed

From: Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle

Chromosome

Start position

End position

Associated trait

Breed

Population frequencya

CNV type

Marginal R2 b

Flanking genes

9

7.28 Mb

7.29 Mb

Weight

CH

3

Deletion

0.0201

ADGRB3

1

9.91 Mb

9.92 Mb

Weight

HF

6

Deletion

0.0276

APP U6

7

10.49 Mb

11.09 Mb

Weight

HF

3

Duplication

0.0286

OR7A89, OR7A95

22

61.33 Mb

61.38 Mb

Weight

HF

3

Mixed

0.0146

CFAP100

2

136.75 Mb

136.91 Mb

Conformation

HF

6

Mixed

0.0047

U6, 5S rRNA

7

23.81 Mb

23.86 Mb

Conformation

HF

25

Mixed

0.0053

GRAMD2B

11

103.48 Mb

103.50 Mb

Conformation

HF

3

Mixed

0.0044

CAMSAP1

11

49.90 Mb

49.91 Mb

Conformation

HF

3

Mixed

0.0056

TMBSB10

21

58.26 Mb

58.28 Mb

Conformation

HF

3

Mixed

0.0049

ITPK1

7

45.49 Mb

45.52 Mb

Conformation

LM

4

Deletion

0.0109

APC2, PCSK4, REEP6

10

39.73 Mb

39.73 Mb

Fat

LM

6

Deletion

0.0045

RPL10L, U1

  1. aThe population frequency is the number of animals in the population with a deletion or duplication variant of the CNV
  2. bThe marginal R2 is the R2 which is attributable to the fixed effect in the linear mixed model, in this case the CNV is the fixed effect