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Table 2 Haplotype blocks, marker and candidate gene information

From: Genetic effects and correlations between production and fertility traits and their dependency on the lactation-stage in Holstein Friesians

      

Effect of Major Allele

r MKG – RZR within genotypes

  

Chr.

HTB size Kb (sig. markers/total)

Most significant marker (bp)

MAF

Traits

DIM

ø first 60 DIM

305-days

A1A1

A2A2

# Genes in HTB

Candidate genes

5

381.05 (1/3)

ARS-BFGL-NGS-116999 (99,656,229)

0.21

FC

41-60

ns

−0.008

−0.26 ***

−0.17

0

 
 

383.08 (2/8)

Hapmap49734-BTA-74577 (101,015,511)

0.09

FC

31-60

ns

−0.011

−0.26 ***

0.08

3

 
 

56.34 (1/3)

Hapmap60021ss46526426 (101,979,582)

0.43

FC

51-60

ns

+0.006

−0.27 ***

−0.20***

2

 

6

322.61 (1/7)

Hapmap50464-BTA-77021 (84,174,079)

0.12

PC

11-20

−0.004

ns

−0.25 ***

−0.41 †

1

 
 

38.98 (1/2)

Hapmap25708-BTC-043671 (88,263,656)

0.27

PC

11-50

−0.003

ns

−0.25 ***

−0.30 ***

1

CSN1S1

 

181.84 (1/3)

ARS-BFGL-NGS-112872 (89,212,072)

0.32

PC

11-40

−0.003

ns

−0.29 ***

−0.20 ***

4

 
 

44.76 (1/2)

ARS-BFGL-NGS-118182 (89,774,922)

0.44

PC

11-60

−0.003

ns

−0.26 ***

−0.22 **

0

 
 

90.40 (1/5)

BTB-00277427 (106,066,499)

0.13

NRh

 

ns

+0.59

−0.23 ***

−0.19

1

KLHL8

14

393.07 (7/7)

ARS-BFGL-NGS-4939 (443,937)

0.32

MY

11-60

+1.435

+66.195

−0.21 ***

−0.39 ***

25

DGAT1

    

FY

11-60

−0.073

−1.905

    
    

PY

51-60

+0.024

+1.051

    
    

FC

11-60

−0.018

−0.028

    
    

PC

11-60

−0.005

−0.009

    
 

83.26 (2/2)

ARS-BFGL-NGS-107379 (679,600)

0.37

MY

11-60

+1.397

+58.401

−0.20 ***

−0.39 ***

3

 
    

FY

11-60

−0.053

−1.415

    
    

PY

31-60

+0.025

+1.040

    
    

FC

11-60

−0.015

−0.023

    
    

PC

11-60

−0.004

−0.007

    
 

21.46 (2/2)

ARS-BFGL-NGS-18365 (741,867)

0.29

MY

41-60

−0.840

−32.466

  

0

 
    

FY

11-60

+0.043

+1.160

    
    

FC

11-60

+0.010

+0.016

    
    

PC

21-60

+0.003

+0.005

    
 

21.84 (2/2)

Hapmap25384-BTC-001997 (835,054)

0.49

MY

21-60

+0.872

+33.402

  

3

 
    

FY

11-60

−0.030

−0.849

    
    

FC

11-60

−0.008

−0.013

    
    

PC

11-60

−0.003

−0.004

    
 

102.73 (3/3)

BTA-35941-no-rs (894,252)

0.44

MY

31-60

+0.824

+30.112

−0.22 ***

−0.30 ***

8

 
    

FY

11-60

−0.044

−1.254

    
    

FC

11-60

−0.010

−0.015

    
    

PC

11-60

−0.003

−0.005

    
  

UA-IFASA-6878 (1,044,041)

0.49

MY

21-60

−1.000

−41.885

−0.29 ***

−0.20 ***

0

 
    

FY

11-60

+0.041

+1.053

    
    

PY

305d

ns

−0.666

    
    

FC

11-60

+0.011

+0.017

    
    

PC

11-60

+0.003

+0.006

    
 

91.70 (3/3)

ARS-BFGL-NGS-103064 (1,193,336)

0.48

MY

31-60

−0.850

−29.853

  

3

CYP11B

    

FY

11-60

+0.027

+0.763

    
    

FC

11-60

+0.007

+0.011

    
    

PC

31-60

+0.002

+0.003

    
 

29.09 (2/2)

Hapmap30086-BTC-002066 (1,490,178)

0.47

MY

31-60

−0.801

−29.959

−0.31 ***

−0.24 ***

2

 
    

FY

11-60

+0.050

+1.338

    
    

FC

11-60

+0.010

+0.016

    
    

PC

21-60

+0.003

+0.004

    
 

60.69 (2/2)

ARS-BFGL-NGS-74378 (1,889,210)

0.34

FC

11-60

−0.005

−0.008

  

1

 
 

115.11 (1/3)

UA-IFASA-9288 (2,201,870)

0.30

FC

305d

ns

−0.007

  

1

 
 

95.92 (1/3)

ARS-BFGL-NGS-56327 (2,580,414)

0.38

FC

41-60

−0.027

−0.811

  

1

 
    

FC

41-60

−0.005

−0.007

    
 

82.03 (1/3)

UA-IFASA-5306 (2,711,615)

0.30

FC

305d

ns

−0.007

  

0

 

18

271.14 (1/3)

ARS-BFGL-NGS-109285 (57,125,869)

0.13

PC

11-30

+0.004

ns

−0.27 ***

−0.26 †

17

SICLEC12

27

89.19 (1/4)

ARS-BFGL-NGS-57448 (38,878,780)

0.35

FY

11-40

+0.030

ns

−0.19 ***

−0.29 ***

2

AGPAT6

    

FC

11-60

+0.006

     

28

21.15 (1/2)

ARS-BFGL-NGS-103007 (6,863,680)

0.13

NRh

 

ns

−0.59

−0.24 ***

−0.27

1

NID1

  1. This table summarizes the information for the most significant marker in each haplotype block. We give the minor allele frequency, trait and the days in milk for which this marker showed significant effects. The days in milk cover one or more intervals used in the analyses and the effects of the major allele are given as an average over all intervals that this marker had significant effects. The correlations r in this table refer to the correlations between the traits milk yield and fertility index where we separated these correlation for homozygous animals carrying the major or minor allele. In the last two columns are the number of genes given that lay within the haplotype block and the possible candidate genes that might have an effect on the traits under investigation.
  2. P-values *** < 0.0001 ** < 0.001 * < 0.01 † < 0.05 NA non-significant.
  3. HTB: haplotype block; MY: milk yield; FY: fat yield; PY: protein yield; FC: fat content; PC: protein content; RZR: fertility index, summarizing all fertility traits; NRh: non-return rate for heifers; DIM: days in milk; ns: non-significant; A1 is the major allele.
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BMC Genomic Data

ISSN: 2730-6844

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