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Table 5 Intercept and slope of regression when deregressed breeding values of validation animals were regressed onto their predicted genomic breeding values

From: Utility of whole-genome sequence data for across-breed genomic prediction

Across-breed, across-country

Scenarios

DH reference, NZJ validation

NZJ reference, DH validation

Intercept

Slope

Intercept

Slope

Full_seq

0.28

0.38 (0.20)

− 0.01

0.36 (0.22)

HD

0.39

0.41 (0.16)

− 0.02

0.73 (0.20)

50k

0.24

0.20 (0.14)

− 0.01

0.63 (0.16)

HD_Top

0.39

0.41 (0.16)

− 0.02

0.74 (0.20)

50k_Top

0.28

0.23 (0.13)

− 0.02

0.73 (0.16)

Pval5

0.30

0.36 (0.08)

− 0.03

0.59 (0.04)

Pval7

0.01

0.01 (0.06)

− 0.04

0.42 (0.03)

COJO3

0.40

0.35 (0.07)

− 0.05

0.71 (0.04)

COJO8

0.13

0.40 (0.07)

− 0.03

0.81 (0.04)

Top_markers

0.46

0.43 (0.08)

− 0.06

0.48 (0.03)

Across-breed, within-country

Scenarios

NZH reference, NZJ validation

NZJ reference, NZH validation

Intercept

Slope

Intercept

Slope

Full_seq

0.37

1.17 (0.01)

− 0.04

0.87 (0.47)

HD

0.47

1.17 (0.01)

0.02

− 0.58 (0.43)

50k

0.45

1.17 (0.01)

0.02

− 0.43 (0.36)

HD_Top

0.47

1.17 (0.01)

0.02

− 0.57 (0.43)

50k_Top

0.46

1.19 (0.01)

0.02

− 0.33 (0.36)

Pval5

0.32

1.19 (0.02)

0.01

0.90 (0.08)

Pval7

0.40

1.16 (0.03)

0.05

0.87 (0.07)

COJO3

0.52

1.20 (0.02)

0.05

0.89 (0.09)

COJO8

0.54

1.13 (0.03)

0.00

0.56 (0.10)

Top_markers

0.51

1.02 (0.04)

0.03

0.70 (0.08)

Within-breed, across-country

Scenarios

DH reference, NZH validation

NZH reference, DH validation

Intercept

Slope

Intercept

Slope

Full_seq

0.45

0.85 (0.04)

− 0.24

1.16 (0.03)

HD

0.40

0.81 (0.04)

− 0.27

1.17 (0.03)

50k

0.36

0.77 (0.04)

− 0.27

1.13 (0.03)

HD_Top

0.40

0.81 (0.04)

− 0.27

1.17 (0.03)

50k_Top

0.38

0.78 (0.04)

− 0.27

1.14 (0.03)

Pval5

0.47

0.72 (0.03)

− 0.27

1.09 (0.02)

Pval7

0.24

0.55 (0.03)

− 0.27

0.98 (0.03)

COJO3

0.44

0.64 (0.03)

− 0.22

0.91 (0.02)

COJO8

0.33

0.55 (0.04)

− 0.22

0.91 (0.02)

Top_markers

0.47

0.69 (0.04)

− 0.16

0.74 (0.02)

  1. The populations are Dutch Holsteins (DH), New Zealand Holsteins (NZH) and New Zealand Jerseys (NZJ). Standard errors for the slopes are given in parentheses
  2. The unselected marker sets are the whole-genome sequence (Full_seq), high-density markers (HD) and markers on the traditional 50k chip (50k). HD_Top and 50k_Top are scenarios in which some pre-selected markers from a meta-GWAS (Top_markers) are added to the HD and 50k markers, respectively. Pval5 and Pval7 are marker sets pre-selected from a meta-GWAS based on their p values. The COJO scenarios are those containing markers that are assumed to be independently significant markers from a meta-GWAS at different significant levels. Top_markers contain the most significant markers in each QTL region from a meta-GWAS
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Genetics Selection Evolution

ISSN: 1297-9686