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Table 4 Accuracy of genomic prediction for post-weaning scanned eye muscle depth (PW-EMD) based on different reference populations, using two genomic relationship matrices (G1 and G2)

From: Comparing genomic prediction accuracy from purebred, crossbred and combined purebred and crossbred reference populations in sheep

Reference population

Breed proportion (%) (number of haplotypes)1

GBV accuracy

G1

G2

Type

Size

BL

Merino

BL

Merino

BL

Merino

(1) = Purebred Merino

1000

0.0 (0)

100 (2000)

0.00 a

0.23 a

0.00 a

0.23 b

(2) = Purebred Merino

2000

0.0 (0)

100 (4000)

0.00 a

0.33 b

−0.01 a

0.33 c

(3) = Purebred Merino

3000

0.0 (0)

100 (6000)

−0.01 a

0.34 b

−0.01 a

0.34 c

BL*Merino

1602

52.0 (1661)

41.6 (1332)

0.17 b

0.18 a

0.19 b

0.17 a

BL*Merino + (1)

2602

31.9 (1661)

64.0 (3332)

0.16 b

0.21 a

0.19 b

0.24 b

BL*Merino + (2)

3602

23.1 (1661)

73.9 (5332)

0.16 b

0.27 b

0.17 b

0.25 b

BL*Merino + (3)

4602

18.1 (1661)

79.6 (7332)

0.16 b

0.33 b

0.18 b

0.26 b

Type

Size

PD

Merino

PD

Merino

PD

Merino

(1) = Purebred Merino

1000

0.0 (0)

100 (2000)

0.00 a

0.23 b

0.00 a

0.23 a

(2) = Purebred Merino

2000

0.0 (0)

100 (4000)

−0.01 a

0.33 cd

−0.01 a

0.33 b

(3) = Purebred Merino

3000

0.0 (0)

100 (6000)

−0.01 a

0.34 d

−0.01 a

0.34 b

PD*Merino

1890

50.1 (1893)

33.7 (1273)

0.08 b

0.15 a

0.07 b

0.19 a

PD*Merino + (1)

2890

32.7 (1893)

56.6 (3273)

0.06b

0.22 b

0.07 b

0.30 b

PD*Merino + (2)

3890

24.3 (1893)

67.8 (5273)

0.06 b

0.28 c

0.08 b

0.33 bc

PD*Merino + (3)

4890

19.3 (1893)

74.4 (7273)

0.06 b

0.35 d

0.07 b

0.36 c

Type

Size

WS

Merino

WS

Merino

WS

Merino

(1) = Purebred Merino

1000

0.0 (0)

100 (2000)

0.00 a

0.23 b

0.00 a

0.23 b

(2) = Purebred Merino

2000

0.0 (0)

100 (4000)

−0.02 a

0.33 c

−0.01 a

0.33 c

(3) = Purebred Merino

3000

0.0 (0)

100 (6000)

−0.02 a

0.34 c

−0.01 a

0.34 c

WS*Merino

1257

45.0 (1331)

26.2 (687)

0.05 b

0.12 a

0.08 b

0.11 a

WS*Merino + (1)

2257

25.0 (1331)

58.7 (2657)

0.05 b

0.17 a

0.08 b

0.21 b

WS*Merino + (2)

3257

17.3 (1331)

71.4 (3657)

0.04 b

0.23 b

0.08 b

0.22 b

WS*Merino + (3)

4257

13.3 (1331)

78.1 (5657)

0.05 b

0.27 b

0.06 b

0.23 b

  1. BL = Border Leicester, PD = Poll Dorset, WS = White Suffolk, G1 = single population genomic relationship matrix, G2 = combined population genomic relationship matrix, accuracies within columns and within breed blocks are significantly different when letter superscripts differ (p < 0.05); 1number of haplotypes calculated as 2 × population size × breed proportion.
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Genetics Selection Evolution

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