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Table 3 Accuracy of genomic prediction for post-weaning weight (PWWT) 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)

−0.02 a

0.53 b

0.00 a

0.53 b

(2) = Purebred Merino

2000

0.0 (0)

100 (4000)

−0.04 a

0.57 bc

−0.01 a

0.57 bc

(3) = Purebred Merino

3000

0.0 (0)

100 (6000)

−0.06 a

0.59 c

−0.03 a

0.59 c

BL*Merino

1514

50.7 (1535)

47.2 (1430)

0.31 c

0.41 a

0.31 b

0.41 a

BL*Merino + (1)

2514

30.5 (1535)

68.2 (3430)

0.27 bc

0.48 bc

0.27 b

0.49 bc

BL*Merino + (2)

3514

21.8 (1535)

77.2 (5430)

0.26 b

0.51 bc

0.27 b

0.50 bc

BL*Merino + (3)

4514

17.0 (1535)

82.3 (7430)

0.26 b

0.54 bc

0.27 b

0.51 bc

Type

Size

PD

Merino

PD

Merino

PD

Merino

(1) = Purebred Merino

1000

0.0 (0)

100 (2000)

−0.00 a

0.53 c

0.00 a

0.53 b

(2) = Purebred Merino

2000

0.0 (0)

100 (4000)

−0.02 a

0.57 cd

−0.01 a

0.57 cd

(3) = Purebred Merino

3000

0.0 (0)

100 (6000)

−0.04 a

0.59 d

−0.03 a

0.59 d

PD*Merino

1847

50.1 (1850)

36.4 (673)

0.28 b

0.36 a

0.29 c

0.36 a

PD*Merino + (1)

2847

32.5 (1850)

58.7 (1671)

0.23 b

0.42 ab

0.23 b

0.41 a

PD*Merino + (2)

3846

24.0 (1850)

69.4 (2669)

0.22 b

0.47 b

0.23 b

0.42 a

PD*Merino + (3)

4847

19.1 (1850)

75.7 (3669)

0.23 b

0.52 b

0.22 b

0.52 b

Type

Size

WS

Merino

WS

Merino

WS

Merino

(1) = Purebred Merino

1000

0.0 (0)

100 (2000)

−0.01 a

0.53 b

0.00 a

0.53 c

(2) = Purebred Merino

2000

0.0 (0)

100 (4000)

−0.02 a

0.57 bc

−0.01 a

0.57 cd

(3) = Purebred Merino

3000

0.0 (0)

100 (6000)

−0.02 a

0.59 c

−0.03 a

0.59 d

WS*Merino

1011

38.3 (773)

35.2 (711)

0.23 b

0.38 a

0.24 b

0.33 a

WS*Merino + (1)

2011

19.2 (773)

67.4 (2711)

0.23 b

0.47 b

0.24 b

0.44 b

WS*Merino + (2)

3011

12.8 (773)

78.2 (4711)

0.23 b

0.50 b

0.24 b

0.48 bc

WS*Merino + (3)

4011

9.6 (773)

83.7 (6711)

0.23 b

0.53 b

0.24 b

0.56 cd

  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.