Predictive performances of animal models using different multibreed relationship matrices in systems with rotational crossbreeding

Poulsen, Bjarke Grove; Ostersen, Tage; Nielsen, Bjarne; Christensen, Ole Fredslund

doi:10.1186/s12711-022-00714-w

Genetics Selection Evolution

Table 2 Median prediction accuracy across replicates

From: Predictive performances of animal models using different multibreed relationship matrices in systems with rotational crossbreeding

Population \(\times\) method	y\(_{A}\)	y\(_{AD}\)
Population \(\times\) method		Purebred	F1	Rotation
Population A (Purebred)
GT	0.41 (0.09)\(^{\mathrm{c}}\)	0.37 (0.11)\(^{\mathrm{c}}\)	0.40 (0.11)\(^{\mathrm{c}}\)	0.39 (0.12)\(^{\mathrm{c}}\)
MF	0.41 (0.09)\(^{\mathrm{c}}\)	0.37 (0.11)\(^{\mathrm{c}}\)	0.40 (0.11)\(^{\mathrm{c}}\)	0.39 (0.12)\(^{\mathrm{c}}\)
NRM	0.39 (0.09)\(^{\mathrm{c}}\)	0.37 (0.09)\(^{\mathrm{c}}\)	0.40 (0.11)\(^{\mathrm{c}}\)	0.37 (0.11)\(^{\mathrm{c}}\)
SM	0.41 (0.09)\(^{\mathrm{c}}\)	0.37 (0.10)\(^{\mathrm{c}}\)	0.41 (0.09)\(^{\mathrm{c}}\)	0.40 (0.12)\(^{\mathrm{c}}\)
ssGT	0.65 (0.06)\(^{\mathrm{a}}\)	0.59 (0.08)\(^{\mathrm{a}}\)	0.60 (0.08)\(^{\mathrm{a}}\)	0.60 (0.08)\(^{\mathrm{a}}\)
ssMF	0.65 (0.06)\(^{\mathrm{a}}\)	0.59 (0.08)\(^{\mathrm{a}}\)	0.60 (0.07)\(^{\mathrm{a}}\)	0.60 (0.08)\(^{\mathrm{a}}\)
ssNRM	0.63 (0.05)\(^{\mathrm{b}}\)	0.56 (0.07)\(^{\mathrm{b}}\)	0.58 (0.06)\(^{\mathrm{b}}\)	0.58 (0.07)\(^{\mathrm{b}}\)
ssSM	0.65 (0.04)\(^{\mathrm{ab}}\)	0.58 (0.08)\(^{\mathrm{a}}\)	0.60 (0.07)\(^{\mathrm{b}}\)	0.60 (0.08)\(^{\mathrm{a}}\)
Population B (Purebred)
GT	0.34 (0.12)\(^{\mathrm{c}}\)	0.31 (0.11)\(^{\mathrm{c}}\)	0.34 (0.12)\(^{\mathrm{c}}\)	0.34 (0.12)\(^{\mathrm{c}}\)
MF	0.33 (0.12)\(^{\mathrm{c}}\)	0.31 (0.12)\(^{\mathrm{c}}\)	0.34 (0.12)\(^{\mathrm{c}}\)	0.34 (0.12)\(^{\mathrm{c}}\)
NRM	0.33 (0.11)\(^{\mathrm{c}}\)	0.30 (0.11)\(^{\mathrm{c}}\)	0.31 (0.13)\(^{\mathrm{c}}\)	0.31 (0.13)\(^{\mathrm{c}}\)
SM	0.35 (0.11)\(^{\mathrm{c}}\)	0.29 (0.11)\(^{\mathrm{c}}\)	0.31 (0.11)\(^{\mathrm{c}}\)	0.32 (0.11)\(^{\mathrm{c}}\)
ssGT	0.53 (0.10)\(^{\mathrm{a}}\)	0.50 (0.08)\(^{\mathrm{a}}\)	0.54 (0.10)\(^{\mathrm{a}}\)	0.53 (0.09)\(^{\mathrm{a}}\)
ssMF	0.55 (0.09)\(^{\mathrm{a}}\)	0.51 (0.07)\(^{\mathrm{a}}\)	0.54 (0.08)\(^{\mathrm{a}}\)	0.54 (0.08)\(^{\mathrm{a}}\)
ssNRM	0.50 (0.11)\(^{\mathrm{b}}\)	0.50 (0.09)\(^{\mathrm{b}}\)	0.50 (0.09)\(^{\mathrm{b}}\)	0.51 (0.08)\(^{\mathrm{b}}\)
ssSM	0.51 (0.11)\(^{\mathrm{b}}\)	0.48 (0.09)\(^{\mathrm{b}}\)	0.49 (0.08)\(^{\mathrm{b}}\)	0.50 (0.08)\(^{\mathrm{b}}\)
Population C (Crossbred)
GT	0.62 (0.03)\(^{\mathrm{b}}\)			0.61 (0.03)\(^{\mathrm{b}}\)
MF	0.62 (0.03)\(^{\mathrm{b}}\)			0.62 (0.03)\(^{\mathrm{b}}\)
NRM	0.48 (0.02)\(^{\mathrm{f}}\)			0.48 (0.02)\(^{\mathrm{e}}\)
SM	0.57 (0.02)\(^{\mathrm{d}}\)			0.57 (0.02)\(^{\mathrm{d}}\)
ssGT	0.63 (0.03)\(^{\mathrm{a}}\)			0.62 (0.03)\(^{\mathrm{a}}\)
ssMF	0.63 (0.03)\(^{\mathrm{a}}\)			0.62 (0.03)\(^{\mathrm{a}}\)
ssNRM	0.48 (0.02)\(^{\mathrm{e}}\)			0.49 (0.03)\(^{\mathrm{e}}\)
ssSM	0.57 (0.02)\(^{\mathrm{c}}\)			0.57 (0.02)\(^{\mathrm{c}}\)

Median absolute deviations are in parentheses
Accuracy: Pearson’s correlation between true breeding values and predicted breeding values
Superscripts: Different superscripts denote that medians are significantly different
Superscripts are comparable within combinations of Population and column
ss-prefix: Relationship matrices include genomic information
y\(_{A}\): A phenotype with additive genetic effects
y\(_{AD}\): A phenotype with both additive and dominant genetic effects
Purebred: True breeding value is for production of purebred animals
F1: True breeding value is for production of F1-animals
Rotation: True breeding value is for mating with rotationally crossbred animals

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ISSN: 1297-9686

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