A Comparison of Genomically Enhanced Breeding Values Predicted by Different Single-Step Approaches

Dawid Słomian; Kacper Żukowski; Joanna Szyda

doi:10.2478/aoas-2025-0088

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A Comparison of Genomically Enhanced Breeding Values Predicted by Different Single-Step Approaches

Annals of Animal Science

Volume 26 (2026): Issue 3 (April 2026)

By: Dawid Słomian, Kacper Żukowski and Joanna Szyda

Open Access

|Apr 2026

Figures & Tables

Pearson correlation coefficients of GEBVs predicted by different model variants

Mean GEBV difference divided by the genetic standard deviation between SNP-BLUP and GT, as well as SNP-BLUP and APY models implementing different scenarios of core individual selection. (A) stature, (B) foot angle

Correlation between full and truncated data set for cows with phenotype records and bulls with a minimum of one daughter. (A) stature, (B) foot angle

An upset plot of bulls with the top 50 GEBVs. (A) stature, (B) foot angle

Validation of GEBV predictions

Model variants	b^0 {{\hat b}_0}	SEb^0 {\rm{SE}}( {{{\hat b}_0}})	b^1 {{\hat b}_1}	SEb^1 {\rm{SE}}( {{{\hat b}_1}})	R²
Stature, 1,727 validation bulls, h² = 0.54
SNP-BLUP	−3.90	0.32	1.01	0.01	0.77
GT	−4.40	0.27	1.01	0.01	0.83
APY3000top	−1.81	0.44	0.94	0.02	0.57
APY3000random	−2.20	0.44	0.99	0.02	0.60
APY10000random	−3.74	0.36	1.02	0.02	0.72
APY15000top	−2.59	0.32	0.96	0.01	0.75
APY15000random	−2.32	0.33	0.96	0.01	0.73
Foot angle, 1,725 validation bulls, h² = 0.09
SNP-BLUP	−2.03	0.18	1.03	0.01	0.76
GT	−1.96	0.18	1.04	0.01	0.76
APY3000top	−0.68	0.21	0.97	0.02	0.62
APY3000random	−0.52	0.26	1.03	0.02	0.60
APY10000random	−2.04	0.21	1.02	0.02	0.69
APY15000top	−2.15	0.18	1.02	0.01	0.75
APY15000random	−2.10	0.19	1.03	0.02	0.73

Number of animals in the analyzed data sets

Category	Sex	Number of animals
Phenotype data (Stature)	Females with phenotypes	1,098,611
Phenotype data (Stature)	Males with MACE DRP	141,397
Phenotype data (Foot angle)	Females with phenotypes	1,098,766
Phenotype data (Foot angle)	Males with MACE DRP	117,482
Genotype data	Females	70,134
Genotype data	Males (bulls and candidates)	64,826
Pedigree data	Females	1,368,487
Pedigree data	Males	187,508

Computational resources utilized by the solvers

Model variants	Wall clock time (min)		Peak RAM consumption (GB)		Number of iterations
Model variants	stature	foot angle	stature	foot angle	stature	foot angle
SNP-BLUP	23	32	5.81	5.81	673	1027
GT	138	143	63.89	63.88	477	629
APY3000top	23	29	49.48	49.47	335	811
APY3000random	23	32	49.48	49.47	390	499
APY10000random	32	34	56.53	56.53	469	652
APY15000top	68	70	61.56	61.56	425	625
APY15000random	54	57	61.56	61.56	477	551

Variance components underlying the analyzed phenotypes

Trait	σ_a²	σ_e²	σ_u²
Stature	5.50	4.63	20%
Foot angle	0.11	1.06	20%

References

Authors

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Articles in this issue

DOI: https://doi.org/10.2478/aoas-2025-0088 | Journal eISSN: 2300-8733 | Journal ISSN: 1642-3402

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Language: English

Page range: 789 - 796

Submitted on: Feb 15, 2025

Accepted on: Aug 8, 2025

Published on: Apr 30, 2026

Published by: National Research Institute of Animal Production

In partnership with: Paradigm Publishing Services

Publication frequency: Volume open

Keywords:

APY,

G-BLUP,

GEBV,

GT,

Related subjects:

Zoology,

© 2026 Dawid Słomian, Kacper Żukowski, Joanna Szyda, published by National Research Institute of Animal Production
This work is licensed under the Creative Commons Attribution 4.0 License.

Volume 26 (2026): Issue 3 (April 2026)

A Comparison of Genomically Enhanced Breeding Values Predicted by Different Single-Step Approaches

Figures & Tables

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Validation of GEBV predictions

Number of animals in the analyzed data sets

Computational resources utilized by the solvers

Variance components underlying the analyzed phenotypes

Paradigm

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