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Sparse single-step method for genomic evaluation in pigs.

Tage Ostersen¹, Ole F Christensen², Per Madsen²

¹SEGES Pig Research Centre, Axeltorv 3, 1609, Copenhagen V, Denmark. tao@seges.dk.

Genetics, Selection, Evolution : GSE

|July 1, 2016

Summary

This summary is machine-generated.

Selecting core animals across all generations and maximizing offspring representation improves genomic breeding value accuracy in animal breeding. This strategy enhances the efficiency of the proven and young (APY) method for genomic evaluations.

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Area of Science:

Animal breeding and genetics
Genomic evaluation methods
Quantitative genetics

Background:

Single-step genomic evaluation is computationally intensive with increasing genotyped animals.
The proven and young (APY) algorithm offers a computationally efficient approximation.
APY divides animals into core and non-core groups, with core computations being intensive.

Purpose of the Study:

To investigate optimal criteria for selecting core animals in the APY method.
To evaluate the impact of core group selection strategies on the accuracy of estimated breeding values (EBV).
To compare different core group compositions for accuracy in genomic evaluations.

Main Methods:

Compared eight core group selection strategies for the APY method across three pig breeds.
Evaluated strategies based on generational representation, minimizing within-group relatedness, and maximizing genotyped offspring.
Used a single-trait model for daily gain and correlated EBVs from sparse approximations with the standard single-step method.

Main Results:

Core groups representing all generations yielded higher EBV correlations (0.977–0.989) than those not distributing across generations (0.934–0.956).
Maximizing genotyped offspring in core groups resulted in higher correlations (0.983–0.989) compared to other methods (0.934–0.981).
No significant association was found between low within-core group relatedness and approximation accuracy.

Conclusions:

Core groups representing all generations and maximizing genotyped offspring provide accurate EBV approximations using the APY method.
The strategy of minimizing relatedness within the core group did not consistently improve accuracy.
Recommended criteria for APY core group selection: ensure generational representation and maximize genotyped offspring for enhanced accuracy.