Crossbreed evaluations in single-step genomic best linear unbiased predictor using adjusted realized relationship...

Area of Science:

• Animal Genetics and Breeding
• Genomic Selection
• Livestock Improvement

Background:

• Combining purebred and crossbred data enhances genetic evaluations in livestock.
• Single-step genomic BLUP (ssGBLUP) traditionally uses a single genomic relationship matrix, potentially limiting accuracy in crossbred populations due to varying allele frequencies.
• Breed-specific allele frequencies are important for accurate genomic relationship matrices.

Purpose of the Study:

• To evaluate the performance of different breed-specific genomic relationship matrices within ssGBLUP for crossbred genetic evaluations.
• To assess the impact of genotyping crossbred animals on the accuracy of genomic predictions.
• To determine if accounting for breed-specific allele frequencies improves genetic gain in crossbred populations.

Main Methods:

• Developed and tested breed-specific genomic relationship matrices (G matrices) using allele frequencies from purebred (AA, BB) and crossbred (F1) pig populations.
• Implemented ssGBLUP with various G matrices, including breed-specific and across-breed matrices, with and without adjustments for selective genotyping.
• Utilized simulated and real pig population data, performing cross-validation on F1 animals to compare prediction accuracies.

Main Results:

• Using breed-specific allele frequencies in G matrices reduced negative relationships between purebreds but did not consistently improve genomic estimated breeding value (GEBV) accuracy in F1 animals.
• Genotyping crossbred animals increased GEBV accuracy by up to 39% compared to using only purebred genotypes.
• For real populations, accuracies for litter size and stillborns were similar across tested G matrices, with minor negative impact from tuning for selective genotyping on one matrix.

Conclusions:

• Accounting for breed-specific allele frequencies in G matrices did not enhance GEBV accuracy in crossbred evaluations.
• Genotyping crossbred animals is essential for maximizing accuracy in crossbreed genetic evaluations.
• The optimal ssGBLUP approach for crossbreed evaluations involves using genotypes from both purebred and crossbred animals without breed-specific adjustments in the realized relationship matrix.