Estimation & Prediction

Single-step GBLUP breeding values for genotyped animals with unknown pedigree

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Abstract

Single-step GBLUP evaluations combine phenotypic records, pedigree and genotypes to predict genomically enhanced breeding values (GEBVs). Single-step evaluations would allow inclusion of genotyped animals with unknown parents but are at present not included in the Polish national genetic evaluation. As the properties of GEBV for such animals are not well documented, the aim of this study was to investigate the effect of missing parent information by masking pedigree for a subset of genotyped animals, predicting GEBV using the masked pedigree and compare with GEBV predicted using the complete pedigree. Data comprised 77.6 million test-day milk yield records for 4.2 million cows with a first calving between 1995 and 2024. In addition, de-regressed MACE breeding values for 151 thousand bulls (32,731 genotyped) were included. Pedigree was traced for three generations and comprised 5.9 million animals. Unknown parents were assigned to unknown parent groups (n=212) constructed based on country of origin, birth year and selection path. Genotypes were available for 238,754 animals and 40,681 markers. The model for evaluation was a single-trait multi-lactation random regression test-day model with lactations included as separate traits. The model included fixed effects of herd-test-day, herd-year of calving, and age-season of calving, and random genetic and permanent environment effects fitted with fourth order Legendre polynomials. De-regressed MACE breeding values were included as pseudo-phenotypes for bulls, with weights that reflect the amount of extra information in the MACE de-regressed breeding values. Breeding values for random regression coefficients were used to calculate breeding values for lactation (305-day) yield, which were subsequently combined into one milk yield breeding value per animal. Single-step evaluations were carried out using the blupf90+ suite of programs, applying the APY algorithm. Either 10% or 40% of genotyped Polish females without offspring were chosen to have their pedigree masked, resulting in 9509 and 38036 animals with masked pedigree. Masking was done in three different ways: mask the male parent, mask the female parent and mask both parents. Masked parents were assigned to unknown parent groups. GEBVs for masked and non-masked animals were examined, correlations, means and standard deviations were calculated. Correlations between GEBVs for animals with masked pedigree where high (≥ 0.99). GEBVs were lower when pedigree was masked, and the mean difference between breeding values with complete and masked pedigree ranged between 24 kg and 80 kg milk (relative to a genetic standard deviation of 855 kg) and was larger with 40% masking compared to 10% masking. Interestingly, GEBV differences were larger when one parent was masked than when both parents were masked. Breeding values for non-masked animals were virtually unaffected. Inclusion of genotyped animals without pedigree in a single-step GBLUP evaluation obtained slightly conservative GEBVs but did not affect GEBVs of other animals.

Keywords: 2026

How to Cite:

Fikse, F., Stachowicz, K., Graczyk-Bogdanowicz, M., Pszczola, M. & Mucha, S., (2026) “Single-step GBLUP breeding values for genotyped animals with unknown pedigree”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285496. doi: https://doi.org/10.31274/wcgalp.23726

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