How pedigree errors affect genetic evaluations and validation statistics.

Area of Science:

• Animal Genetics
• Quantitative Genetics
• Bioinformatics

Background:

• Pedigree data is crucial for genetic evaluations, but errors can compromise accuracy.
• Previous studies examined pedigree error effects without genomic information.
• The impact of pedigree errors on advanced single-step genetic evaluation models remains less understood.

Purpose of the Study:

• To investigate the impact of pedigree errors on genetic evaluations using the single-step model.
• To assess how pedigree errors affect forward prediction validation studies.
• To quantify the consequences of varying rates of pedigree errors (5-20%) in Fleckvieh cattle.

Main Methods:

• Utilized real pedigree and genotype data from Fleckvieh cattle.
• Simulated true breeding values (TBV) and phenotypes based on a heritability of 0.25.
• Conducted genetic evaluations using conventional and single-step animal models with correct and error-containing pedigrees (5%, 10%, 20% errors).
• Introduced errors by randomly assigning incorrect sires to nongenotyped females.

Main Results:

• Increasing pedigree error rates decreased the correlation between TBV and estimated breeding values (EBV).
• Higher error rates led to lower standard deviations in predictions, reducing observed genetic variation.
• Variation reduction was more pronounced in progeny-tested bulls than young candidates.
• In forward prediction, reduced variation caused apparent inflation of early predictions.

Conclusions:

• Pedigree errors significantly reduce the accuracy of genetic evaluations in single-step models.
• The random exchange of daughters among bulls due to errors artificially homogenizes genetic groups.
• Observed inflation in early predictions during validation studies may be partly explained by pedigree error effects.