Heterogeneity of Variance Components for Milk Protein Yield in Different Levels of Herd-year Production and Its Effects on Genetic Parameters and Estimated Breeding Value of Iranian Holsteins

This study was carried out to investigate different data transformation methods on homogeneity and heterogeneity of variance components. Data included 305-day lactation records for protein yield from the first three lactations of Iranian Holstein cows collected from 1983 to 2014 by the Animal Breeding Center and Promotion of Animal Products of Iran. Data included 141670 records for 1st lactation, 115395 records for 2nd lactation and 82529 records for 3rd lactation. Records were categorized to 3 classes according to the average of herd-year production. For testing the heterogeneity of variance components Bartlet test was used and it was significant among all three lactations. A pre-correction method and two different data transformation methods including Box-Cox and Square root were used to correct for heterogeneity of variance. Genetic parameter and heritability estimates were estimated by VCE program, under an animal model. Spearman correlations and proportion of animals selected before and after data transformation were also estimated. Application of the Visscher adjustment method resulted in slightly higher heritabilities, which may be due to the more accurate estimation of additive genetic effects when heterogeneity is considered. Heterogeneity of variance had a significant effect on re-ranking and selection of 5% top sires and 1% of top dams. Pre-correction, Box-Cox and Square root method caused a proportion of 4%, 19% and 10% of top sires and 10%, 21% and 7% of top dams, respectively, to be excluded from selection when compared to the homogenous variance scenario. The results of this research indicate that the variance between different levels of herd-year production is not homogeneous and may influence the ranking and genetic evaluation of top cows.