Genetic Analysis of Production Traits in Iranian Holstein Cows Considering Genetic Grouping

The lack of sufficient information in the pedigree of the animals prevents the correct estimation of the breeding values. Henderson proposed a genetic grouping for a more realistic estimation of breeding values for phenotypic records in different years. For these groups, the birth year, the year that the first daughter of the male had recorded, or the year that the male animal was used for insemination were used for grouping. In fact, this grouping was considered for calculating the genetic trend over the years. The incomplete recording of the animals in the population will result in the elimination of true genetic relationships between animals. Although, these animals are considered as the base animal in the analysis, but not born at the same time, and can affect the accuracy of estimated breeding values. The available pedigree information in Iran does not have a good quality index. So that the average of pedigree completeness criterion for Iranian Holstein cows has been reported less than 0.7. Genetic evaluation of Iranian Holstein cows with unknown parents may cause a bias in estimating genetic parameters and breeding values. The use of genetic groups in genetic analysis can partly correct the problem of animals with unknown parents. In this regard, the purpose of this study was to estimate the genetic parameters and breeding values of the production traits (milk, fat, protein) of Iranian Holstein cows with and without genetic grouping in model.

In this study, the pedigree of 1555702 heads of the Iranian Holstein cattle from 14623 sires and 697940 dams that collected by Animal breeding center of Iran till 2013, were used. Production traits, including milk, fat and protein corrected for 305 days and twice milking from first to third lactation periods were used to estimate variance components and breeding values. Herds under 100 heads were not considered for analysis and for all production traits; pedigree related to animals with the record was extracted from the general pedigree using CFC software and used. For animals with unknown parents, genetic grouping was performed based on the sex and the birth year. Traits at different lactation periods analyzed with (model 2) and without (model 1) genetic grouping in the model and genetic trend was calculated. Then the accuracy of breeding values and genetic trend of traits obtained from different models were compared with each other. The Spearman rank correlation was used to investigate the change in animal ranking in a result of considering the genetic grouping.

The additive genetic variance and their standard error were lower for milk, fat and protein production traits in model with genetic grouping (model 21) than the model without genetic grouping (model 1). The estimated heritability range for milk, fat and protein production in three lactation periods with model 1 was 0.094-0.162, 0.069-0.114, and 0.079-0.123, respectively, that these values were higher than model 21 in terms of magnitude. Spearman rank correlation between the estimated breeding values with model 1 and 21 was significantly different from 1, indicating a change in animal rank with consideration of genetic grouping in the model. The spearman rank correlation was lower for males than females, suggesting a higher change in male animal's rank than females. The average accuracy estimated breeding values with model 21 was higher than model 1 and the average accuracy difference was significant between two models. The genetic trend in the first, second and third lactation periods with the model 21 was estimated 63.06, 59.60 and 44.64 for milk production, 1.346, 1.095 and 0.943 for fat and 1.542, 1. 514 and 1.035 kg per year for protein, which were higher than the estimates of model 1.

The results showed that consideration of genetic grouping in the model reduced the additive genetic variances of traits and the heritability estimated were higher without consideration of genetic grouping. The significance of the Spearman rank correlation indicates that the rank of males and females changed by inserting genetic groups into the model and change in the animal's rank for males was higher than females. The high accuracy of estimated breeding values and the genetic trends of traits in the model with genetic grouping suggests that genetic grouping for animals with unknown parents has been done and entered into the model in order to more accurately estimate the breeding values and to better reflect the performance of the breeding programs.