The Effect of Pedigree Error on Heritability and Accuracy of Prediction of Breeding Value in Threshold Traits

Complete information of relationship matrix is ​​an important principle to achieve reliable results in genetic evaluations. Two kinds of pedigree errors, including incorrect pedigree information and missing pedigree information, reduce the capability of the livestock model in traditional methods. The purpose of this study was to investigate the different levels of missing pedigree information such as sire, dam and both parents (sire and dam together) on heritability, accuracy of prediction and estimation of breeding value in threshold traits.

Sex-limited traits with heritability of 0.05, 0.1, and 0.2, were simulated. In order to create threshold phenotypes of litter size, 20% of the top-phenotypes were considered as two and the rest were considered as one. Different ratios of missing sire information (zero, 5, 10, 15 and 20), missing dam information (zeros, 5 and 10) and a combination of both missing information (sire and dam together) were created. A threshold model was considered. Heritability, breeding values ​​and accuracy of prediction were calculated by Bayesian statistical method.

With the introduction of different levels of missing pedigree information to the complete pedigree, the amount of heritability decreased. The lowest values ​​of heritability were 0.018, 0.084 and 0.16 for heritability of 0.05, 0.1 and 0.2, respectively. In the complete pedigree, the lowest and highest accuracy of prediction were 0.375 (h2 =0.05) and 0.521 (h2 =0.2), respectively. The lowest values of accuracy of prediction for heritability of 0.05, 0.1, and 0.2 were 0.309 (30% in paternal pedigree defects and 10% in maternal pedigree defects), 0.353 (paternal pedigree defects 20% and maternal pedigree defects 10%), and 0.459 (5% defect in paternal pedigree and 10% defect in maternal pedigree), respectively. Furthermore, missing pedigree information led to a decrease in the average breeding value.

The results showed that, compared to the paternal or maternal missing pedigree information separately, paternal and maternal missing pedigree information together, further reduces the estimation of genetic evaluations.