The effect of missed sire pedigree on genetic parameters and accuracy of selection of two related quantitative traits using computer simulation

Introduction: According to the FAO in 2017, Iran, with 40 milion head of sheep and 291200 ton sheep meat, is the eighth country in the world of sheep production(http://www.fao.org/faostat/en/#data). One of the most important factors influencing accuracy of the estimated breeding value is complete sire pedigree information. Registration of father's number in sheep flocks of Iran is a big problem, through not having  any program for the control of matting program and artificial insemination. Therefore, the information of sire pedigree is not complete in sheep flocks. Incomplete pedigree causes incorrect relationship matrix and reduces accuracy of the selection and estimation of the genetic parameters of the traits and increases errors in the estimates(Clement et al., 2001). So, the existence of false and missing father’s information reduces genetic gain that this decrease in traits with low heritability have steeper slope. Imperfect sires pedigree data increase standard deviation between different repetitions of estimating variance components and cause bias estimation of genetic and phenotypic parameters(Sanders et al., 2006). Therefore, increase of unknown father's will be decreased direct and maternal heritability and breeding value, but the phenotypic variance will not be affected(Senneke et al., 2004).The estimation of heritability in complete and unbiased pedigree is similar to its actual value. But, random excluding of  50% of father’s ID led to bias estimation of heritability. If 50% of parent’s ID removed  from pedigree, the estiomation of heritability will be incorrect(Cantet et al.,2000). Generally, incomplete pedigree increases the standard error of estimations(Dong et al., 1988). Comparing random and consecutive exclusion pedigree methods (consecutive From zero to the last generation) for a trait with heritability of 0.15 showed random exclusion method leaded to a slight reduction in genetic variation, which consequently declined estimation of heritability. But for other trait with heritability of 0.30 different estimation of variance components leaded to significant decrease in estimation of heritability. In the consecutive exclusion method, the reduction of heritability was not significant with an increase  missing in pedigree of sires(Abbasi et al., 2011). Our objective in this study was investigation of influence of incomplete sire's pedigree on estimation of (co) variance components, genetic parameters and accuracy.
Material and methods: In this study we simulated a population with weaning weight (WW) and average daily gain(ADG) records. Heritability for weaning weight (WW) and average daily gain(ADG) were 0.15 and 0.30 respectively and genetic, environmental and phenotypic correlation for two traits were 0.5. Average of weaning weight was 22.29 kg, genetic variance was 1.7525, environmental variance was 9.759, phenotypic variance was 11.5, and heritability was 0.15. The average amount of  genetic variance,  environmental variance, and  phenotypic variance for daily weight gain were 190 g, 1078.2 , 2515.8, 3594, respectively and heritability was 0.3. The pedigree file and performance data were included of animal ID, father and mother ID, phenotypic variance, breeding value, and environmental effects for two traits. Visual Basic 6 program was used for simulation. Mating was random in both populations and the maximum maintenance age of sire and dam was 3 and 6 years, respectively. The ratio of female to male was15:1. In the generated data file, the sire numbers were eliminated asrandom and sequential with proportions 0 to 100 perecnt.The resulted data file were analyzed based on  two traits animal model. The accuracy of selection calculated from correlation between actual and predicted breeding values.
Results and discussion: The simulation of data file consist of 20625 head of sheep and base population was 2075 head in this study. Data file included animal ID, sire ID, dam ID, phenotypic value for weaning weight and daily weight gain. Random 10% deletion  of father’s ID increaed unknown fathers from 2750 to 4490 ,while unknown fathers for random 80% deletion  was  equal to 16973. In random and consecutive deletion method, phenotypic variances for two traits were slightly constant. The variance of daily weight gain for random deletion in diferent levels was stable. But the genetic variances were decreased and the environmental variances were slightly increased. The heritabilities of two traits were significantly (p < 0.05) reduced in random deletion method.  These results were almost contrary to the results of the randomization method in analysis of a trait with heritability of 0.15, in which the reduction of heritability was not significant(Abbasi et al., 2011). Standard error of heritability in final removal percentage with increase in defect of father's ID slightly increased. In randomization method, variation of variance components led to decrease estimated heritability in 0-80% exclusion of father's ID. In exclusion of father's ID estimated heritability slightly increased by 90 and 100 percent,  which were significant compared with base population (p < 0.05). The reduction of genetic variances and heritabilities with increasing in deletion proportion of sire pedigree were only significant(p < 0.05) for 50 to 90 percent of sire pedigree sequential deletion. The accuracy of selection were reduced from 0.767 to 0.493 and 0.933 to 0.614 for WW and ADG, respectively. Genetic correlations were reduced with increasing in missing proportion of sire number in random deletion method. But in sequential deletion method, the reductions of genetic correlations were only significant for the proportions of 60 and 80 percent in deletion of sire ID.
Conclusion: Incomplete pedigree generates incorrect relationship matrix and bias in the estimation of variance components, genetic parameters of traits and the accuracy of selection. so that , the percentage of  father's ID deletion had a slight influence on phenotypic variance, phenotypic, and environmental correlation. The effect of random deletion of father’s ID on pedigree information had more influence than consecutive deletion method; then, this effect depends on the actual heritability, kind of traits, and the structure of simulated data. Generally, genetic variances, heritabilities, the accuracy of selection and genetic correlation between two traits were reduced with inceasing the proportional deletion  of sire number. The reduction of accuracy associated with genetic progress of traits; then, it is necessary to develop artificial insemination and others control mating method in order to record father's ID.