The effect of using cow genomic information in reference population on the accuracy ‎of genomic estimated breeding values in Iranian Holstein cattle

Document Type : Research Paper


1 Ph.D. Cnadidate, Aras International Campus, University of Tehran, Jolfa, Iran‎

2 Professor, Department of Animal Science, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran

3 Assistant Professor, Department of Animal Science, University of Guelph, Canada


Accurate genomic evaluation depend on large reference population with reliable performance information such as predicted breeding value (PBVs). The aim of this study was to identify the most appropriate reference population to predict the genomic breeding value for Iran Holstein dairy breeding programs. Phenotypes and genotypes were simulated based on the dairy cattle Iran population program (open breeding nucleus with gene flows between the nucleus and the commercial population). Medium (0.3) and low (0.05) heritability levels were considered independently. All simulations were performed with 10 replications and the results were evaluated. In the first study, female cows were selected for genotyping in four scenarios: random selection, individuals with upper and lower extremities of phenotypic value, highest phenotypic value and highest breeding value with maximum accuracy; and these females are added to the reference population. Single Step BLUP (SSBLUP) was used to predict the genomic breeding value for individuals in the population. The accuracy and unbiased coefficient of predicted breeding value were investigated. The results showed that when female animals with the highest and lowest phenotypic values were selected (the second scenario of determining females), the highest accuracy of prediction of breeding value was observed compared to other scenarios. Determination of substances with high phenotypic value (third scenario of female selection) showed the least bias. The use of imported males with genotype and their use alone as a reference population showed the least accuracy and the most bias. The combination of males and females showed an increase in accuracy and a decrease in bias compared to the scenarios for males or females alone. However, in relation to the size of the population similar to females, no improvement in the prediction of the breeding value was observed. Therefore, in terms of economic conditions (genotyping costs), the use of only female cows in the reference population (2000 females genotyped), according to the second scenario of female selection, is the best strategy to form a reference population and genomic evaluation at the lowest cost, in Iran.


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