Effect of Marker Genotyping Error on the Prediction Accuracy of Genomic Breeding Value in Threshold Traits

The purpose of this study was to investigate the effect of different rates marker genotyping error and the type of mating and selection design (breeding value and phenotypic) on the accuracy of genomic prediction assessment under different levels of heritability (0.05, 0.1 and 0.3) and marker density (500, 1000 and 1500) by simulation in threshold trait. The genome consisted of two chromosomes, each 100 cM, and 125 QTLs were randomly distributed on each chromosome. In order to simulation a threshold trait, 20 percent of the top-level phenotypes were considered to be 2, and the rest were considered as 1. Genomic breeding value was predicted using marker effects estimated by Bayes B statistical method. Comparison of the accuracy of genomic evaluations showed that selection and mating designs of breeding value was more accurate than the selection and mating designs of phenotypic. The accuracy of genomic prediction decreased with increasing marker genotyping error in both selection and mating designs of breeding value and phenotypic. The results showed that with increasing the percentage of marker genotyping error, increasing the number of markers leads to increasing the accuracy of genomic breeding value prediction.