This article addresses a currently relevant topic of detecting associations of copy number polymorphisms with traits and will be of interest to readers of Genetics Research. The simulation study showed that the additional CNP information could increase the accuracy of the predicted genotypic value, compared to using SNP information alone in an association study. Accuracy was highly dependent on the heritability of CNP phenotypes (correlation of CNP genotype and phenotype) (Table 3). The higher prediction accuracy with CNP information could also result in lower prediction root mean square errors (Table 4). On the other hand, the authors found that the linkage disequilibrium (LD) between SNP and CNP was not much different from that between two SNPs. The authors demonstrated that an increased mutation rate and a larger number of segregating alleles hardly affect LD with a nearby SNP. I have the following main comments. 1) One possible reason for high accuracy in using CNP information was that CNP was the causal gene itself in the simulation. If the CNP had negligible effects and was simply linked to a causal gene, the performance might not be very different from that of the SNPs, because, as noted above, the structure of the LD was not very different between the SNP and the CNP. In this situation, the success of using CNP information to predict genotypic values ​​would be conditional on 1) effects due to the causal CNP should explain a significant proportion of genetic variation, 2) these causal CNPs should be genotyped, and 3) l accuracy of genotyping. for CNP should be reasonably high. In general, how easily and accurately are causal NOCs identified? What is the underlying distribution of effects due to CNPs? Can we expect the right Middle of Paper......the same effect from the same direction and magnitude. Would this be realistic?10) Line 158, If the copy number is the same (c=b), the equation would result in zero. Is this true?11) Line 171, SNP phenotypes -> CNP phenotypes?12) Line 242, 2 or 3 alleles > 2 or 3 copies?13) Table 2. It may be useful to have a likelihood ratio for each model.14) Lineage 267, phenotype -> phenotype?15) The introduction is human/livestock oriented, but the rest of the article is presented in livestock terminology. A discussion of the relevance of the results to human populations would be helpful. 16) Line 343 "Assuming that x copies at a CNP locus lead to an effect x times greater than that of one copy", is this a realistic assumption? Is the 4 copy CNP genotype likely to have the same functional impact for individuals with 2/2 alleles vs 4/0.