Level-biases in estimated breeding values due to the use of different SNP panels over time in ssGBLUP.

Because, historically, different SNP chips have been used for genotyping different parts of a population, fine-tuning of imputation within and across SNP chips and handling of missing genotypes are crucial for reducing bias. Although all the SNPs used for estimating breeding values are present on the chip used for genotyping young animals, incompleteness and some genotype errors might lead to level-biases in breeding values.