Deregressed genomic breeding values from single-step evaluations of test-day traits using all genotype data

Abstract

Single-step model has become the Golden Standard for routine genetic evaluation in dairy cattle. For various statistical analyses or genomic validation, (daughter) yield deviations or deregressed genomic breeding values may be considered as pseudo-phenotype that are more independent from early genomic prediction. The aims of this study were to assess GEBV deregression methods for cows and bulls, and to validate the deregressed GEBV via a reversibility test. A total of 13.5 million animals with phenotypic records, evaluated with a single-step model using the German genotypic and phenotypic data from April 2023, were considered in the cow GEBV deregression. Likewise, all bulls with daughters and all reference cows were included in the bull GEBV deregression. Both GEBV deregression processes used the same genotype data and pedigree file as the preceding single-step evaluation. Deregressed GEBV of the cows or the bulls were moderately or highly correlated with their GEB, respectively. For the four test-day traits, milk, fat and protein yields and somatic cell scores, the deregressed GEBV seemed to have a lower trend than their original GEBV. Equal GEBV were obtained in a special single-step evaluation using the deregressed GEBV as phenotypic data, in comparison to those GEBV from the original single-step evaluation. We obtained equal GEBV not only for the cows with test-day records and bulls with daughters but nearly equal also for young, genotyped candidates without own phenotypic records. The validation results confirmed that the GEBV deregression was a reversible process and the deregressed GEBV were proven to be correct.