Comparison between genomic predictions using daughter yield deviation and conventional estimated breeding value as response variables.

This study compared genomic predictions using conventional estimated breeding values (EBV) and daughter yield deviations (DYD) as response variables based on simulated data. Eight scenarios were simulated in regard to heritability (0.05 and 0.30), number of daughters per sire (30, 100, and unequal numbers with an average of 100 per sire) and numbers of genotyped sires (all or half of sires were genotyped). The simulated genome had a length of 1200 cM with 15,000 equally spaced Single-nucleotide polymorphism (SNP) markers and 500 randomly distributed Quantitative trait locus (QTL). In the simulated scenarios, the EBV approach was as effective as or slightly better than the DYD approach at predicting breeding value, dependent on simulated scenarios and statistical models. Applying a Bayesian common prior model (the same prior distribution of marker effect variance) and a linear mixed model (GBLUP), the EBV and DYD approaches provided similar genomic estimated breeding value (GEBV) reliabilities, except for scenarios with unequal numbers of daughters and half of sires without genotype, for which the EBV approach was superior to the DYD approach (by 1.2 and 2.4%). Using a Bayesian mixture prior model (mixture prior distribution of marker effect variance), the EBV approach resulted in slightly higher reliabilities of GEBV than the DYD approach (by 0.3-3.6% with an average of 1.9%), and more obvious in scenarios with low heritability, small or unequal numbers of daughters, and half of sires without genotype. Moreover, the results showed that the correlation between GEBV and conventional parent average (PA) was lower (corresponding to a relatively larger gain by including PA) when using the DYD approach than when using the EBV approach. Consequently, the two approaches led to similar reliability of an index combining GEBV and PA in most scenarios. These results indicate that EBV can be used as an alternative response variable for genomic prediction.