Marker weighting improves single-step genomic prediction reliabilities of udder health traits in Nordic Red and Jersey dairy cattle populations

The standard single-step genomic prediction model assumes that all SNP markers explain an equal amount of genetic variance, which, however, may not be true. This is because SNPs are located in or near different genes with different functions. Therefore, it seems logical to consider SNP marker-specific weights when predicting genomic breeding values. We hypothesized that allowing differences in the amount of genetic variance explained by each SNP marker will improve prediction reliability and response to selection. To investigate this hypothesis, we first developed multitrait standard single-step genomic models based on the current multitrait random regression evaluation models for udder health traits of the Nordic Red (RDC) and Jersey (JER) dairy cattle populations. The models included 4 clinical mastitis (CM) traits, 3 test-day SCS traits, and the conformation traits fore udder attachment and udder depth. In the second step, we investigated the effect of applying different SNP marker weighting scenarios in the single-step genomic prediction models, for which a single-step SNP best linear unbiased prediction model was applied. We investigated the prediction reliability of the different models by forward prediction, where the last 4 years of the data were removed to estimate breeding values for validation candidates. In addition, genetic trends of the pedigree-based estimated breeding values (PEBV) and GEBV were examined. The datasets for RDC and JER included 6.9 million and 1.2 million animals, of which 5.6 million and 0.9 million cows had records, respectively. The number of genotyped animals was 125,789 and 64,777 for RDC and JER, respectively. Cows had repeated SCS observations but only single observations for all other traits and breeding values for all traits were modeled by one covariance function. This required modeling 12 eigenvalue breeding value coefficients for each cow and developing SNP marker weights for the principal components rather than for the biological traits. We investigated 3 SNP marker weighting scenarios: (1) a nonlinear method similar to BayesA, (2) using the classical formula 2pqû² that accounts for allele heterozygosity, and (3) applying a mean SNP weight calculated by 2pqû² for every 20 adjacent SNP markers. Bias, dispersion, and prediction reliability were calculated using PEBV or GEBV from the evaluation based on the full dataset on those using the reduced dataset. We found that the recent favorable genetic trend in CM and SCS has been accelerated since the introduction of genomic selection. The study also shows that a significant increase in prediction reliability, i.e., 0.74 versus 0.48 for RDC and 0.72 versus 0.41 for JER cows for CM, can be achieved with a standard single-step genomic prediction model compared with a pedigree-based prediction model. Almost all scenarios with SNP marker weighting further improved the prediction reliability between 0.5% and 12.7%. The highest improvement was achieved by weighing the SNP markers based on the 2pqû² formula.