Single-step SNPBLUP evaluation in six German beef cattle breeds.

The implementation of genomic selection for six German beef cattle populations was evaluated. Although the multiple-step implementation of genomic selection is the status quo in most national dairy cattle evaluations, the breeding structure of German beef cattle, coupled with the shortcoming and complexity of the multiple-step method, makes single step a more attractive option to implement genomic selection in German beef cattle populations. Our objective was to develop a national beef cattle single-step genomic evaluation in five economically important traits in six German beef cattle populations and investigate its impact on the accuracy and bias of genomic evaluations relative to the current pedigree-based evaluation. Across the six breeds in our study, 461,929 phenotyped and 14,321 genotyped animals were evaluated with a multi-trait single-step model. To validate the single-step model, phenotype data in the last 2 years were removed in a forward validation study. For the conventional and single-step approaches, the genomic estimated breeding values of validation animals and other animals were compared between the truncated and the full evaluations. The correlation of the GEBVs between the full and truncated evaluations in the validation animals was slightly higher in the single-step evaluation. The regression of the full GEBVs on truncated GEBVs was close to the optimal value of 1 for both the pedigree-based and the single-step evaluations. The SNP effect estimates from the truncated evaluation were highly correlated with those from the full evaluation, with values ranging from 0.79 to 0.94. The correlation of the SNP effect was influenced by the number of genotyped animals shared between the full and truncated evaluations. The regression coefficients of the SNP effect of the full evaluation on the truncated evaluation were all close to the expected value of 1, indicating unbiased estimates of the SNP markers for the production traits. The Manhattan plot of the SNP effect estimates identified chromosomal regions harbouring major genes for muscling and body weight in breeds of French origin. Based on the regression intercept and slope of the GEBVs of validation animals, the single-step evaluation was neither inflated nor deflated across the six breeds. Overall, the single-step model resulted in a more accurate and stable evaluation. However, due to the small number of genotyped individuals, the single-step method only provided slightly better results when compared to the pedigree-based method.

Genomic evaluation of carcass traits of Korean beef cattle Hanwoo using a single-step marker effect model.

Hanwoo beef cattle are well known for the flavor and tenderness of their meat. Genetic improvement programs have been extremely successful over the last 40 yr. Recently, genomic selection was initiated in Hanwoo to enhance genetic progress. Routine genomic evaluation based on the single-step breeding value model was implemented in 2020 for all economically important traits. In this study, we tested a single-step marker effect model for the genomic evaluation of four carcass traits, namely, carcass weight (CW), eye muscle area, backfat thickness, and marbling score. In total, 8,023,666 animals with carcass records were jointly evaluated, including 29,965 genotyped animals. To assess the prediction stability of the single-step model, carcass data from the last 4 yr were removed in a forward validation study. The estimated genomic breeding values (GEBV) of the validation animals and other animals were compared between the truncated and full evaluations. A parallel conventional best linear unbiased prediction (BLUP) evaluation with either the full or the truncated dataset was also conducted for comparison with the single-step model. The estimates of the marker effect from the truncated evaluation were highly correlated with those from the full evaluation, ranging from 0.88 to 0.92. The regression coefficients of the estimates of the marker effect for the full and truncated evaluations were close to their expected value of 1, indicating unbiased estimates for all carcass traits. Estimates of the marker effect revealed three chromosomal regions (chromosomes 4, 6, and 14) harboring the major genes for CW in Hanwoo. For validation of cows or steers, the single-step model had a much higher R2 value for the linear regression model than the conventional BLUP model. Based on the regression intercept and slope of the validation, the single-step evaluation was neither inflated nor deflated. For genotyped animals, the estimated GEBV from the full and truncated evaluations were more correlated than the estimated breeding values from the two conventional BLUP evaluations. The single-step model provided a more accurate and stable evaluation over time.

Hanwoo beef cattle are well known for the flavor and tenderness of their meat. Genetic improvement programs have been successful over the last 40 yr. Recently, genomic selection was initiated in Hanwoo to enhance genetic progress. A routine genomic evaluation based on the single-step breeding value model was implemented in 2020 for all economically important traits. In this study, we tested a single-step marker effect model for the genomic evaluation of four carcass traits. In total, 8,023,666 cows or steers with carcass records were jointly evaluated, including 29,965 genotyped animals. To assess the prediction accuracy of the single-step model, carcass data from the last 4 yr were removed in a forward validation study. Estimated genomic breeding values (GEBV) of validation animals were compared between truncated and full evaluations. A parallel conventional best linear unbiased prediction (BLUP) evaluation with either the full or truncated dataset was conducted for comparison with the single-step model. Plots of the estimates of the marker effect showed three chromosomal regions harboring the major genes for carcass weight in Hanwoo. The single-step model yielded a more accurate and stable evaluation over time than the conventional BLUP model.

Replacement of microsatellite markers by imputed medium-density SNP arrays for parentage control in German warmblood horses.

In horses, parentage control is currently performed based on an internationally standardized panel of 17 microsatellite (MS) markers comprising 12 mandatory and five optional markers. Unlike MS, single nucleotide polymorphism (SNP) profiles support a wider portfolio of genomic applications, including parentage control. A transition to SNP-based parentage control is favorable, but requires additional efforts for ensuring generation-overlapping availability of marker genotypes of the same type. To avoid double genotyping of either parents or offspring for changing to SNP technology and enable efficient transition, we tested whether MS genotypes used for parentage control could be reliably imputed from a medium-density SNP panel in German warmblood horses. Imputation accuracy was tested in a tenfold cross-validation with two approaches: within breed (option A) and across breeds (option B). Average imputation accuracies of 97.98% (A) and 96.17% (B) were achieved, respectively. Due to interbreed differences in genotyping rates, five MS markers of low genotyping rate (GTR; < 90%) could be imputed with higher accuracy within breed (98.18%) than across breeds (90.73%). MS markers with high GTR performed homogeneously well in option B (98.44%) and showed slightly lower accuracy in option A (97.90%). Among these markers, AHT5 proved to be problematic for imputation regardless of the approach, revealing accuracies of 86.40% (A) and 88.70% (B). Better results for MS markers with high GTR and savings in computational processing justified the choice of option B for routine implementation. To date, more than 9500 horses have undergone the new parentage control based on imputed MS genotypes.