Abstract
BackgroundAll progeny-tested bucks from the two main French dairy goat breeds (Alpine and Saanen) were genotyped with the Illumina goat SNP50 BeadChip. The reference population consisted of 677 bucks and 148 selection candidates. With the two-step approach based on genomic best linear unbiased prediction (GBLUP), prediction accuracy of candidates did not outperform that of the parental average. We investigated a GBLUP method based on a single-step approach, with or without blending of the two breeds in the reference population.MethodsThree models were used: (1) a multi-breed model, in which Alpine and Saanen breeds were considered as a single breed; (2) a within-breed model, with separate genomic evaluation per breed; and (3) a multiple-trait model, in which a trait in the Alpine was assumed to be correlated to the same trait in the Saanen breed, using three levels of between-breed genetic correlations (ρ): ρ = 0, ρ = 0.99, or estimated ρ. Quality of genomic predictions was assessed on progeny-tested bucks, by cross-validation of the Pearson correlation coefficients for validation accuracy and the regression coefficients of daughter yield deviations (DYD) on genomic breeding values (GEBV). Model-based estimates of average accuracy were calculated on the 148 candidates.ResultsThe genetic correlations between Alpine and Saanen breeds were highest for udder type traits, ranging from 0.45 to 0.76. Pearson correlations with the single-step approach were higher than previously reported with a two-step approach. Correlations between GEBV and DYD were similar for the three models (within-breed, multi-breed and multiple traits). Regression coefficients of DYD on GEBV were greater with the within-breed model and multiple-trait model with ρ = 0.99 than with the other models. The single-step approach improved prediction accuracy of candidates from 22 to 37% for both breeds compared to the two-step method.ConclusionsUsing a single-step approach with GBLUP, prediction accuracy of candidates was greater than that based on parent average of official evaluations and accuracies obtained with a two-step approach. Except for regression coefficients of DYD on GEBV, there were no significant differences between the three models.
Highlights
All progeny-tested bucks from the two main French dairy goat breeds (Alpine and Saanen) were genotyped with the Illumina goat SNP50 BeadChip
Estimates were close to those estimated between Holstein and Normande and between Montbéliarde and Normande dairy cattle breeds [18], i.e. from 0.38 to 0.46 for milk yield and from 0.35 to 0.56 for fat content, but lower than the correlations between Holstein and Montbeliarde breeds (0.79 for milk yield and 0.66 for fat content). These results suggest that French Holstein and Montbeliarde dairy cattle breeds are genetically closer than the Alpine and Saanen goat breeds, perhaps due to the introgression of Red Holstein genes in the Montbéliarde breed in the 1980’s
Quality of the predictions was similar for the three models, except for the dispersion of the genomic breeding values (GEBV), which was better with the within-breed model
Summary
All progeny-tested bucks from the two main French dairy goat breeds (Alpine and Saanen) were genotyped with the Illumina goat SNP50 BeadChip. We investigated a GBLUP method based on a single-step approach, with or without blending of the two breeds in the reference population. With the recent availability of the Illumina goat SNP50 BeadChip [1], it has become possible to study the implementation of genomic selection in French dairy goat. In this species, as in dairy cattle, genomic selection has the ability to shorten the generation interval for the sire-son pathway (5.5 years with progeny-testing [2]) by selecting Considering the relatively small sample size and the genetic structure of this population, the prediction accuracy of GEBV is not expected to be as high in these populations as in dairy cattle [4]
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