A first step toward genomic selection in the multi-breed French dairy goat population

The objectives of this study were to describe, using the goat SNP50 BeadChip (Illumina Inc., San Diego, CA), molecular data for the French dairy goat population and compare the effect of using genomic information on breeding value accuracy in different reference populations. Several multi-breed (Alpine and Saanen) reference population sizes, including or excluding female genotypes (from 67 males to 677 males, and 1,985 females), were used. Genomic evaluations were performed using genomic best linear unbiased predictor for milk production traits, somatic cell score, and some udder type traits. At a marker distance of 50 kb, the average r(2) (squared correlation coefficient) value of linkage disequilibrium was 0.14, and persistence of linkage disequilibrium as correlation of r-values among Saanen and Alpine breeds was 0.56. Genomic evaluation accuracies obtained from cross validation ranged from 36 to 53%. Biases of these estimations assessed by regression coefficients (from 0.73 to 0.98) of phenotypes on genomic breeding values were higher for traits such as protein yield than for udder type traits. Using the reference population that included all males and females, accuracies of genomic breeding values derived from prediction error variances (model accuracy) obtained for young buck candidates without phenotypes ranged from 52 to 56%. This was lower than the average pedigree-derived breeding value accuracies obtained at birth for these males from the official genetic evaluation (62%). Adding females to the reference population of 677 males improved accuracy by 5 to 9% depending on the trait considered. Gains in model accuracies of genomic breeding values ranged from 1 to 7%, lower than reported in other studies. The gains in breeding value accuracy obtained using genomic information were not as good as expected because of the limited size (at most 677 males and 1,985 females) and the structure of the reference population