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Background  Genomic best linear unbiased prediction methods assume that all markers explain the same fraction of the genetic variance and do not account effectively for genes with major effects such as the  α   s1   casein  polymorphism in dairy goats. In this study, we investigated methods to include the available  α   s1   casein  genotype effect in genomic evaluations of French dairy goats.    Methods  First, the  α   s1   casein  genotype was included as a fixed effect in genomic evaluation models based only on bucks that were genotyped at the  α   s1   casein  locus. Less than 1 % of the females with phenotypes were genotyped at the  α   s1   casein  gene. Thus, to incorporate these female phenotypes in the genomic evaluation, two methods that allowed for this large number of missing  α   s1   casein  genotypes were investigated. Probabilities for each possible  α   s1   casein  genotype were first estimated for each female of unknown genotype based on iterative peeling equations. The second method is based on a multiallelic gene content approach. For each model tested, we used three datasets each divided into a training and a validation set: (1) two-breed population (Alpine + Saanen), (2) Alpine population, and (3) Saanen population.    Results  The  α   s1   casein  genotype had a significant effect on milk yield, fat content and protein content. Including an  α   s1   casein  effect in genetic and genomic evaluations based only on male known  α   s1   casein  genotypes improved accuracies (from 6 to 27 %). In genomic evaluations based on all female phenotypes, the gene content approach performed better than the other tested methods but the improvement in accuracy was only slightly better (from 1 to 14 %) than that of a genomic model without the  α   s1   casein  effect.    Conclusions  Including the  α   s1   casein  effect in a genomic evaluation model for French dairy goats is possible and useful to improve accuracy. Difficulties in predicting the genotypes for ungenotyped animals limited the improvement in accuracy of the obtained estimated breeding values.

Including α s1 casein gene information in genomic evaluations of French dairy goats