Including αs1casein gene information in genomic evaluations of French dairy goats

BackgroundGenomic 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 αs1casein polymorphism in dairy goats. In this study, we investigated methods to include the available αs1casein genotype effect in genomic evaluations of French dairy goats.MethodsFirst, the αs1casein genotype was included as a fixed effect in genomic evaluation models based only on bucks that were genotyped at the αs1casein locus. Less than 1 % of the females with phenotypes were genotyped at the αs1casein gene. Thus, to incorporate these female phenotypes in the genomic evaluation, two methods that allowed for this large number of missing αs1casein genotypes were investigated. Probabilities for each possible αs1casein 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.ResultsThe αs1casein genotype had a significant effect on milk yield, fat content and protein content. Including an αs1casein effect in genetic and genomic evaluations based only on male known αs1casein 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 αs1casein effect.ConclusionsIncluding the αs1casein 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.