Genetic evaluation of test day milk yields from smallholder dairy production systems in Kenya using genomic relationships: genetic evaluation in smallholder dairy cattle

Efforts to improve dairy production in smallholder farming systems of Eastern Africa over the past decade have had limited impact due to the lack of records on performance to guide targeted breeding programs. Estimates of genetic parameters in these systems are lacking. Using data generated through a project on “Germplasm for Dairy Development in East Africa” in Kenya, and a genomic relationship matrix from genotypic records, we examine the potential impact of different models handling contemporary groups or herd effects on estimates of genetic parameters using a fixed regression model (FRM) for test-day (TD) milk yields, and the covariance structure for TD milk yield at various stages of lactation for animals using a random regression model (RRM). Models where herd groups were defined using production levels derived from the data fitted the data better than those in which herds were either grouped depending on management practices or were random. Lactation curves obtained for animals under different production categories did not display a typical peak yield characteristic of improved dairy systems in developed countries. Heritability estimates for TD milk yields using FRM varied greatly with the definition of contemporary herd groups ranging from 0.05 ± 0.03 to 0.27 ± 0.05. The analysis using a RRM fitted the data better than the FRM. The heritability estimates for specific TD yields obtained by RRM were higher than those obtained by the FRM. Genetic correlations between TD yields were high and positive for measures within short consecutive intervals but decreased as the intervals between TDs increased beyond 60 days and became negative with intervals that were more than five months between TD. The magnitude of the genetic correlation estimates among TD records indicates that it would not be optimum to use TD milk records beyond a 60-day interval for genetic evaluation of animals on the smallholder farms as repeated measures of the same trait. Though each individual smallholder farmer retains only a few animals, using the genomic relationship between animals to link the large number of farmers operating under specified environments provide a sufficiently large “herd-group” for which a breeding program could potentially be developed.