Feasibility of joint genomic evaluations for smallholder dairy data in Tanzania and Ethiopia

Abstract

One of the approaches to increasing the accuracy of genomic predictions when the reference population size is limited is by joint across country evaluations. Such an approach is straightforward only when one breed is involved. However, in small holder dairy systems in East Africa, the cows are mostly crossbreds and breeds and breed types used in the crossing and the breed composition of cows tend to be different among countries.  The feasibility and benefits of joint across country evaluations have not been demonstrated for such systems. This paper therefore examines the feasibility of across joint country genomic evaluations for milk yield in Tanzania and Ethiopia. PCA analysis indicated that the first principal component accounted for about 50 percent of the variation between bulls and cows genotyped in both countries. The genetic correlation between both countries from a bivariate analysis was rather low at 0.12±0.10. Marginal increases in the accuracy for genomic prediction of about 2.5% were observed for Ethiopia from a joint analysis of all data from both countries or only including a sub-set of 500 related from Tanzania. The increase was only 1.7% for Tanzania when a sub-set of 500 related cows were included from Ethiopia. The current data structure indicates no advantage from joint analysis of data from both countries, but the study does highlight the need to deliberately exchange top ranking bulls between both countries.