Genetic structure and diversity of dairy cows in commercial herds in Burkina Faso using microsatellite markers

Abstract

The present study provides knowledge about the genetic diversity and population structure of cows in peri-urban cattle herds that are urgently needed for the planning of systematic selection programs. We considered 21 microsatellite markers to identify genetic clusters for 112 dairy cows from Burkina Faso and a reference dataset of European cattle breeds (n = 179). Unsupervised clustering and a model-based approach were used for identification of latent classes and inference of genetic diversity within classes. Overall, the genetic diversity of cows in commercial dairy herds in Burkina Faso was high. Clustering results suggest four genetic clusters. Almost all cows from Burkina Faso shared the same ancestry and were grouped together in cluster 3. The highest expected heterozygosity (H_E = 0.74) and inbreeding coefficient (F_IS = 0.08) were obtained for this cluster. The other genetic clusters included Original Braunvieh and Tarentaise (cluster 1), Red Holstein (cluster 2) and Fleckvieh (cluster 4). The genetic distances of cluster 3 to the other clusters were large. In conclusion, the poor population structuring, and the low genetic contribution of European cattle breeds underline the need for effective (cross-)breeding strategies for optimal exploitation of heterosis effects and maintaining genetic diversity in dairy cows in Burkina Faso.