Genetic variability and relationships in nine South African cattle breeds using microsatellite markers

Tropical Animal Health and Production - Genetic variability within and between breeds allows adaptation to a changing environment and consequently prepares producers for the future. Eleven...     

Use of SNP genotyping to determine pedigree and breed composition of dairy cattle in Kenya

High levels of inbreeding in East African dairy cattle are a potential concern because of use of a limited range of imported germplasm coupled with strong selection, especially by disease, and sparse performance recording. To address this, genetic relationships and breed composition in an admixed population of Kenyan dairy cattle were estimated by means of a 50K SNP scan. Genomic DNA from 3 worldwide Holstein and 20 Kenyan bulls, 71 putative cow‐calf pairs, 25 cows from a large ranch and 5 other Kenyan animals were genotyped for 37 238 informative SNPs. Sires were predicted and 89% of putative dam‐calf relationships were supported by genotype data. Animals were clustered with the HapMap population using Structure software to assess breed composition. Cows from a large ranch primarily clustered with Holsteins, while animals from smaller farms were generally crosses between Holstein and Guernsey. Coefficients of relatedness were estimated and showed evidence of heavy use of one AI bull. We conclude that little native germplasm exists within the genotyped populations and mostly European ancestry remains.     

Across breed multi‐trait random regression genomic predictions in the Nordic Red dairy cattle

The current study evaluates reliability of genomic predictions in selection candidates using multi‐trait random regression model, which accounts for interactions between marker effects and breed of origin in the Nordic Red dairy cattle (RDC). The population structure of the RDC is admixed. Data consisted of individual animal breed proportions calculated from the full pedigree, deregressed proofs (DRP) of published estimated breeding values (EBV) for yield traits and genotypic data for 37 595 single nucleotide polymorphic markers. The analysed data included 3330 bulls in the reference population and 812 bulls that were used for validation. Direct genomic breeding values (DGV) were estimated using the model under study, which accounts for breed effects and also with GBLUP, which assume uniform population. Validation reliability was calculated as a coefficient of determination from weighted regression of DRP on DGV (), scaled by the mean reliability of DRP. Using the breed‐specific model increased the reliability of DGV by 2 and 3% for milk and protein, respectively, when compared to homogeneous population GBLUP. The exception was for fat, where there was no gain in reliability. Estimated validation reliabilities were low for milk (0.32) and protein (0.32) and slightly higher (0.42) for fat.