Population structure, admixture analysis anddifferentiation in local Gudali and its crossbred withItalian Simmental, in Cameroon

Abstract Information on population structure and diversity in cattle breeds is critical for understanding environmental adaptation, aswell as optimal utilisation of genetic resources and breed improvement. In this study, we investigated at the genomic level thepopulation structure, genetic diversity and admixture of the local Gudali breed and its crossbred with the Italian Simmental(Simgud) in three agroecological zones of Cameroon. A total of 717 Gudali and 139 Simgud were genotyped using the GGPBovine 100K array and analyzed together with reference breed data from public databases. PCA and admixture analysisseparated European Bos taurus from Asian Bos indicus, African Bos taurus and African Bos indicus breeds. These analyses showed that, except for recently admixed cattle, all African indigenous breeds are either pure African Bos taurus (N’Dama)or admixtures of African Bos taurus and Bos indicus. Analysis revealed ancient admixture from Asian origin in Gudali and amore recent and ongoing European introgression. Simgud is an admixed population of 25% and 50% Simmental proportion. Differentiation analysis showed that Gudali and Simgud have high genetic diversity (He=0.34 and He=0.41) respectively.Inbreeding measures based on the FIS coefficient were 0.03 for Gudali and 0.07 for Simgud. A general decline in effectivepopulation size was observed in Gudali from a large population 959 generations ago. This is not surprising given breedingefforts throughout the (period here) that involved introduction of Simmental genetics. This has affected the effective populationsize of Gudali, despite the general increase in cattle population in the ranches over that period. These results highlight theneed for a structured breeding program in Cameroon for improving productivity, while maintaining a large genetic base of thepure Gudali population.