Genomic diversity of Cameroonian Gudali and Gudali-cross cattle

Information on population structure and diversity in cattle breeds is critical for understanding environmental adaptation, as well as optimal utilisation of genetic resources and breed improvement. In this study, we investigated at the genomic level the population 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 GeneSeek® Genomic ProfilerTM (GGP) Bovine 100K array and analyzed together with reference breed data from public databases. Principal component (PCA) and admixture analysis separated 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 an ancient admixture from Asian origin in Gudali and a more recent and ongoing European introgression. Simgud is an unmanaged crossbreed expected to be primarily a 50% admixture of Gudali and Simmental. We show here that Simgud is, in actuality, composed of two genetic groups representing admixture of between ∼25% to ∼50% Simmental proportion. Diversity analysis revealed high average heterozygosity (Ho = 0.34 ± 0.14, He = 0.35 ± 0.13) for the Gudali and (Ho = 0.42 ± 0.13 , He = 0.40 ± 0.11) for Simgud respectively. Inbreeding measures based on the mean FIS coefficient were 0.03 for Gudali and 0.07 for Simgud. A general decline in effective population size was observed in Gudali from a large population (Ne=2475), 959 generations (4797 years ago), back to 13 generations (65 years) (Ne=1404) ago. These results were expected, given the breeding efforts that began in 1952 with the introduction of various exotic (imported taurine) breeds and the Gudali selection initiative. This has affected the effective population size of Gudali, despite the general increase in cattle population in the ranches over that period. These results highlight the need for a structured breeding program in Cameroon for improving productivity, while maintaining a large genetic base of the pure Gudali population.