In previous studies, significant differences in Mycobacterium bovis infection prevalence was reported between two Chadian cattle breeds. Those findings and the established differentiation due to phenotypic characteristics suggest that the two breeds (Arab and Mbororo) are genetically different. To evaluate the genetic structure and the differences between these breeds, the genetic diversity within and between breeds was evaluated based on a total of 205 multilocus genotypes (21 microsatellite loci).
All of the loci under investigation were polymorphic and the number of alleles ranged from 4 to14 within the two populations. The analysis of population fixation resulted in a FST value of 0.006. Further the population assignment of the individual genotypes and the exact test of population differentiation did not support the hypothesis that the samples drawn from the two populations are genetically different. Population admixture and sample collection are discussed as possible reasons for the rejection of the hypothesis. Finally, recommendations for sample collection in extensive systems are given.