A total of 304 individuals from eight Ankole cattle populations of Uganda were analysed based on 19 microsatellite markers to investigate genetic diversity, relationships and population structure. Across all loci, 200 alleles were observed. A high mean number of alleles (MNA) per locus, ranging from 5.89 to 6.79 per population, was observed. Polymorphic information content (PIC) ranged from 0.403 (ILSTS013) to 0.817 (ILSTS036), with an overall mean over all loci of 0.688. The average observed heterozygosity (Ho) was highest in Kaibanda (0.727) and lowest in Kituuha (0.648), while the expected heterozygosity (He) ranged from 0.722 (Nshaara) to 0.664 (Kituuha), though for all populations the differences were not significant. Significant deviations from Hardy–Weinberg proportions were observed over eight loci, however, all 152 loci–population combination tests were in equilibrium after Bonferroni correction. FST estimates for all loci and between all populations were highly significant (P < 0.001), suggesting little if any gene flow between the populations. F-statistics at respective loci among all populations were significant, with the exception of the FIT. For all population pairs, FST values were generally low, with an overall mean of 0.041 ± 0.08. Significant (P < 0.01) inbreeding effect (FIS) was detected in only the Nasasira population. The mean number of migrants per generation (Nm) across all populations was 3.82. Relationship analysis showed populations from the same geographical counties group together. These results illustrate at the molecular level the fairly wide genetic variation found within the Ankole breed and therefore the potential for genetic improvement.
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