Genetic Diversity of Ugandan Local Chicken Genotypes Inferred from Mitochondrial DNA D-loop Sequences

This study aimed to examine the genetic relationship and structure of the local chicken genotypes in Uganda to serve as an essential component for improvement and conservation strategies. A set of 46 mitochondrial DNA D-loop sequences among 7 chicken strain populations across Uganda was evaluated. The results revealed 5 polymorphic sites defining 7 haplotypes with the dominant (80%) haplotype, UGA01, shared among the populations. Maximum genetic variation was observed among frizzle and rose comb strains which had 2 haplotypes each, followed by the normal feathered which showed the highest (5) haplotypes and crested chickens with 3 haplotypes, however, naked neck, ptilopody, polydactylous chickens were the least diverse with highly conserved sequences. Overall, both haplotype (0.353±0.090) and nucleotide diversities (0.0007±0.0021) revealed a high sequence conversation among the strains, corresponding to a low genetic variation with no genetic structure detected. However, the highest genetic distance observed was between the naked neck / rose comb (0.300) and naked neck/ frizzle (0.300) chickens. A close phylogenetic relationship was observed among the strains suggesting a single founder population adapting to prevailing keeping conditions and high gene flows among the strains. All observed haplotypes were exclusively haplogroup E1 ancestry believed to have its roots in the Indian subcontinent. Keywords: Gallus gallus, chicken genotypes, phylogenetic structure, mutant genes, mtDNA control region, genetic relationship.