Maternal lineage diversity and genetic relationships of Sukuma chicken ecotype with other Tanzanian indigenous chickens based on mitochondrial DNA D-loop region

Understanding the genetic diversity, phylogenetic relationships, and demographic history of chickens is crucial for elucidating domestication processes, conserving indigenous genetic resources, and improving productivity and resilience in sustainable poultry production systems. This study investigates the genetic diversity, phylogenetic relationships, and demographic history of six Tanzanian indigenous chicken ecotypes, namely, Sukuma, Kuchi, Unguja, Pemba, Morogoro Medium, and Ching’wekwe, using mitochondrial DNA (mtDNA) D-loop sequences. A total of 100 mitochondrial DNA (mtDNA) D-loop sequences of 310 base pairs, representing six Tanzanian chicken ecotypes (Sukuma, Kuchi, Unguja, Pemba, Morogoro Medium, and Ching’wekwe), were analyzed. Genetic variation among the six Tanzanian chicken ecotypes was evaluated using several statistical approaches. Molecular diversity indices revealed substantial heterogeneity, with Sukuma chickens exhibiting the highest haplotype diversity (Hd = 0.95789) and nucleotide diversity ( π = 0.30299), reflecting multiple maternal origins and deep evolutionary history. Conversely, Kuchi chickens showed the lowest diversity (Hd = 0.36316; π = 0.00158), consistent with founder effects. Analysis of molecular variance (AMOVA) indicated significant genetic differentiation (FST = 0.35452, p < 0.001), with 35.45% variation among populations and 64.55% within populations. Pairwise FST values and phylogenetic analyses revealed clear clustering, with Sukuma, Kuchi, and Morogoro Medium forming distinct clades, while coastal and Island ecotypes showed closer relationships. Neutrality tests suggested demographic stability in most ecotypes, except Kuchi, which showed signals of past expansion. These findings highlight Sukuma chickens as a critical genetic resource for breeding programs, while the low diversity of Kuchi chickens underscores the need for genetic management. The results provide a foundation for conservation strategies aimed at preserving the adaptive potential and genetic heritage of Tanzania’s indigenous chickens.