Haplotype analysis of the mitochondrial DNA d‐loop region reveals the maternal origin and historical dynamics among the indigenous goat populations in east and west of the Democratic Republic of Congo

Abstract

This study aimed at assessing haplotype diversity and population dynamics of three Congolese indigenous goat populations that included Kasai goat (KG), small goat (SG), and dwarf goat (DG) of the Democratic Republic of Congo (DRC). The 1169 bp d‐loop region of mitochondrial DNA (mtDNA) was sequenced for 339 Congolese indigenous goats. The total length of sequences was used to generate the haplotypes and evaluate their diversities, whereas the hypervariable region (HVI, 453 bp) was analyzed to define the maternal variation and the demographic dynamic. A total of 568 segregating sites that generated 192 haplotypes were observed from the entire d‐loop region (1169 bp d‐loop). Phylogenetic analyses using reference haplotypes from the six globally defined goat mtDNA haplogroups showed that all the three Congolese indigenous goat populations studied clustered into the dominant haplogroup A, as revealed by the neighbor‐joining (NJ) tree and median‐joining (MJ) network. Nine haplotypes were shared between the studied goats and goat populations from Pakistan (1 haplotype), Kenya, Ethiopia and Algeria (1 haplotype), Zimbabwe (1 haplotype), Cameroon (3 haplotypes), and Mozambique (3 haplotypes). The population pairwise analysis (FST) indicated a weak differentiation between the Congolese indigenous goat populations. Negative and significant (p‐value <.05) values for Fu's Fs (−20.418) and Tajima's (−2.189) tests showed the expansion in the history of the three Congolese indigenous goat populations. These results suggest a weak differentiation and a single maternal origin for the studied goats. This information will contribute to the improvement of the management strategies and long‐term conservation of indigenous goats in DRC.

Bioinformatics and Molecular Analyses Identified the Control Region as the Most Powerful Mitogenomic Marker for Distinguishing the Main Maternal Haplogroups in Goats

“…In contrast to the results of 13 coding and 2 ribosomal genes, sequences of the mitochondrial control region were suitable for differentiation the main maternal haplogroups from each other (Figure 2; Appendices Figure S16; Appendices Table S2). Our findings are well corroborated by previous research that used the control region in which the six highly divergent haplogroups in domestic goats were identified (Vacca et al, 2010;Ghernouti et al, 2017;Nguluma et al, 2021;Baenyi Simon et al, 2022).…”

Mitochondrial DNA D-Loop Polymorphisms among the Galla Goats Reveals Multiple Maternal Origins with Implication on the Functional Diversity of the HSP70 Gene

“…The high genetic variation observed within populations could be attributed to a lack of selective breeding, random mating within the population, mutations that can generate completely new alleles in a population, or even reshuffling of alleles within an organism's offspring during homologous recombination [ 45 , 46 ].…”

Phylogeographic Patterns of the Greater Cane Rat (Thryonomys Swinderianus) Populations from Eastern, Western and Southern Africa and Implications for Wildlife Conservation

“…Further, the median joining network revealed that the populations from Ghana have little divergence and share the most common haplotypes between the three agro-ecological zones. Less-divergent haplotypes within animals and geographical locations suggest that gene flow has occurred on a regional scale during the recent past and the animals have not been subdivided by long-term biogeographic barriers (Simon et al, 2022). The AGC populations from Tanzania on the other hand were more structured with some haplotypes unique to a single population (Udzungwa South) while other haplotypes were shared between populations (Udzungwa North, Uluguru urban and Uluguru rural), indicating low genetic exchange among the Udzungwa South, Udzungwa North, and Uluguru urban and rural populations.…”