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 1,169 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 (1,169 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 (F_ST) indicated a weak differentiation between the Congolese indigenous goat populations. Negative and significant (p-value < 0.05) 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.

Blood samples representing three Congolese indigenous goat populations (Kasai goat, dwarf goat, and small goat) were sampled from farmer’s flocks from three AEZs of DRC (representing in this study by Kinshasa, Tshopo and South Kivu). Efforts were made to avoid closely related individuals during sampling. The socio-economic factors associated to goat keeping, the environmental characteristics (the high land volcanic mountain) and the proximity to neighboring countries (Tanzania, Rwanda, and Burundi, with which animal exchanges can readily occur leading to an uncontrolled inter crossbreeding between goat populations), were the main reasons for choosing the South Kivu region. Tshopo was chosen based on its geographic location (the equatorial forest region) which could affect goat management and productivity, while Kinshasa (capital city) was chosen based on the environmental characteristic (high temperature), the commercial transaction with surrounding regions including Bandundu, Kasai central, Congo central, and the productivity history of goats. Genomic DNA was extracted from blood samples using the QIAamp® DNA Mini kit (Qiagen) according to the manufacturer’s protocol. DNA quality control (QC) was done using a spectrophotometer (NanoDrop 2000, Thermo Fisher Scientific, USA) and DNA integrity was checked on 1% agarose gel electrophoresis. The 1,169 bp of the mtDNA d-loop region was amplified using primers designed (F: 5’-ACCAGAAAAGGAGAATAGCC-3’; R: 5’–GGTACACTCATCTAGGCATT-3’) using a three steps PCR. PCR reactions were carried out in 25 µl reaction volumes composed of Phusion master mix (2x concentrated solution which included Taq DNA polymerase (0.05 U/µl), reaction buffer, 4 mM MgCl₂ and 0.4 mM of each dNTP), 0.2 µM of each primer (F and R), 2% of Dimethyl Sulfoxide (DMSO) and 40 ng of template DNA. The three steps PCR involved an initial denaturation at 98°C for 30 seconds following by 35 cycles of amplification (denaturation at 98°C for 10 seconds, annealing at 61°C for 30 seconds, and extension at 72°C for 30 seconds) and completed by the final extension step at 72°C for 7 minutes. The PCR products were purified using the QIAquick® PCR purification kit (Qiagen) following the manufacture’s protocol. The reverse primer (R: 5’ –GGTACACTCATCTAGGCATT -3’) and a pair of GDLS2 primers (GDLS-2F: 5’-ACCTAAAATCGCCCACTC-3’; GDLS-2 R: 5’ TGATCTAGTGGACGGGATAC-3) were respectively used as external and internal primers to sequence the purified PCR products. Default values and parameters inherent in algorithms and software were used for all analyses undertaken in this study. Only deviations from the default were mentioned. Before the analyses, all the chromatograms were visualized using CLC Genomics workbench v8.0 software. MEGA v6.4 software was used for the multiple sequence alignments with the ClustalW algorithm . The variable sites were scored against the Capra hircus reference sequence (GenBank accession number: GU223571: direct submission).