Conservation & local programs

Genomic diversity, population structure and admixture in native cattle breeds of Benin

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Abstract

This study investigates the genetic diversity, population structure, admixture patterns, and effective population size of indigenous cattle breeds in Benin, providing insights into their evolutionary relationships and adaptation to the West African environment. Hair samples were collected from 348 cattle representing eight indigenous populations, including taurine breeds Lagunaire, Borgou, Pabli, and Somba, zebu breeds Gudali, Zebu Peulh, and Yakana, as well as a crossbred group. Genomic DNA was extracted and genotyped using the Axiom Bovine Genotyping BovMDv3 array and combined with reference data from European, Asian, and West African cattle populations. After quality control, 28591 SNPs from 838 individuals were retained for analyses of genetic diversity, differentiation, admixture, and effective population size. Pairwise FST values indicated significant genetic differentiation between local taurine and zebu populations, with values ranging from 0.05 to 0.15, with some populations showing close genetic relationships, while others, such as the Borgou and N'Dama breeds, exhibiting more distinct separation. The admixture analysis indicated that zebu cattle had contributed to the genetic composition of local taurine breeds, suggesting adaptive interbreeding driven by factors such as heat tolerance and disease resistance. Effective population size was estimated using a linkage disequilibrium-based approach implemented in SNeP and revealed higher values in taurine populations compared to zebu populations. Among taurine breeds, estimated Ne values increased over recent generations and reached approximately 3000 in N'dama, around 4000 in Borgou and Lagunaire, and up to about 6000 in Pabli, indicating relatively high genetic diversity and demographic stability. In Beninese zebu breeds, Ne estimates peaked at approximately 3800 in Gudali, around 4000 in Zebu Peulh, and close to 5000 in Yakana, reflecting moderate demographic expansion. These results indicate generally favorable genetic health in indigenous cattle populations, particularly taurine breeds, likely supported by open communal mating systems. This genetic structure reflects the influence of both historical domestication and ongoing introgression from Asian zebu cattle. The results highlight the importance of maintaining genetic diversity through regional breeding strategies that consider environmental and adaptive pressures. However, the study is limited by its sampling, which was limited to just three municipalities in Benin. Future research could expand to broader sampling across Benin and other West African countries to gain deeper insights into the regional genomic landscape.

Keywords: 2026

How to Cite:

Zorobouragui, L., Tapsoba, S., Traore, A., Periasamy, K., Pichler, R., Mavunga, T., Assani, A., Worogo, H., Taba, N., Azalou, M., Iwaka, C., Alkoiret, I. & Houaga, I., (2026) “Genomic diversity, population structure and admixture in native cattle breeds of Benin”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286427. doi: https://doi.org/10.31274/wcgalp.24000

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