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

Abstract This study investigates the genetic diversity, population structure, and admixture patterns of indigenous cattle breeds in Benin, shedding light on their evolutionary relationships and adaptation to the West African environment. A total of 348 cattle from eight indigenous breeds of Benin, including taurine (Lagune, Borgou, Pabli, and Somba), zebu (Gudali, Zebu Peuhl, and Yakana) and one crossbred (Bourgou X Zebu) cattle were genotyped along with a reference dataset of cattle from Europe, Asia, and West Africa. After quality control, 28.591 SNPs from 838 cattle were analyzed for genetic diversity, differentiation, and admixture. Pairwise F ST values revealed significant genetic differentiation between local taurine and zebu breeds (F ST = 0.05 – 0.15), with some populations showing close genetic relationships, while others, such as the Borgou and N’Dama breeds, exhibiting relatively more divergence. The admixture analysis indicated significant gene flow from zebu cattle into local taurine breeds, suggesting adaptive introgression driven by factors such as heat tolerance and disease resistance. Additionally, the effective population size ( N e ) was relatively higher in Benin’s taurine breeds as compared to zebu, likely attributable to traditional open communal mating practices. The genetic structure also reflected the influence of both historical 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. The results of the present study will serve as a basis for the development of Community Based Breeding Programs (CBBPs) for Beninese cattle adapted to local contexts, integrating information on admixture levels, breeders’ preferences, production performance, and the conservation of local genetic diversity.