The indigenous cattle population of Benin is a diverse mix of taurine and hybrid breeds shaped by diverse ecological and climatic conditions with eight agro-ecological zones (AEZ). Presumably, the taurine breeds face current endangerment due to ongoing indicine introgression following climate change and transboundary transhumance. The aim of the study was to investigate the genetic diversity and population structure of the indigenous breeds Lagune, Somba, Pabli and Borgou considering spatial agro-ecological and socio-economic factors (transhumance) based on 50k SNP and microsatellite data. Among the four sampled breeds, six genetic clusters were identified using model-free (discriminant analysis of principal components) and model-based (TESS and ADMIXTURE) methods separating taurine from hybrid breeds. Results based on an extension with publicly available historic SNP data sets from taurine and indicine West African cattle and additional outgroups provided additional insight into changes of genetic structure in the sampled breeds over time. Both taurine breeds, Somba and Lagune, showed a stable foundation but also spatially limited partial indicine introgression associated with transhumance leading to high genetic diversity. In addition, we found evidence for spatial diversity and changes in genetic structure over time in the Borgou breed in comparison of our samples with the historic samples which could be explained by potential continuous indicine introgression into the Borgou breed in two sample regions. Results for the Pabli breed do not conclusively point to full absorbance by the Borgou in comparison with all available Borgou samples. Further research is needed in this regard.

中文翻译：

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农业生态因素和跨界迁徙在塑造贝宁四个土著牛群遗传多样性中的作用

贝宁的土著牛群是牛磺酸和杂交品种的多样化组合，由不同的生态和气候条件形成，拥有八个农业生态区 (AEZ)。据推测，由于气候变化和越境迁徙后的持续性基因渗入，牛磺酸品种目前面临着濒临灭绝的危险。该研究的目的是基于 50k SNP 和微卫星数据，考虑空间农业生态和社会经济因素（迁徙），调查本土品种 Lagune、Somba、Pabli 和 Borgou 的遗传多样性和种群结构。在四个采样品种中，使用无模型（主成分判别分析）和基于模型（TESS 和 ADMIXTURE）方法将牛磺酸与杂交品种分离，确定了六个遗传簇。基于对来自牛磺酸和 indicine 西非牛和其他外群的公开历史 SNP 数据集的扩展，结果提供了对采样品种遗传结构随时间变化的更多了解。牛磺酸品种 Somba 和 Lagune 都表现出稳定的基础，但在空间上有限的部分 indicine 基因渗入与迁徙相关，导致高遗传多样性。此外，通过将我们的样本与历史样本进行比较，我们发现了 Borgou 品种空间多样性和遗传结构随时间变化的证据，这可以通过两个样本区域中潜在的连续 indicine 渗入 Borgou 品种来解释。与所有可用的 Borgou 样品相比，Pabli 品种的结果并不能最终表明 Borgou 的完全吸光度。