Data from: Genome-wide insights into population structure and genetic history of Tunisian local cattle using the Illumina BovineSNP50 Beadchip

Background: Tunisian local cattle populations are at risk of extinction as
they were massively crossed with imported breeds. Preservation of
indigenous livestock populations is important because each of them
comprises a unique set of genes resulting from a local environment-driven
selection that occurred over hundreds of years. The diversity and genetic
structure of Tunisian local cattle populations are poorly understood.
However, such information is crucial to the conservation and sustainable
use of genetic resources. In addition, comparing the genomic structure of
population sets from different parts of the world could help yield insight
into their origin and history. In the present study, we provide a detailed
assessment of the population structure of the three Tunisian local cattle
populations using various methods, and we highlight their origin and
history by investigating approximately ~38,000 SNPs in a broad panel of
878 individuals from 37 worldwide cattle breeds representative of African,
European and indicine populations. Results: Our study revealed a low level
of divergence and high genetic diversity in Tunisian local cattle
reflecting low levels of genetic drift. A Comparison with the worldwide
cattle panel pinpointed the admixed origin of the genome of the three
Tunisian populations with the two main European and African ancestries.
Our results were in agreement with previous historical and archaeological
reports about the past gene flow that existed between North African and
South European breeds, in particular with Iberian cattle. We also detected
a low-level indicine introgression in the three Tunisian populations and
we inferred that indicine ancestry was inherited via African ancestors.
Conclusions: Our results represent the first study providing genetic
evidence about the origin and history of Tunisian local cattle. The
information provided by the fine-scale genetic characterization of our
study will enhance the establishment of a national conservation strategy
for these populations. These results may enable the identification of
genetic variants involved in adaptation to harsh environmental conditions.

背景：突尼斯本地牛种群因大量与进口品种杂交而面临灭绝风险。保护本土家畜种群（indigenous livestock populations）至关重要，因为每个种群都包含一套独特的基因集合，这些基因源于数百年来由本地环境驱动的选择过程。突尼斯本地牛种群的多样性与遗传结构尚不清楚，然而此类信息对于遗传资源的保护及可持续利用至关重要。此外，比较全球不同地区种群的基因组结构，有助于深入了解其起源与历史。本研究通过多种方法对三个突尼斯本地牛种群的结构进行了详细评估，并通过分析来自全球37个代表非洲、欧洲及瘤牛（indicine）种群的牛品种的878个个体组成的广泛样本中的约38000个单核苷酸多态性（Single Nucleotide Polymorphisms，SNPs），揭示了其起源与历史。

结果：本研究发现突尼斯本地牛的遗传分化水平较低且遗传多样性较高，反映出较低的遗传漂变水平。与全球牛样本面板对比后，明确了三个突尼斯种群基因组的混合起源，其主要祖先成分来自欧洲和非洲。我们还在三个突尼斯种群中检测到低水平的瘤牛基因渗入（introgression），并推断瘤牛祖先成分是通过非洲祖先遗传而来。

结论：本研究首次为突尼斯本地牛的起源与历史提供了遗传学证据。本研究的精细遗传特征分析所提供的信息，将有助于制定针对这些种群的国家保护策略。这些结果或可助力识别与适应恶劣环境条件相关的遗传变异。