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.

研究背景：突尼斯本地牛种群因大量与外来培育品种杂交，正面临灭绝风险。保护本土家畜种群具有重要意义，因为每一个本土种群均拥有历经数百年本地环境适应性选择所形成的独特基因组合。目前学界对突尼斯本地牛种群的遗传多样性与遗传结构尚缺乏深入认知，然而此类信息对于遗传资源的保护与可持续利用至关重要。此外，对比全球不同区域种群的基因组结构，有助于揭示其起源与演化历史。本研究采用多种方法对3个突尼斯本地牛种群的种群结构进行了细致评估；同时，通过对涵盖非洲、欧洲及瘤牛（indicine）代表性类群的37个全球牛品种的878份个体样本开展约38000个单核苷酸多态性（Single Nucleotide Polymorphisms，SNPs）位点分型分析，阐明了这三个种群的起源与演化历史。
研究结果：本研究发现，突尼斯本地牛种群的分化程度较低且遗传多样性较高，这反映出其遗传漂变水平较低。与全球牛种群基因分型面板的对比分析证实，这三个突尼斯牛种群的基因组均为欧洲与非洲两大主要血统的混合起源。本研究结果与此前关于北非与南欧牛品种（尤其是伊比利亚牛）之间存在历史基因交流的历史学、考古学研究结论相一致。本研究还在三个突尼斯牛种群中检测到低水平的瘤牛基因渐渗现象，并推断其瘤牛血统源自非洲祖先种群。
研究结论：本研究是首个为突尼斯本地牛种群的起源与演化历史提供遗传学证据的研究。本研究通过高精度遗传特征解析所获得的信息，将有助于推动针对这些种群的国家级保护策略的制定。本研究结果还有助于鉴定出与极端环境适应性相关的遗传变异。