Genome Diversity and the Origin of the Arabian Horse

The Arabian horse, one of the world’s oldest breeds of any domesticated animal, is characterized by natural beauty, graceful movement, athletic endurance, and, as a result of its development in the arid Middle East, the ability to thrive in a hot, dry environment. Here we studied 378 Arabian horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing to examine hypotheses about genomic diversity, population structure, and the relationship of the Arabian to other horse breeds. We identified a high degree of genetic variation and complex ancestry in Arabian horses from the Middle East region. Also, contrary to popular belief, we could detect no significant genomic contribution of the Arabian breed to the Thoroughbred racehorse, including Y chromosome ancestry. However, we found strong evidence for recent interbreeding of Thoroughbreds with Arabians used for flat-racing competitions. Genetic signatures suggestive of selective sweeps across the Arabian breed contain candidate genes for combating oxidative damage during exercise, and within the “Straight Egyptian” subgroup, for facial morphology. Overall, our data support an origin of the Arabian horse in the Middle East, no evidence for reduced global genetic diversity across the breed, and unique genetic adaptations for both physiology and conformation. This deposition includes sample annotation and Plink format filesets for genotyping data generated for the associated publication. Full methods can be found in the publication, in summary: Genotype calls from each genotyping array batch and the whole genome sequences were combined sequentially using PLINK v. 1.90 [58]. First, Affymetrix and GeneSeek calls were merged using PLINK with filters set to 90% SNP genotyping rate and 1% minor allele frequency. A subset of multi-origin ancestry Arabians (from mixed origins) were used to test all SNPs for Hardy Weinberg Equilibrium. Autosomal variants with P-values &lt; 0.005 (corrected for multiple testing) were removed from the genotype files. SNPs derived from whole genome sequencing were then merged to generate the final set of variant calls for downstream analysis, removing any variant with lower than 80% genotyping rate, 1% minor allele frequency, or flagged as multi-allelic. Finally, samples with genotyping rate &lt;95% were removed. After applying these filters, the data set included 343,367 SNPs.阿拉伯马是全球现存最古老的家养动物品种之一，兼具自然美感与优雅步态，拥有卓越的运动耐力；又因演化于干旱的中东地区，同时具备在炎热干燥环境中存活的优异适应性。本研究针对来自12个国家的378匹阿拉伯马，利用马科单核苷酸多态性（single nucleotide polymorphism, SNP）芯片与全基因组重测序技术，对阿拉伯马的基因组多样性、种群结构，以及该品种与其他马品种的亲缘关系相关假说开展验证分析。研究团队在中东地区的阿拉伯马群体中，检测到高度的遗传变异与复杂的血统起源。与学界普遍认知相悖的是，本研究未发现阿拉伯马品种对纯血赛马（Thoroughbred racehorse）存在显著的基因组贡献，包括Y染色体血统谱系。但研究显示，用于平地竞速赛事的阿拉伯马与纯血马近期存在频繁的杂交事件。阿拉伯马群体中检出的选择性清除遗传特征，包含了与运动过程中抗氧化损伤相关的候选基因；而在“纯种埃及阿拉伯马（Straight Egyptian）”亚群中，该特征则与面部形态发育相关。综上，本研究数据支持阿拉伯马起源于中东地区，未发现该品种全球遗传多样性降低的证据，同时揭示了其在生理机能与体型结构上独特的遗传适应性。本数据集存档包包含与该关联论文配套的基因型数据样本注释文件与PLINK格式数据集文件集。完整实验方法可参见原论文，简要流程如下：使用PLINK v1.90 [58] 对各批次基因型芯片数据与全基因组测序数据依次进行合并。首先，通过PLINK将Affymetrix与GeneSeek平台的基因型分型结果合并，筛选阈值设置为：SNP分型率≥90%、次要等位基因频率（minor allele frequency, MAF）≥1%。选取多血统起源的阿拉伯马亚群，对所有SNP进行哈迪-温伯格平衡（Hardy Weinberg Equilibrium, HWE）检验，剔除经多重检验校正后P值<0.005的常染色体变异位点。随后将全基因组测序得到的SNP位点并入，生成最终的变异位点集用于后续分析，期间剔除分型率<80%、次要等位基因频率<1%或被标记为多等位基因的变异位点。最后移除分型率<95%的样本。经上述过滤步骤后，最终数据集共包含343367个SNP位点。