Data from: Genetic diversity of Persian Arabian horses and their relationship to other native Iranian horse breeds

The principal aims of this study were to explore genetic diversity and genome-wide selection signatures in Persian Arabian horses and to determine genetic relationship of Persian Arabians with other Iranian horse breeds. We evaluated 71 horses from 8 matrilineal strains tracing to 47 mares from the mid to late 19th century, using the equine 670k SNP BeadChip. Mean observed and expected heterozygosity were (0.43) and (0.45), respectively, average inbreeding measures (FROH and FPED) were low, indicating high genetic diversity in Persian Arabian horses. Analysis of population genetic structure using STRUCTURE and Principal Component Analysis suggested that Persian Arabian horses can be divided into three groups, however the groups do not match traditional matrilineal strains. In total, 15 genomic regions were identified by at least two of the three implemented methods, Tajima's D, H, and H12, as potentially under selection in Persian Arabian horses. Most of these peaks were found on chromosome 9, overlapping with QTLs previously associated with horse temperament. Biological function analysis of identified candidate genes highlighted enrichment of GO term "response to lipopolysaccharide" and KEGG pathway "chemokine-mediated signaling pathway", which are associated with immune responses and may have been targets of selection in Persian Arabian horses. Independent analyses of SNP data from 30 horses of four other Iranian breeds suggested distinct population structure between Persian Arabian, and Turkemen and Caspian horse breeds. Overall, the results of this study suggest a rich genetic diversity in the Persian Arabian horses and a clear genetic differentiation with Turkemen and Caspian breeds.

本研究的核心目标为探究波斯阿拉伯马（Persian Arabian Horses）的遗传多样性与全基因组选择信号，并明确波斯阿拉伯马与其他伊朗马品种间的遗传亲缘关系。本研究采用马670K SNP基因芯片（equine 670k SNP BeadChip），对源自19世纪中后期47匹奠基母马的8个母系谱系的71匹波斯阿拉伯马开展了基因分型分析。观测杂合度与期望杂合度的均值分别为0.43与0.45；平均近交系数（FROH与FPED）处于较低水平，表明波斯阿拉伯马具有较高的遗传多样性。采用STRUCTURE软件与主成分分析（Principal Component Analysis）对种群遗传结构进行解析，结果显示波斯阿拉伯马可划分为3个类群，但该类群划分与传统母系谱系并不匹配。本研究通过Tajima's D、H以及H12三种检测方法中的至少两种，共鉴定出15个可能在波斯阿拉伯马中受到选择的基因组区域。其中多数选择信号峰位于9号染色体，且与此前报道的与马性情相关的数量性状基因座（quantitative trait locus, QTL）存在重叠。对鉴定得到的候选基因开展生物学功能富集分析后发现，其显著富集于基因本体（Gene Ontology, GO）术语"脂多糖应答（response to lipopolysaccharide）"以及京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）通路"趋化因子介导的信号通路（chemokine-mediated signaling pathway）"，上述通路均与免疫应答相关，可能是波斯阿拉伯马受选择的靶标通路。对另外4个伊朗马品种的30匹马匹的SNP数据进行独立分析后发现，波斯阿拉伯马与土库曼马（Turkemen）、里海马（Caspian）之间存在显著的种群遗传分化。综上，本研究结果表明波斯阿拉伯马拥有丰富的遗传多样性，且与土库曼马、里海马品种间存在清晰的遗传分化。