Data from: Application of genomic estimation methods of inbreeding and population structure in an Arabian horse herd

Horse breeders rely heavily on pedigrees for identification of ancestry in breeding stock. Inaccurate pedigrees may erroneously assign individuals to false lineages or breed memberships resulting in wrong estimates of inbreeding and coancestry. Moreover, discrepancies in pedigree records can lead breeders seeking to limit inbreeding into making misguided breeding decisions. Genome-wide SNPs provide a quantitative tool to aid in the resolution of lineage assignments and the calculation of genomic measures of relatedness. The aim of this project was to pilot a comparison between pedigree and genomic relatedness and inbreeding measures in a herd of 36 pedigreed Egyptian Arabian horses genotyped using the Equine SNP70 platform (Geneseek, Inc.). Moreover, we sought to estimate the minimum number of markers sufficient for genomic inbreeding calculations. Pedigree inbreeding values were moderately correlated with genomic inbreeding values (r = 0.406), whereas genomic relationships and pedigree relationships have a high correlation (r = 0.77). Although first degree relationships were successfully reconstructed, more distant relationships were difficult to resolve. Multi-dimensional scaling and clustering analysis agreed with within-herd pedigree information. In comparing the herd to a reference sample of United States, Polish, and Egyptian Arabian horses, the herd's historically recorded Egyptian lineage was successfully recovered. We conclude that genomic estimates of inbreeding and relationships are superior to their pedigree counterparts. They can be thus utilized in conservation of valuable lines of livestock, and in breeds at risk for loss of genomic diversity. We also postulate a minimum of 2000 markers in linkage equilibrium to be used for inbreeding estimation.

马育种者严重依赖系谱来识别育种种群的祖先血统。不准确的系谱可能会错误地将个体归入虚假谱系或品种类群，导致近交与共祖系数的估算出现偏差。此外，系谱记录的差异会令试图控制近交的育种者做出失当的繁育决策。全基因组单核苷酸多态性（Single Nucleotide Polymorphism，SNPs）提供了一种量化分析工具，可辅助明确谱系归属并计算基因组层面的亲缘关系指标。本研究旨在以36头具有完整系谱记录的埃及阿拉伯马为研究对象，开展系谱与基因组亲缘关系、近交系数测算结果的对比预实验，这些马匹通过Equine SNP70平台（Geneseek, Inc.）完成基因分型。此外，本研究还尝试估算用于基因组近交系数测算的最少标记数量。系谱近交值与基因组近交值呈中等程度相关（r=0.406），而基因组亲缘关系与系谱亲缘关系的相关性较高（r=0.77）。尽管一级亲缘关系可被成功重构，但较远的亲缘关系较难分辨。多维标度分析与聚类分析结果与该马群内部的系谱信息一致。将该马群与美国、波兰及埃及阿拉伯马的参考样本进行比对后，该马群历史记录的埃及血统得以成功复原。本研究得出结论：基因组层面的近交与亲缘关系估算结果优于系谱测算结果，该方法可用于珍贵畜禽品系的保护，以及面临基因组多样性丧失风险的品种保育。本研究还推测，用于近交系数估算的连锁平衡标记数量至少需达到2000个。