Knowledge of population structure and breed composition of a population can be advantageous for a number of reasons; these include designing optimal (cross)breeding strategies in order to maximise non-additive genetic effects, maintaining flockbook integrity by authenticating animals being registered and as a quality control measure in the genotyping process. The objectives of the present study were to 1) describe the population structure of 24 sheep breeds, 2) quantify the breed composition of both flockbook-recorded and crossbred animals using single nucleotide polymorphism BLUP (SNP-BLUP), and 3) quantify the accuracy of breed composition prediction from low-density genotype panels containing between 2000 and 6000 SNPs. In total, 9334 autosomal SNPs on 11 144 flockbook-recorded animals and 1172 crossbred animals were used. The population structure of all breeds was characterised by principal component analysis (PCA) as well as the pairwise breed fixation index (Fst). The total number of animals, all of which were purebred, included in the calibration population for SNP-BLUP was 2579 with the number of animals per breed ranging from 9 to 500. The remaining 9559 flockbook-recorded animals, composite breeds and crossbred animals represented the test population; three breeds were excluded from breed composition prediction. The breed composition predicted using SNP-BLUP with 9334 SNPs was considered the gold standard prediction. The pairwise breed Fst ranged from 0.040 (between the Irish Blackface and Scottish Blackface) to 0.282 (between the Border Leicester and Suffolk). Principal component analysis revealed that the Suffolk from Ireland and the Suffolk from New Zealand formed distinct, non-overlapping clusters. In contrast, the Texel from Ireland and that from New Zealand formed integrated, overlapping clusters. Composite animals such as the Belclare clustered close to its founder breeds (i.e., Finn, Galway, Lleyn and Texel). When all 9334 SNPs were used to predict breed composition, an animal that had a majority breed proportion predicted to be ≥0.90 was defined as purebred for the present study. As the panel density decreased, the predicted breed proportion threshold, used to identify animals as purebred, also decreased (≥0.85 with 6000 SNPs to ≥0.60 with 2000 SNPs). In all, results from the study suggest that breed composition for purebred and crossbred animals can be determined with SNP-BLUP using ≥5000 SNPs.

中文翻译：

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使用全基因组范围的单核苷酸多态性基因型预测多品种绵羊种群的种群结构和品种组成。

出于多种原因，了解种群的种群结构和品种组成可能是有利的。这些措施包括设计最佳的（杂交）育种策略，以最大程度地发挥非加性遗传效应，通过验证被注册的动物并作为基因分型过程中的质量控制措施来保持羊皮簿的完整性。本研究的目标是：1）描述24个绵羊品种的种群结构，2）使用单核苷酸多态性BLUP（SNP-BLUP）量化羊群记录和杂交动物的品种组成，以及3）量化准确性包含2000至6000个SNP的低密度基因型面板预测品种组成的方法。总共使用了11 144张由书本记录的动物和1 172只杂交动物的9334个常染色体SNP。通过主成分分析（PCA）和成对的固定指数（Fst）来表征所有品种的种群结构。SNP-BLUP的校正种群中包括纯种在内的动物总数为2579，每个品种的动物数量在9至500之间。其余9559个由书本记录的动物，复合品种和杂交动物代表测试人群；从品种组成预测中排除了三个品种。使用具有9334个SNP的SNP-BLUP预测的品种组成被认为是金标准预测。成对繁殖的Fst范围从0.040（在爱尔兰黑脸和苏格兰黑脸之间）到0.282（在边境莱斯特和萨福克之间）。主成分分析表明，来自爱尔兰的萨福克和来自新西兰的萨福克形成了独特的，不重叠的簇。相比之下，来自爱尔兰和来自新西兰的特塞尔形成了相互重叠的综合集群。诸如Belclare之类的复合动物聚集在其始祖品种（即Finn，Galway，Lleyn和Texel）附近。当所有9334个SNP都用于预测品种组成时，本研究将多数品种比例预计≥0.90的动物定义为纯种。随着面板密度的降低，用于识别动物为纯种的预测品种比例阈值也降低了（6000个SNP时≥0.85，2000 SNP时≥0.60）。总体而言，研究结果表明，可以使用≥5000个SNP的SNP-BLUP确定纯种和杂交动物的品种组成。