USDA, ARS, National Animal Germplasm Program, 1111 S. Mason St., Fort Collins, CO 80521, USA.
Department of Animal Science, 350 W. Pitkin St., Colorado State University, Fort Collins, CO 80523, USA.
J Hered. 2022 Jul 23;113(4):431-443. doi: 10.1093/jhered/esac026.
Long-term sustainability of breeds depends on having sufficient genetic diversity for adaptability to change, whether driven by climatic conditions or by priorities in breeding programs. Genetic diversity in Suffolk sheep in the United States was evaluated in four ways: 1) using genetic relationships from pedigree data [(n = 64 310 animals recorded in the US National Sheep Improvement Program (NSIP)]; 2) using molecular data (n = 304 Suffolk genotyped with the OvineHD BeadChip); 3) comparing Australian (n = 109) and Irish (n = 55) Suffolk sheep to those in the United States using molecular data; and 4) assessing genetic relationships (connectedness) among active Suffolk flocks (n = 18) in NSIP. By characterizing genetic diversity, a goal was to define the structure of a reference population for use for genomic selection strategies in this breed. Pedigree-based mean inbreeding level for the most recent year of available data was 5.5%. Ten animals defined 22.8% of the current gene pool. The effective population size (Ne) ranged from 27.5 to 244.2 based on pedigree and was 79.5 based on molecular data. Expected (HE) and observed (HO) heterozygosity were 0.317 and 0.306, respectively. Model-based population structure included 7 subpopulations. From Principal Component Analysis, countries separated into distinct populations. Within the US population, flocks formed genetically disconnected clusters. A decline in genetic diversity over time was observed from both pedigree and genomic-based derived measures with evidence of population substructure as measured by FST. Using these measures of genetic diversity, a framework for establishing a genomic reference population in US Suffolk sheep engaged in NSIP was proposed.
长期可持续性的品种取决于是否有足够的遗传多样性，以适应变化，无论是由气候条件驱动还是由育种计划的优先事项驱动。美国萨福克羊的遗传多样性通过以下四种方式进行评估：1）使用来自系谱数据的遗传关系[（在美国国家绵羊改良计划（NSIP）中记录的 n = 64310 只动物）]；2）使用分子数据（n = 304 只萨福克羊，用 OvineHD BeadChip 进行基因分型）；3）使用分子数据比较澳大利亚（n = 109）和爱尔兰（n = 55）萨福克羊与美国的萨福克羊；4）评估 NSIP 中活跃的萨福克羊群（n = 18）的遗传关系（连通性）。通过描述遗传多样性，目标是定义一个参考群体的结构，用于该品种的基因组选择策略。基于系谱的最近可用数据的平均近交水平为 5.5%。10 只动物定义了当前基因库的 22.8%。基于系谱的有效种群大小（Ne）范围为 27.5 至 244.2，基于分子数据的 Ne 为 79.5。预期（HE）和观察（HO）杂合度分别为 0.317 和 0.306。基于模型的群体结构包括 7 个子群体。从主成分分析来看，各国分为不同的群体。在美国种群中，羊群在遗传上形成了不相连的集群。从系谱和基于基因组的衍生指标来看，遗传多样性随时间呈下降趋势，这表明存在种群亚结构，如 FST 所衡量的。使用这些遗传多样性的衡量标准，提出了在美国 NSIP 中建立萨福克羊基因组参考群体的框架。
