Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30 - 2472, 3001 Leuven, Belgium.
Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30 - 2472, 3001 Leuven, Belgium.
Animal. 2024 Oct;18(10):101315. doi: 10.1016/j.animal.2024.101315. Epub 2024 Aug 23.
Assessing the genetic diversity of local breeds is essential for conserving these unique breeds, which may possess unique traits. This study provides the genomic characterisation of eight indigenous sheep breeds in Belgium based on pedigree and single nucleotide polymorphism (SNP) analysis. A total of 687 sheep were genotyped and were subjected to a rigorous quality control, resulting in a set of 45 978 autosomal SNPs. Pedigree analysis showed breed-average inbreeding estimates between 3.3% and 11.3%. The genomic analysis included an assessment of runs of homozygosity (ROH) to examine the genomic inbreeding coefficient, with breed-average inbreeding coefficients estimated between 4.1% and 8.5%. Runs of homozygosity islands were identified in six of the eight breeds studied, with some exhibiting an incidence of up to 58%. Interestingly, several ROH islands overlapped with other breeds included in this study, as well as with international sheep breeds. Pedigree-based effective population sizes were estimated below 100 for all breeds, whereas genomic-based effective population sizes were below 24, indicating that these eight local sheep breeds are endangered. Principal component analysis, admixture analyses, and F computations were used to study the population structure and genetic differences. A neighbour-joining tree using 95 international sheep breeds positioned the eight local breeds in the group of milksheep, Texel sheep and the Scandinavian breeds. Additionally, the investigation of paternal oY1 genotypes revealed diverse lineage origins within the Belgian sheep population. This study refines and deepens our knowledge about the local sheep breeds in Belgium, thereby improving their management and conservation. Moreover, as these breeds are linked to other international breeds, these insights are significant for the global scientific community.
评估地方品种的遗传多样性对于保护这些独特的品种至关重要，因为它们可能具有独特的特征。本研究基于系谱和单核苷酸多态性（SNP）分析，对比利时的 8 个本地绵羊品种进行了基因组特征描述。共对 687 只绵羊进行了基因分型，并进行了严格的质量控制，得到了一组 45978 个常染色体 SNP。系谱分析显示，各品种的平均近交估计值在 3.3%至 11.3%之间。基因组分析包括对纯合子片段（ROH）的评估，以检查基因组近交系数，各品种的平均近交系数估计值在 4.1%至 8.5%之间。在所研究的 8 个品种中有 6 个发现了纯合子片段岛，其中一些品种的发生率高达 58%。有趣的是，几个 ROH 岛与本研究中包括的其他品种以及国际绵羊品种重叠。基于系谱的有效种群数量估计所有品种均低于 100，而基于基因组的有效种群数量则低于 24，这表明这 8 个本地绵羊品种处于濒危状态。主成分分析、混合分析和 F 计算用于研究种群结构和遗传差异。使用 95 个国际绵羊品种的邻接树将 8 个本地品种定位在乳用绵羊、特克塞尔绵羊和斯堪的纳维亚品种组中。此外，对父本 oY1 基因型的研究揭示了比利时绵羊群体中多样化的谱系起源。本研究深化和完善了我们对比利时本地绵羊品种的认识，从而提高了它们的管理和保护水平。此外，由于这些品种与其他国际品种有关，因此这些见解对全球科学界具有重要意义。
