Ma Keyan, Song Juanjuan, Li Dengpan, Li Taotao, Ma Youji
College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
Animals (Basel). 2024 Sep 26;14(19):2784. doi: 10.3390/ani14192784.
This research is designed to examine the genetic diversity and kinship among Hu sheep, as well as to discover genes associated with crucial economic traits. A selection of 50 unrelated adult male Hu sheep underwent genotyping with the SNP50K BeadChip. Seven indicators of genetic diversity were assessed based on high-quality SNP data: effective population size (), polymorphic information content (), polymorphic marker ratio (), expected heterozygosity (), observed heterozygosity (), effective number of alleles, and minor allele frequency (). Plink software was employed to compute the IBS genetic distance matrix and detect runs of homozygosity (ROHs), while the G matrix and principal component analysis were performed using GCTA software. Selective sweep analysis was carried out using ROH, Pi, and Tajima's D methodologies. This study identified a total of 64,734 SNPs, of which 56,522 SNPs remained for downstream analysis after quality control. The population displayed relatively high genetic diversity. The 50 Hu sheep were ultimately grouped into 12 distinct families, with families 6, 8, and 10 having the highest numbers of individuals, each consisting of 6 sheep. Furthermore, a total of 294 ROHs were detected, with the majority having lengths between 1 and 5 Mb, and the inbreeding coefficient was 0.01. In addition, 41, 440, and 994 candidate genes were identified by ROH, Pi, and Tajima's D methods, respectively, with 3 genes overlapping (, and ). These results offer valuable insights for future Hu sheep breeding, genetic assessment, and population management.
本研究旨在检测湖羊的遗传多样性和亲缘关系，并发现与关键经济性状相关的基因。选取50只无亲缘关系的成年雄性湖羊，使用SNP50K基因芯片进行基因分型。基于高质量的SNP数据评估了七个遗传多样性指标：有效种群大小（）、多态信息含量（）、多态标记比例（）、期望杂合度（）、观察杂合度（）、有效等位基因数和次要等位基因频率（）。使用Plink软件计算IBS遗传距离矩阵并检测纯合子连续片段（ROH），同时使用GCTA软件进行G矩阵和主成分分析。使用ROH、Pi和Tajima's D方法进行选择清除分析。本研究共鉴定出64,734个SNP，其中56,522个SNP在质量控制后用于下游分析。该群体表现出相对较高的遗传多样性。50只湖羊最终被分为12个不同的家系，其中家系6、8和10的个体数量最多，每个家系由6只羊组成。此外，共检测到294个ROH，大多数长度在1至5 Mb之间，近交系数为0.01。此外，分别通过ROH、Pi和Tajima's D方法鉴定出41、440和994个候选基因，其中有3个基因重叠（、和）。这些结果为未来湖羊的育种、遗传评估和群体管理提供了有价值的见解。
