Genomic structure analysis and construction of DNA fingerprint for four sheep populations

• Published in: Animal (Cambridge, England) England), 2024-04, Vol.18 (4), p.101116-101116, Article 101116
• Main Authors: Ma, Ke-Yan, Song, Juan-Juan, Li, Deng-Pan, Wu, Yi, Wang, Chun-Hui, Liu, Zi-Long, Li, Tao-Tao, Ma, You-Ji
• Format: Article
• Language: English
• Subjects: DNA fingerprint; Genetic diversity; Germplasm resources; Population structure; Selective sweep
• ISSN: 1751-7311; 1751-732X
• DOI: 10.1016/j.animal.2024.101116

•The genetic diversity and population structure of Yongdeng Qishan sheep were studied.•A genetic differentiation between Yongdeng Qishan sheep and other populations.•DNA fingerprints were constructed for four sheep populations.•It provides a basis for the identification of new resources of Yongdeng Qishan sheep.•DNA fingerprinting can serve as a tool for a variety of identification. The Yongdeng Qishan sheep (QS) is a sheep population found locally in China. To gain in-depth knowledge of its population characteristics, three control groups were chosen, comprising the Lanzhou fat-tailed sheep (LFT), TAN sheep (TAN), and Minxian black fur sheep (MBF), inhabiting the nearby environments. This study genotyped a total of 120 individuals from four sheep populations: QS, LFT, TAN, and MBF. Using Specific-Locus Amplified Fragment Sequencing, we conducted genetic diversity, population structure, and selective sweep analysis, and constructed the fingerprint of each population. In total, there were 782 535 single nucleotide polymorphism (SNP) variations identified, with most being situated within regions that are intergenic or intronic. The genetic diversity analysis revealed that the QS population exhibited lower genetic diversity compared to the other three populations. Consistent results were obtained from the principal component, phylogenetic tree, and population structure analysis, indicating significant genetic differences between QS and the other three populations. However, a certain degree of differentiation was observed within the QS population. The linkage disequilibrium (LD) patterns among the four populations showed clear distinctions, with the QS group demonstrating the most rapid LD decline. Kinship analysis supported the findings of population structure, dividing the 90 QS individuals into two subgroups consisting of 23 and 67 individuals. Selective sweep analysis identified a range of genes associated with reproduction, immunity, and adaptation to high-altitude hypoxia. These genes hold potential as candidate genes for marker-assisted selection breeding. Additionally, a total of 86 523 runs of homozygosity (ROHs) were detected, showing non-uniform distribution across chromosomes, with chromosome 1 having the highest coverage percentage and chromosome 26 the lowest. In the high-frequency ROH islands, 79 candidate genes were associated with biological processes such as reproduction and fat digestion and absorption. Furthermore, a DNA fingerprint was con