关键词: 全基因组重测序, 遗传多样性, 群体进化, 武雪山羊, 群体结构

Abstract:

This study aimed to provide an in-depth understanding of its population structure, which can explore the genetic variation and differentiation within populations and genetic differences between populations as well as geographic distribution characteristics, and provide an important basis for germplasm resource utilization and development of this breed. Ear tissues of 18 Wuxue goats (WXG), 9 Xiangdong Black goats (XDB), 9 Hechuan White goats (HCW), 9 Dazu Black goats (DZB), 11 Maguan Poll goat (MGG), and 10 Yunling goats (YLG) were collected and used for whole genome resequencing, with an average sequencing depth of about 10×. In this study, principal component analysis, phylogenetic analysis, population genetic structure analysis, heterozygosity analysis, population differentiation analysis, and linkage disequilibrium analysis were performed on 6 populations based on genome-wide data using GCTA, Plink, Admixture, Vcftools, and PopLDdecay software, respectively. The results of principal component analysis showed that Wuxue goats and Xiangdong Black goats were clustered into the same category, indicating that these two goat breeds have similar genetic backgrounds. In the phylogenetic analysis, Wuxue goats and other breeds of goat populations could be clustered into a single cluster, and were genetically closer to Xiangdong Black goats in the evolutionary tree. The results of the analysis of the genetic structure of the population showed that when the CV value was the smallest (K=3), Wuxue goats and Xiangdong Black goats had the same genetic components, indicating that the degree of genetic differentiation index between the two populations was small and the genetic backgrounds were similar. The results of heterozygosity analysis showed that Wuxue goats had lower nucleotide polymorphism (π), the lowest observed heterozygosity (Ho) and lower than the expected heterozygosity (He); ROH (runs of homozygosity) analyses showed that the number and length of ROHs in Wuxue goats were also significantly higher than those in other breeds, and the genomic inbreeding coefficient (F_ROH) was significantly higher than that of the other 5 populations, which suggests that there was a significant accumulation of purity fragments and a decrease in genetic diversity at the genomic level in Wuxue goats. The results of linkage disequilibrium analyses showed that Wuxue goats exhibited the highest degree of linkage disequilibrium, which further illustrated the low genetic diversity of the population. In conclusion, this study systematically analysed the genetic characteristics and population structure of the Wuxue goat, and found that the genetic background of Wuxue goats is similar to that of Xiangdong Black goats, and that the genetic diversity of their populations is low and there is a certain tendency of inbreeding, which suggests that we should pay attention to the expansion of the population size and the control of the inbreeding coefficient in the subsequent work of breeding conservation. These findings not only provide a scientific basis for the in-depth understanding of the genetic background, but also provide an important theoretical reference for the conservation and rational development and utilization of genetic resources of this breed.

Key words: whole genome resequencing, genetic diversity, population evolution, Wuxue goat, population structure