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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Genomic analysis reveals specific patterns of homozygosity and heterozygosity in inbred pigs
Animals, Volume 9, No. 6, Article 314, Year 2019
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Description
The inbred strain of miniature pig is an ideal model for biomedical research due to its high level of homozygosity. In this study, we investigated genetic diversity, relatedness, homozygosity, and heterozygosity using the Porcine SNP60K BeadChip in both inbred and non-inbred Wuzhishan pigs (WZSPs). Our results from multidimensional scaling, admixture, and phylogenetic analyses indicated that the inbred WZSP, with its unique genetic properties, can be utilized as a novel genetic resource for pig genome studies. Inbreeding depression and run of homozygosity (ROH) analyses revealed an average of 61 and 12 ROH regions in the inbred and non-inbred genomes of WZSPs, respectively. By investigating ROH number, length, and distribution across generations, we further briefly studied the impacts of recombination and demography on ROH in these WZSPs. Finally, we explored the SNPs with higher heterozygosity across generations and their potential functional implications in the inbred WZSP. We detected 56 SNPs showing constant heterozygosity with He = 1 across six generations in inbred pigs, while only one was found in the non-inbred population. Among these SNPs, we observed nine SNPs located in swine RefSeq genes, which were found to be involved in signaling and immune processes. Together, our findings indicate that the inbred-specific pattern of homozygosity and heterozygosity in inbred pigs can offer valuable insights for elucidating the mechanisms of inbreeding in farm animals. © 2019 by the authors.
Authors & Co-Authors
Xu, Lingyang
China, Beijing
Chinese Academy of Agricultural Sciences
Li, Kui
China, Beijing
Chinese Academy of Agricultural Sciences
Han, Jianlin
China, Beijing
Chinese Academy of Agricultural Sciences
Hou, Guanyu
China, Haikou
Chinese Academy of Tropical Agricultural Sciences
Yang, Shulin
China, Beijing
Chinese Academy of Agricultural Sciences
He, Xiaohong
China, Beijing
Chinese Academy of Agricultural Sciences
Liu, George E.
United States, Washington, D.c.
United States Department of Agriculture
Statistics
Citations: 8
Authors: 7
Affiliations: 3
Identifiers
Doi:
10.3390/ani9060314
ISSN:
20762615
Research Areas
Genetics And Genomics
Mental Health
Study Design
Cross Sectional Study