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Open AccessArticle

Genomic Analysis Reveals Specific Patterns of Homozygosity and Heterozygosity in Inbred Pigs

1
Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
2
Institute of Tropical Crop Variety Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
3
Animal Genomics and Improvement Laboratory, U.S. Department of Agriculture-Agricultural Research Services, Beltsville, MD 20705, USA
*
Authors to whom correspondence should be addressed.
These authors contribute equally to this work.
Animals 2019, 9(6), 314; https://doi.org/10.3390/ani9060314
Received: 26 April 2019 / Revised: 27 May 2019 / Accepted: 28 May 2019 / Published: 1 June 2019
(This article belongs to the Collection Applications of Quantitative Genetics in Livestock Production)
The inbred strain of miniature pig is an ideal model for biomedical research due to its high level of homozygosity. Our results from multidimensional scaling, admixture, and phylogenetic analyses indicated that the inbred Wuzhishan pig (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. ROH number, length, and distribution across generations indicate the impacts of recombination and demography on ROHs in these WZSPs. Finally, we detected 56 single nucleotide polymorphisms (SNPs) showing constant heterozygosity with heterozygosity (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.
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. View Full-Text
Keywords: Wuzhishan pig (WZSP); genetic structure; inbred; homozygosity; heterozygosity Wuzhishan pig (WZSP); genetic structure; inbred; homozygosity; heterozygosity
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MDPI and ACS Style

Wang, L.; Mu, Y.; Xu, L.; Li, K.; Han, J.; Wu, T.; Liu, L.; Gao, Q.; Xia, Y.; Hou, G.; Yang, S.; He, X.; Liu, G.E.; Feng, S. Genomic Analysis Reveals Specific Patterns of Homozygosity and Heterozygosity in Inbred Pigs. Animals 2019, 9, 314. https://doi.org/10.3390/ani9060314

AMA Style

Wang L, Mu Y, Xu L, Li K, Han J, Wu T, Liu L, Gao Q, Xia Y, Hou G, Yang S, He X, Liu GE, Feng S. Genomic Analysis Reveals Specific Patterns of Homozygosity and Heterozygosity in Inbred Pigs. Animals. 2019; 9(6):314. https://doi.org/10.3390/ani9060314

Chicago/Turabian Style

Wang, Ligang; Mu, Yulian; Xu, Linyang; Li, Kui; Han, Jianlin; Wu, Tianwen; Liu, Lan; Gao, Qian; Xia, Ying; Hou, Guanyu; Yang, Shulin; He, Xiaohong; Liu, George E.; Feng, Shutang. 2019. "Genomic Analysis Reveals Specific Patterns of Homozygosity and Heterozygosity in Inbred Pigs" Animals 9, no. 6: 314. https://doi.org/10.3390/ani9060314

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