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Genomic Analysis Reveals Specific Patterns of Homozygosity and Heterozygosity in Inbred Pigs
Ligang Wang1, Yulian Mu2, Linyang Xu3
1Key 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. ligwang@126.com.
Animals : an Open Access Journal From MDPI
|June 5, 2019
Summary
Inbred Wuzhishan pigs (WZSPs) exhibit unique genetic patterns, with significantly more homozygous regions than non-inbred WZSPs. This study highlights their potential as a novel resource for pig genome research and understanding inbreeding.
Area of Science:
- Animal Genetics
- Genomics
- Biomedical Research
Background:
- Inbred miniature pigs are valuable biomedical research models due to high homozygosity.
- Wuzhishan pigs (WZSPs) offer a unique genetic resource for studying inbreeding.
Purpose of the Study:
- Investigate genetic diversity, relatedness, homozygosity, and heterozygosity in inbred and non-inbred WZSPs.
- Characterize runs of homozygosity (ROH) and identify highly heterozygous single nucleotide polymorphisms (SNPs) in inbred WZSPs.
- Explore the functional implications of identified SNPs in pig genome studies.
Main Methods:
- Utilized the Porcine SNP60K BeadChip for genotyping.
- Performed multidimensional scaling, admixture, and phylogenetic analyses.
- Analyzed inbreeding depression and runs of homozygosity (ROH) across generations.
Main Results:
- Inbred WZSPs showed significantly higher ROH (average 61 regions) compared to non-inbred WZSPs (average 12 regions).
- Identified 56 SNPs with constant heterozygosity (He = 1) across six generations in inbred pigs, versus one in non-inbred pigs.
- Nine of these SNPs were located in swine RefSeq genes involved in signaling and immune processes.
Conclusions:
- Inbred WZSPs possess distinct genetic properties making them a novel resource for pig genome research.
- The study elucidates the impact of recombination and demography on ROH patterns.
- Findings provide insights into inbreeding mechanisms in farm animals through analysis of homozygosity and heterozygosity patterns.
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