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

Ligang Wang,Tianwen Wu,Shutang Feng,Shulin Yang,Ying Xia,George E Liu,Jianlin Han,Lan Liu,Qian Gao,Guanyu Hou,Xiaohong He,Yulian Mu,Kui Li,Linyang Xu

doi:10.3390/ani9060314

Abstract

Simple SummaryThe 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.

Highlights

Inbred animals are an ideal model for conservation genetics, and can be utilized as a valuable genetic resource for human medical research [1]
We found that the average heterozygosity (He ) was clearly lower across six generations in the inbred Wuzhishan pigs (WZSPs) compared to the non-inbred population (Supplementary Table S1)
K = 3 and 4, we found the inbred WZSP could not be separated by generation, indicating similar cannot be separated by generations

Summary

Introduction

Inbred animals are an ideal model for conservation genetics, and can be utilized as a valuable genetic resource for human medical research [1]. ROHs have been previously explored in humans, cattle, pigs, and other farm animals [4,5,6,7,8]. The size and position of ROHs were expected to be associated with multiple causes, including recombination and demography [6,9]. Keller et al found that inbreeding coefficients estimated from ROHs are much better at detecting the overall burden of rare recessive mutations (the likely cause of inbreeding depression) than several alternatives, including inbreeding coefficients defined based on single nucleotide polymorphism (SNP) and those defined from pedigrees [10]

Methods

Results

Conclusion