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

Abstract

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.

Comparative genomic analysis of inbred rat strains reveals the existence of ancestral polymorphisms

“…These regions seem to be still heterozygous to some extent because heterozygous sites are also enriched in discordant site-rich regions. These findings are concordant with some previous reports for other inbred species (Lilue et al 2018;Wang et al 2019), providing valuable insights for understanding the genetic characteristics and diversity in highly polymorphic loci in the process of inbreeding. Indeed, in the process of naturally occurring inbreeding, such loci are thought to be under balancing selection and are shown to be heterozygous (Sato et al 2002;Aguilar et al 2004;Lins et al 2018).…”

“…Indeed, in the process of naturally occurring inbreeding, such loci are thought to be under balancing selection and are shown to be heterozygous (Sato et al 2002;Aguilar et al 2004;Lins et al 2018). Our results, together with the findings in other previously reported species (Lilue et al 2018;Wang et al 2019), suggest that balancing selection may also act on such loci in the process of artificial inbreeding.…”

The Nero Lucano Pig Breed: Recovery and Variability

“…Results obtained by the Illumina PorcineSNP60 BeadChip genotyping evidenced that: (i) the percentage of SNPs having an MAF > 0.05 was lower (51.38%) than those observed in three cosmopolitan breeds (Duroc 67.5%, Landrace 80.6% and Yorkshire 80.4%) [ 25 ]; (ii) SNPs in Hardy–Weinberg disequilibrium were mainly due to excess of homozygotes; (iii) the inbreeding coefficients based on molecular data (F MOL ) were very high and comparable with those observed in some small, closed and endangered Spanish (Guadyerbas 0.80 and Torbiscal 0.74) and Chinese (Wuzhishan 0.44) populations [ 26 , 27 , 28 ]; and (iv) the overlapping of the F MOL curves in the two inbred generations could be the consequence of breeders activities (for example, boar exchanges) to avoid an excessive increase of inbreeding.…”

Detection of runs of homozygosity in conserved and commercial pig breeds in Poland

“…These conserved breeds are considered to be unselected, as their current major breeding goal is to maintain their primitive character and maximize genetic diversity. To supplement the previously reported data on pig ROH (Bosse et al., 2012; Gomez‐Raya, Rauw, Dunkelberger, & Dekkers, 2019; Wang et al., 2019; Xu et al., 2019; Yang et al., 2017; Zanella et al., 2016; Zhang et al., 2018; and many others) with information regarding ROH characteristics in Polish pigs, we detected and compared ROH in the genomes of the aforementioned breeds. Our study provides additional insights into the genetic differences between the breeds, and our results can be utilized to observe the effect of selection and population demography on the distribution of ROH in the pig genome.…”