Abstract
Investigating the patterns of homozygosity, linkage disequilibrium, effective population size and inbreeding coefficients in livestock contributes to our understanding of the genetic diversity and evolutionary history. Here we used Illumina PorcineSNP50 Bead Chip to identify the runs of homozygosity (ROH) and estimate the linkage disequilibrium (LD) across the whole genome, and then predict the effective population size. In addition, we calculated the inbreeding coefficients based on ROH in 305 Piétrain pigs and compared its effect with the other two types of inbreeding coefficients obtained by different calculation methods. A total of 23,434 ROHs were detected, and the average length of ROH per individual was about 507.27 Mb. There was no regularity on how those runs of homozygosity distributed in genome. The comparisons of different categories suggested that the formation of long ROH was probably related with recent inbreeding events. Although the density of genes located in ROH core regions is lower than that in the other genomic regions, most of them are related with Piétrain commercial traits like meat qualities. Overall, the results provide insight into the way in which ROH is produced and the identified ROH core regions can be used to map the genes associated with commercial traits in domestic animals.
Highlights
4 samples were removed for low genotyping, 1788 single nucleotide polymorphism (SNP) were filtered in missingness test, 2179 markers were excluded based on HWE test and 11,616 SNPs failed in the minor allele frequency test
We found that the total physical length of runs of homozygosity (ROH) on 18 autosomes per individual was about 507.267 Mb on average
We have investigated the relationship between the inbreeding coefficients based on8 of three categories of ROHs and FHOM
Summary
It was founded by crossing local swine with Berkshire, English Large White and Bayeux pig and was exported to other countries after 1950s. Piétrain pig has medium size, well-developed muscles and white skin with black spots. It is unavoidable to create close inbreeding during breed formation [1]. Whereas those strong inbreeding and selection shaped the Piétrain’s important characteristics like high lean percentages [2]. This breed is popular around the world, and it is commonly used as terminal sire in the commercial crossing system
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