Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes in Three Pig Breeds

摘要

Simple SummaryRuns of homozygosity (ROH) are the DNA segments that harbor uninterrupted stretches of homozygous genotype segments in the genome that are present in an individual due to the transmission of identical haplotypes from parents to their offspring. ROHs are widely used as predictors of whole-genome inbreeding levels in animals and identify highly selected genomic regions. In this study, we investigated the ROH distributions on the whole genome in three pig populations (Landrace, Songliao black and Yorkshire pigs). Moreover, inbreeding coefficients based on ROH were calculated and genes were annotated in the genomic regions with a high frequency of ROH. Results showed that Songliao black pigs had higher inbreeding in recent generations and ten genes related to economically important traits were located within ROH regions. Our findings provide a reference for developing breeding programs to maintain diversity and fitness in these breeds.