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

Runs of homozygosity (ROH) are contiguous homozygous genotype segments in the genome that are present in an individual since the identical haplotypes are inherited from each parent. The aim of this study was to investigate the frequency and distribution of ROH in the genomes of Landrace, Songliao black and Yorkshire pigs. We calculated two types of genome inbreeding coefficients and their correlation, including the inbreeding coefficient based on ROH (FROH) and the inbreeding coefficient based on the difference between the observed and expected number of homozygous genotypes (FHOM). Furthermore, we identified candidate genes in the genomic region most associated with ROH. We identified 21,312 ROH in total. The average number of ROH per individual was 32.99 ± 0.38 and the average length of ROH was 6.40 ± 0.070 Mb in the three breeds. The FROH results showed that Yorkshire pigs exhibited the highest level of inbreeding (0.092 ± 0.0015) and that Landrace pigs exhibited the lowest level of inbreeding (0.073 ± 0.0047). The average correlation between FROH and FHOM was high (0.94) within three breeds. The length of ROH provides insight into the inbreeding history of these three pig breeds. In this study, Songliao black pigs presented a higher frequency and average length of long ROH (>40 Mb) compared with those of Landrace and Yorkshire pigs, which indicated greater inbreeding in recent times. Genes related to reproductive traits (GATM, SPATA46, HSD17B7, VANGL2, DAXX, CPEB1), meat quality traits (NR1I3, APOA2, USF1) and energy conversion (NDUFS2) were identified within genomic regions with a high frequency of ROH. These genes could be used as target genes for further marker-assisted selection and genome selection.