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

Runs of homozygosity (ROH) are continuous segments of the genome that arose as a result of inbreeding, resulting in the inheritance of identical haplotypes from both parents who shared a common ancestor. In the present study, we performed a detailed characterization and comparison of ROH in four pig breeds, including intensively selected Polish Landrace as well as native unselected animals of Pu?awska and two Z?otnicka breeds (White and Spotted). We used a medium-density PorcineSNP60 BeadChip assay (Illumina) and cgaTOH software to detect ROH covering a minimum of 30 adjacent SNPs and maintaining a size over 1 Mb. By analysing ROH distribution and frequency across the genome, we also identified genomic regions with high ROH frequency (so-called “ROH hotspots”). The obtained results showed that the analysed conserved breeds were characterized by a higher ROH span and higher ROH-based inbreeding coefficients (F_ROH), which likely result from past population bottlenecks, increasing the overall inbreeding level within these populations. The analysis of ROH distribution across the genomes revealed the presence of both shared and breed-specific ROH hotspots. These hotspots, presumably representing genome regions under selection, overlapped with a variety of genes associated with processes connected with immune system functioning, reproduction, glucose homeostasis and metabolism. The genome regions with ROH hotspots overlapping in all analysed populations, located on SSC4 (51.9–55.9 Mb) and 13 (92.6–97.8 Mb), covered thirty-one different genes, including MMP16, SLC7A13, ATP6V0D2, CNGB3, WWiP1, RiMDN1 and CPNE3. These genes are primarily associated with biological regulation and metabolism, processes that could be responsible for the variety of the selected production and functional features.