Characterizing Runs of Homozygosity and Inbreeding in American Mink Using SNP Data and Pedigree Information

Inbreeding increases the likelihood of deleterious recessive alleles becoming homozygous and consequently affecting economically important traits. Runs of homozygosity (ROH), the continuous homozygous segments of the genome and the higher than expected homozygosity (HOM) are genomic indicators of inbreeding, quantified as F_ROH and F_HOM, respectively. Previous ROH analyses in American mink (Neogale vison) were restricted to scaffold-level references and could not resolve long autozygous segments. In this study, we characterized ROH in 1413 mink genotyped with the Affymetrix Mink 70K panel (50,902 autosomal SNPs after quality control) on the chromosome-level genome assembly and compared F_ROH with F_HOM and with pedigree-based inbreeding (F_PED) derived from 24,633 pedigree records. ROH were detected in all individuals, with a mean of 149.61 ± 13.82 segments per individual. Segments longer than 8 Mb, not detectable in earlier studies of this population, represented 12.86% of all ROH and accounted for 0.10 of the mean F_ROH of 0.28. Mean F_HOM and F_PED were -0.03 and 0.02, respectively. ROH were unevenly distributed across chromosomes and chromosomes 1, 2, 3, 4, 6 and 11 harboured 78.59% of all segments. The Pearson correlation coefficient was highest (0.72) between F_ROH and F_HOM and moderate (0.34) between genomic inbreeding and F_PED, increasing with ROH length to 0.35 for segments longer than 16 Mb. Because the density of the marker panel limits the resolution of short segments, quantitative inference was restricted to ROH longer than 4 Mb. Our results indicate that recent autozygosity in this closed population is concentrated in a small number of long genomic segments, providing an opportunity to inform mating decisions.