Runs of Homozygosity Reveal Associations Between Autozygosity and Production Traits in Three Commercial Pig Populations

Runs of homozygosity (ROH) provide a genome-wide measure of autozygosity and are useful for evaluating the genomic consequences of selection and inbreeding in commercial pig populations. This study investigated ROH architecture and associations between ROH-based genomic inbreeding coefficients ( F_ROH ) and production-related traits in American Duroc (DD), American Landrace (LL), and American Yorkshire (YY) pigs. After quality control, 5,859 genotyped pigs were analysed. Using a 1 Mb ROH definition restricted to SSC1-18, we detected 416,225 ROH segments and observed the highest individual-level ROH in DD. Mixed models incorporating a genomic relationship matrix (GRM) identified 19 nominally significant F_ROH –trait associations (P < 0.05) among 51 population–trait tests, of which 13 remained significant after Benjamini–Hochberg FDR correction, with the broadest pattern in LL, fewer associations in DD, and nominal associations in YY restricted to BL and BH, with only BH surviving FDR correction. Sex-specific analyses detected F_ROH × Sex interactions that were nominally significant in DD, none of which remained significant after FDR correction across 45 estimable interaction tests. Segmented models further showed 25 nominally significant threshold responses (P < 0.05), none of which survived FDR correction (minimum q = 0.118); these exploratory patterns suggested that nominal candidate F_ROH breakpoints differed by population, trait, and ROH length class. These results indicate that the effects of genomic autozygosity on production traits vary across commercial pig populations with trait-dependent associations supported by FDR correction and sex- and ROH-length-class-related patterns remaining exploratory. The population-specific F_ROH associations and threshold responses observed in this study provide insight into how different sources of inbreeding may influence production performance. These findings provide a basis for population-specific evaluation of inbreeding load and for improving genomic management strategies in commercial pig breeding.