Genomic inbreeding estimated through runs of homozygosity in Moura pigs and four commercial swine breeds

Abstract

The transmission of identical haplotypes from a common ancestor creates long stretches of homozygous genotypes, known as runs of homozygosity (ROHs). Longer haplotypes are inherited from recent common ancestors, and shorter haplotypes, from distant ancestors. In this study, we performed a comparative analysis of the genomic data of the Moura pig breed, a locally adapted breed from Brazil, that typically grows in extensive or semi-intensive systems, in comparison to the commercial breeds Duroc, Landrace, Large White, and Pietrain. We investigated ROH patterns and different inbreeding coefficients in order to guide long-term breeding programs, rescue efforts, and breed evaluation programs. To understand these patterns, we performed a detailed genome characterization of 459 animals, of which 84 were Moura, 87 Duroc, 138 Landrace, 84 Large White and 66 Pietrain swine, performed using Illumina Porcine v2 BeadChip markers. Inbreeding coefficients based on the genomic relationship matrix and ROH were calculated, indicating that Moura pigs displayed the highest ROH frequency (greater than 8 Mb) compared to the other swine breeds. This demonstrates that Moura pigs exhibit greater inbreeding in recent generations, probably due to severe reductions in the number of animals. Furthermore, genes related to meat quality were detected on the ROH islands superimposed on the Moura and Duroc breeds, comprising one of the main characteristics of both breeds. Kinship analysis revealed notable genetic diversity among Moura pigs, with the majority of comparisons indicating the absence of direct parentage. Our findings contribute to a better understanding of the genomic profile of the locally adapted Moura breed. Additionally, they underscore the importance of monitoring inbreeding as a starting point for genetic improvement programs and genomic studies of this breed.