Towards a genomic-driven conservation strategy for the autochthonous Mora Romagnola pig breed by leveraging population genomic parameters, genomic inbreeding and signature of selection analyses

The Mora Romagnola is an endangered pig breed, native to the Emilia-Romagna region in northern Italy, where it is considered part of the local agricultural traditions. Currently, there are approximately 320 boars and sows registered in the breed herd book. In this study, we genotyped a total of 246 Mora Romagnola pigs using the GGP 70K Porcine HD array. The low mean minor allele frequency, high frequency of single nucleotide polymorphisms fixed in the population, small effective population size and high mean genomic inbreeding level, as estimated with various parameters, including runs of homozygosity (ROH), indicate that the breed has experienced genetic events that reduced within-population variability. This has led this breed to have one of the highest average genomic inbreeding levels among autochthonous European pig breeds, with F-ROH equal to 0.406. Signatures of selection were identified using two complementary approaches based on within breed genomic data: identification of ROH islands and applying the integrated haplotype score (iHS). A total of 22.02 Mb of the pig genome, encompassing nine different regions, were covered by ROH islands identified with a stringent criterion. With the second approach, 14 iHS signals were identified, two of which overlapped with ROH islands. Functional enrichment analysis of genes in these signatures of selection reported obesity-related terms, which describe a peculiar-breed characteristic, such as the tendency to deposit high levels of fat. This study provided useful information to develop a genomic-driven conservation strategy, supporting breeders in maintaining long-term genetic diversity and ensuring the sustainability of this breed population.