Genetic diversity and population structure of a Creole sheep flock from Uruguay

Abstract

Since 2020, the National Agricultural Research Institute (INIA) has conserved a Creole sheep flock at INIA Las Brujas. This study genetically characterised this population and compared it with six others: San Miguel National Park Creoles, commercial farms Creoles, Brazilian Creoles, Corriedale, Merilin and Soay sheep. The analysis included 628 individuals and 31 392 autosomal SNPs. Soay and San Miguel National Park Creoles exhibited the lowest genetic diversity (Ho = 0.266 and 0.279) and highest inbreeding (FHOM: 0.283 and 0.249; FROH: 0.199 and 0.202). Merilin and Corriedale showed the highest genetic diversity (Ho = 0.351 and 0.364), while Brazilian Creoles had the highest Ho (0.327) among Creoles. Short runs of homozygosity (ROH) segments (≤4 Mb) predominated, with San Miguel National Park and INIA Las Brujas Creoles exhibiting the highest numbers of ROH (22 773 and 16 762, respectively). Fixation index (Fst) and Reynolds distances highlighted INIA Las Brujas Creoles and Soay as the most distinct (0.318 and 0.321, respectively). INIA Las Brujas Creoles also showed notable differentiation from San Miguel National Park Creoles (Fst = 0.269; Reynolds = 0.272). Principal component analysis (PCA) revealed clear clustering, with Corriedale and Merilin closely related (Fst = 0.060; Reynolds = 0.068). Admixture analysis indicated distinct ancestries for Soay, Corriedale and San Miguel National Park Creoles, while commercial and Brazilian Creoles showed significant admixture. INIA Las Brujas Creoles exhibited a distinct ancestry with traces of Corriedale. Phylogenetic analysis confirmed the divergence between Creole and Corriedale/Merilin populations. Results suggest the historical genetic exchange among INIA Las Brujas Creoles, Corriedale, and commercial farms Creoles, while high differentiation of San Miguel National Park Creoles reflects their closed status since 1929.