SNP-based genetic signatures revealed breeding effects in indigenous Livni compared with Landrace and Large White breeds

Livni is one of the Russian local pig breeds. We previously reported that this breed was more distinct from Duroc breed than from Landrace and the Large White breeds, which participated in the Livni breed creation. The aim of the study was to determine the SNP-based genetic signatures in fat-type Livni breed shared with commercial Landrace and the Large White breeds, and ones that are affected by putative selection. The genome-wide SNP genotyping was carried out using the Porcine GGP HD BeadChip, which contains ~ 80 000 SNPs. Obtained breed relationship and admixture results indicated the insignificant participation of the Landrace and the Large White breeds in the formation of the modern allelofund of Livni pigs. 238 candidate genes were found in the genomic regions with selection signatures, 182 genes with described functions were identified. In the Livni and Landrace breeds, 35 common genes were detected which formed one cluster with enrichment coefficient = 4.94 and predominant HOXD genes. In the Livni and Large White breeds, the largest amounts of common genes were detected (62 in average), which formed two clusters. Cluster 1, with enrichment coefficient = 2.11, was characterized with genes involved in glucose metabolism. Cluster 2, with enrichment coefficient = 1.60, demonstrated helicase genes. Annotated clusters were not determined for the Livni breed. However, 50 candidate genes were specific to Livni pigs and associated with various growth, carcass and reproductive traits, essential for thermoregulation. Results revealed common SNP-based genetic signatures and breeding effects in indigenous Livni compared with Landrace and Large White breeds.