Linkage disequilibrium and genetic diversity estimation in three Sicilian autochthonous dairy sheep breeds

Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. In the present study, we used the OvineSNP50K BeadChip to characterize LD, identify haplotype blocks and to analyze genetic diversity in the Valle del Belice (VDB), Comisana (COM) and Pinzirita (PIN) dairy sheep breeds. LD between adjacent SNPs and for all pairwise combinations of SNPs on each chromosome was measured using r2. Haplotype blocks were estimated using D’ based method. Genetic diversity and Principal Component Analysis (PCA) were calculated using PLINK. Small differences in average LD value for adjacent SNPs on each chromosome were observed between VDB and COM (0.155±0.204 and 0.156±0.208, respectively), whereas a low value was found in PIN breed (0.128±0.188). The same differences were observed across the genome; for example, for SNPs separated by 50-100 kb, the average r2 was 0.117, 0.113 and 0.084, respectively. In all breeds, the chromosome showing the highest number of blocks, the highest number of SNPs involved in block and the highest value of r2 was OAR2. This result suggesting that there is a similarity of conserved haplotypes among Sicilian breeds. PCA indicated that while VDB and PIN are clearly separated populations, the individuals of COM breed occupied different areas of the cluster, showing the presence of substructure. The low level of inbreeding and high genetic diversity (expected heterozigosity) were found in PIN breed, and this result reflect the short extent of LD. Our results for average LD within chromosome and breed are in agreement with the block structure across the genome; moreover, the different levels of LD among chromosomes and breeds, indicate different selection pressure.