Linkage disequilibrium, historical effective population size and haplotype blocks in selected native sheep breeds

Abstract

This study was conducted to investigate linkage disequilibrium (LD), historical effective population size (Ne) and haplotype blocks structure in genomes of nine Polish conserved sheep breeds or varieties: Black-headed (BH), Colored Mountain Sheep (CMS), Old-type Merino (MPOT), Podhale Zackel (PZ), Polish Merino of Coloured Variety (MPC), Polish Mountain Sheep (PMS), Świniarka (SW), Uhruska (UHR) and Wrzosówka (WRZ), based on single nucleotide polymorphisms (SNPs) from the OvineSNP50 DNA Analysis Kit (Illumina, San Diego, CA). LD analysis was performed based on the pairwise r2 statistic of SNPs at a distance up to 5 Mb. At a short distance, up to 100 kb, the lower average r2 was observed in PZ (0.10) breed and the highest average r2 was observed in MPC (0.21) breed. At a distance of 4–5 Mb, the highest average r2 was observed in SW (0.08) breed and the lowest average r2 was observed in PZ (0.02) and PMS (0.02) breeds. All studied Polish sheep breeds, showed mean r2 > 0.3 (‘useful’ LD level for QTL mapping) at shorter distances than average distances between adjacent SNP markers and only for MPC, SW, UH, WRZ breeds mean r2 > 0.2 (high enough to attain an accuracy of 0.85 for genomic breeding value estimation) was observed at similar or longer distances than average distances between adjacent SNP markers. Obtained results showed that the Illumina OvineSNP50 BeadChip assay is not a suitable tool to perform reliable genome-wide association for all studied Polish sheep breeds and only for MPC, SW, UH and WRZ it is potentially possible to perform reliable genomic breeding value estimation. For most of the studied sheep breeds, effective population size 5 generations ago was close or less to the FAO recommended Ne of 50 per generation required to maintain fitness in breed. From 2,051 (SW) to 1,265 (PZ) haplotype block structures, spanning from 148.9 (SW) to 26.3 (PZ) of the genome were detected. Across all studied sheep breeds the highest average block length was observed in MPC (82.5 ± 114 kb) breed and the lowest average block length was observed in PZ (20.9 ± 43 kb) breed. For all studied Polish sheep breeds, as many as 280 haplotype block structures with overlapping segments were detected, within which 182 genes were identified.